Auto-upload batch data to clear storage

.gitattributes

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data/__notebook__.ipynb

@@ -38075,6 +38075,1783 @@
      },
      "metadata": {},
      "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> Upload thành công!\n",
+      "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> Đã làm trống thư mục. Dung lượng hiện tại: 0.00 GB\n",
+      "--------------------------------------------------\n",
+      "[4620/10000] (15.27GB) Downloading: 4f6114a2-0125-4bf5-8d62-d890fa751ee9_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4621/10000] (0.01GB) Downloading: 4f6114a2-0125-4bf5-8d62-d890fa751ee9_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4622/10000] (0.02GB) Downloading: TCGA-E2-A15L-01Z-00-DX1.626032DC-D396-48E7-B888-DFEBCF7102FF.svs (1433.22 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4623/10000] (1.42GB) Downloading: TCGA-A7-A6VV-01A-11-A43F-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4624/10000] (1.42GB) Downloading: TCGA-A7-A6VV-01A-02-TS2.B2C40F30-C888-4D29-8972-90912466A8B7.svs (122.55 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4625/10000] (1.54GB) Downloading: DLP_REDO_FROM_COPAL_E08.grch38.seg.v2.txt (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4626/10000] (1.54GB) Downloading: TCGA-GM-A2DF-01A-11D-A89B-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4627/10000] (1.54GB) Downloading: TCGA-BRCA.e96765f9-45a3-446f-924a-45202dd4b7db.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4628/10000] (1.54GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_F03_741528.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4629/10000] (1.54GB) Downloading: TCGA-E2-A15L-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4630/10000] (1.54GB) Downloading: 8204d38d-337a-4cba-9482-c84b6e0134b5.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4631/10000] (1.54GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_C03_844800.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4632/10000] (1.54GB) Downloading: TCGA-E2-A15L-01A-21-A13E-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4633/10000] (1.54GB) Downloading: TCGA-A8-A095-01A-01-TS1.6e35462c-2639-48ee-9503-d2689ebb0346.svs (512.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4634/10000] (2.04GB) Downloading: TCGA-E2-A15L.C04B3267-9833-44D6-8C3D-45D7F829C38C.PDF (0.17 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4635/10000] (2.04GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H05_628424.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4636/10000] (2.04GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A095.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4637/10000] (2.04GB) Downloading: TCGA-GM-A2DF-01A-01-TSA.92173C4D-78C6-4213-BE01-673760EF899C.svs (141.92 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4638/10000] (2.18GB) Downloading: TCGA-BRCA.1fdda772-80cf-45f4-ae85-79ebf4000fb7.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4639/10000] (2.18GB) Downloading: 481b3e69-fff7-4f32-9ab0-3052a37f0834.wxs.aliquot_ensemble_masked.maf.gz (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4640/10000] (2.18GB) Downloading: TCGA-BRCA.e96765f9-45a3-446f-924a-45202dd4b7db.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4641/10000] (2.18GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A095.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4642/10000] (2.18GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A15L.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4643/10000] (2.18GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_F03_741528.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4644/10000] (2.18GB) Downloading: e7a1cdcf-ec99-44fd-a13b-604cf15b2bd4.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4645/10000] (2.19GB) Downloading: TCGA-E9-A22A.BC3061B7-9C99-4270-84EE-B1306FA01AE2.PDF (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4646/10000] (2.19GB) Downloading: 44f1c070-57db-475a-979a-d384eabe4589_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4647/10000] (2.19GB) Downloading: 66705e98-15ad-4eab-9901-7d1f6c0c2e57.methylation_array.sesame.level3betas.txt (0.73 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4648/10000] (2.19GB) Downloading: TCGA-BRCA.3b807901-2667-4023-8210-20c0ebb5d189.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4649/10000] (2.19GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_B03_628532.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4650/10000] (2.19GB) Downloading: TCGA-BRCA.3b807901-2667-4023-8210-20c0ebb5d189.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4651/10000] (2.20GB) Downloading: 57ffb618-af4e-40fc-96aa-f88b7759fb62.mirbase21.isoforms.quantification.txt (0.26 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4652/10000] (2.20GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A22A.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4653/10000] (2.20GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_B03_628532.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4654/10000] (2.20GB) Downloading: 8927b32d-b478-4f7d-b2eb-ae7dfc5071b2.mirbase21.isoforms.quantification.txt (0.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4655/10000] (2.20GB) Downloading: TCGA-A8-A095-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4656/10000] (2.20GB) Downloading: 825905d3-c2e6-4cff-872c-ae9fcb789173.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4657/10000] (2.20GB) Downloading: TCGA-A8-A095-01Z-00-DX1.97072E53-7323-4836-9D58-22B7C346A7CE.svs (357.41 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4658/10000] (2.55GB) Downloading: 26bf8794-67fc-4e56-8264-05437a996f91_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4659/10000] (2.55GB) Downloading: TCGA-E9-A22A-01A-01-TSA.cb4979a2-8b33-4983-9f84-53307fb392ad.svs (166.99 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4660/10000] (2.71GB) Downloading: TCGA-BRCA.8bb0471f-9d25-4c27-9a4c-ecc00090a7da.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4661/10000] (2.71GB) Downloading: 44f1c070-57db-475a-979a-d384eabe4589.methylation_array.sesame.level3betas.txt (12.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4662/10000] (2.73GB) Downloading: 825905d3-c2e6-4cff-872c-ae9fcb789173.mirbase21.isoforms.quantification.txt (0.30 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4663/10000] (2.73GB) Downloading: TCGA-BH-A0BW-01Z-00-DX1.39B0C363-46A2-4FFB-B1C5-C054A86F4A25.svs (1309.14 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4664/10000] (4.00GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_D02_787546.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4665/10000] (4.00GB) Downloading: TCGA-BH-A0BZ-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4666/10000] (4.00GB) Downloading: TCGA-BH-A0BZ-11A-06-TSF.8926f914-ba66-41ff-b779-574f25cb99b4.svs (123.85 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4667/10000] (4.13GB) Downloading: nationwidechildrens.org_clinical.TCGA-A2-A25B.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4668/10000] (4.13GB) Downloading: 20f5ce9d-da3c-462e-a82d-3e0d0c8d28ed.methylation_array.sesame.level3betas.txt (0.73 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4669/10000] (4.13GB) Downloading: e558015e-969b-4354-9bc9-219a60092734.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4670/10000] (4.13GB) Downloading: TCGA-BH-A0BZ-01A-03-TSC.18e04e86-9ccb-4773-bcf3-d7f0c54c6e2a.svs (601.48 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4671/10000] (4.72GB) Downloading: TCGA-BH-A0BW-11A-01-TSA.a70c68c4-87db-48b3-ab77-c82a3f3e8c73.svs (460.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4672/10000] (5.17GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_C06_748044.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4673/10000] (5.17GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_G03_735058.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4674/10000] (5.17GB) Downloading: 847cc85a-7133-4693-b222-5b2f0aea3c7c.wxs.aliquot_ensemble_masked.maf.gz (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4675/10000] (5.17GB) Downloading: efffe4d8-78f7-4acf-b27c-3daed222831a.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4676/10000] (5.17GB) Downloading: TCGA-BH-A0BW.14CE78F3-8FB4-476D-A09C-AE87F7919D77.PDF (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4677/10000] (5.17GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0BZ.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4678/10000] (5.17GB) Downloading: 57ffb618-af4e-40fc-96aa-f88b7759fb62.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4679/10000] (5.17GB) Downloading: TCGA-BRCA.6eee21c1-5bc4-4eb7-bf40-151fc831d5b9.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4680/10000] (5.17GB) Downloading: TCGA-BRCA.6eee21c1-5bc4-4eb7-bf40-151fc831d5b9.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4681/10000] (5.17GB) Downloading: TCGA-BH-A0BW-11A-01-BSA.06e78372-88dc-4e56-ac02-219351b122b5.svs (280.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4682/10000] (5.44GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_A02_735170.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4683/10000] (5.44GB) Downloading: TCGA-BH-A0BZ.1B56E5A6-35B8-4C60-8BC5-68716C946799.PDF (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4684/10000] (5.45GB) Downloading: TCGA-BRCA.43ba3339-996b-4477-878f-4a62c471ab5f.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4685/10000] (5.45GB) Downloading: TCGA-BRCA.43ba3339-996b-4477-878f-4a62c471ab5f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4686/10000] (5.45GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_G04_735070.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4687/10000] (5.45GB) Downloading: TCGA-B6-A0IA-01A-01-TSA.77975eac-fd36-4fd6-915f-279f8ede5437.svs (294.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4688/10000] (5.74GB) Downloading: 7adaa246-6cbf-4be8-818a-75e3237dd669.mirbase21.isoforms.quantification.txt (0.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4689/10000] (5.74GB) Downloading: TCGA-B6-A0IA-01Z-00-DX1.8A868F0A-6CE2-46A7-AF0C-C5FC5D657D86.svs (1496.57 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4690/10000] (7.20GB) Downloading: 4c5f6397-fd33-4346-8044-829d85e273b5.wxs.aliquot_ensemble_masked.maf.gz (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4691/10000] (7.20GB) Downloading: 272aaf82-6a11-48c8-a195-c67f5d2c7179_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4692/10000] (7.20GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0BW.xml (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4693/10000] (7.20GB) Downloading: TCGA-BRCA.75a4c81e-50fb-4ea4-b973-9e6e666f0e19.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4694/10000] (7.20GB) Downloading: TCGA-BRCA.1427907e-73c9-42c0-ab7b-64cd9b64d874.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4695/10000] (7.20GB) Downloading: 427217a0-b24a-4c7f-bc17-c0094b490bdc.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4696/10000] (7.20GB) Downloading: TCGA-BH-A0BW-01A-11D-A890-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4697/10000] (7.21GB) Downloading: TCGA-BRCA.9817a432-9c60-42d5-928e-531e3fd480dd.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4698/10000] (7.21GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-B6-A0IA.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4699/10000] (7.21GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_E06_667172.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4700/10000] (7.21GB) Downloading: c039beb5-6e40-481c-a2e9-e138c65a401f_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4701/10000] (7.21GB) Downloading: TCGA-BRCA.1609caae-f341-4227-ac2a-a76a6c253e95.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4702/10000] (7.21GB) Downloading: TCGA-A8-A07F-01Z-00-DX1.E6FE5B3A-A412-4E7B-A710-7DFD3596F4E3.svs (588.96 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4703/10000] (7.78GB) Downloading: aa7994b6-8924-4e0c-b074-df337441195e_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4704/10000] (7.78GB) Downloading: TCGA-A8-A07F.D1456192-83E7-4FC8-B783-90D615830156.PDF (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4705/10000] (7.78GB) Downloading: TCGA-BH-A1FE-11B-01-TSA.64df3bc1-a7ca-4bc6-bd99-e619d76f5cb0.svs (64.92 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4706/10000] (7.85GB) Downloading: 2e1410fb-4799-4a85-97e2-0d05c9255977.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4707/10000] (7.85GB) Downloading: 6366b160-c124-4a56-b6a7-e159ea8a096d_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4708/10000] (7.86GB) Downloading: nationwidechildrens.org_clinical.TCGA-B6-A0IA.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4709/10000] (7.86GB) Downloading: 8f08cee9-a91f-4305-bf8d-efeee9cd386c.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4710/10000] (7.86GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_D03_667110.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4711/10000] (7.86GB) Downloading: TCGA-BRCA.1609caae-f341-4227-ac2a-a76a6c253e95.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4712/10000] (7.87GB) Downloading: TCGA-B6-A0IA.55F3F917-E441-4C10-A3E3-0645A4E8374E.PDF (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4713/10000] (7.87GB) Downloading: 30671b2b-1583-4908-bfab-25a9ccb16997.mirbase21.isoforms.quantification.txt (0.33 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4714/10000] (7.87GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A1FE.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4715/10000] (7.87GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A0FZ.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4716/10000] (7.87GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_C11_667238.grch38.seg.v2.txt (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4717/10000] (7.87GB) Downloading: TCGA-A8-A07F-01A-11D-A89H-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4718/10000] (7.87GB) Downloading: nationwidechildrens.org_clinical.TCGA-A2-A3XX.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4719/10000] (7.87GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D10_628322.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4720/10000] (7.87GB) Downloading: d313dc0e-3840-487d-be90-817a1ef43f82_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4721/10000] (7.88GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D10_628322.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4722/10000] (7.88GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A07F.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4723/10000] (7.88GB) Downloading: 228e6710-39f0-4772-bbf7-8c515fde3737.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4724/10000] (7.88GB) Downloading: nationwidechildrens.org_ssf.TCGA-E2-A15T.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4725/10000] (7.88GB) Downloading: TCGA-E2-A15T.8FEBDA40-59FF-4E76-A9B1-F46BAB7C3E4A.PDF (0.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4726/10000] (7.88GB) Downloading: TCGA-BRCA.93d6d838-9563-4daa-ab69-5ba0073c9d1d.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4727/10000] (7.88GB) Downloading: d313dc0e-3840-487d-be90-817a1ef43f82_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4728/10000] (7.88GB) Downloading: nationwidechildrens.org_ssf.TCGA-A2-A3XX.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4729/10000] (7.88GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_B03_760348.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4730/10000] (7.88GB) Downloading: bdbef11e-3900-4bb9-b23e-d90303c82418.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4731/10000] (7.88GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A3XX.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4732/10000] (7.88GB) Downloading: 0fd2afd4-9b49-4aa5-9804-99356a092ef2.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4733/10000] (7.88GB) Downloading: f9506da9-20a3-4124-a614-eb525787ea45.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4734/10000] (7.89GB) Downloading: TCGA-A2-A3XX-01Z-00-DX1.03C6D70F-2833-4E97-91B7-DE70CD083D92.svs (986.82 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4735/10000] (8.85GB) Downloading: 7135f14b-e84f-4ebf-8d95-b2a3c843fd4d.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4736/10000] (8.85GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_F09_760364.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4737/10000] (8.85GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A15T.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4738/10000] (8.86GB) Downloading: TCGA-A2-A3XX-01A-41-A24A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4739/10000] (8.86GB) Downloading: 3de3aa60-a593-4421-9cec-21da1a171366.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4740/10000] (8.86GB) Downloading: EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6_A09_1244872.grch38.seg.v2.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4741/10000] (8.86GB) Downloading: TCGA-BRCA.93d6d838-9563-4daa-ab69-5ba0073c9d1d.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4742/10000] (8.86GB) Downloading: TCGA-BRCA.1a12cd14-3f98-41bd-b89f-c0fb2848f8d5.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4743/10000] (8.86GB) Downloading: d504a28c-f8e7-4c5e-b01a-23b4cdd1dd8a.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4744/10000] (8.87GB) Downloading: TCGA-BH-A1EN-11A-01-TSA.bd9b9222-c982-4cfa-b9b1-5d770243ed00.svs (90.86 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4745/10000] (8.95GB) Downloading: TCGA-A1-A0SH-01A-01-TSA.79c64fec-53ef-405a-b830-da132de9149d.svs (292.46 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4746/10000] (9.24GB) Downloading: TCGA-BRCA.43ba3339-996b-4477-878f-4a62c471ab5f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4747/10000] (9.24GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_G04_698124.grch38.seg.v2.txt (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4748/10000] (9.24GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_G04_698124.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4749/10000] (9.24GB) Downloading: acc69d43-989d-4ee9-a767-9470c099ad78.mirbase21.isoforms.quantification.txt (0.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4750/10000] (9.24GB) Downloading: nationwidechildrens.org_ssf.TCGA-A1-A0SH.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4751/10000] (9.24GB) Downloading: EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6_A05_1244724.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4752/10000] (9.24GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A1EN.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4753/10000] (9.24GB) Downloading: 2ee148f9-f142-417b-85e4-f689380e1315_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4754/10000] (9.25GB) Downloading: TCGA-BH-A1EN.809F294F-8C48-4719-866B-7169FB1CE24D.PDF (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4755/10000] (9.25GB) Downloading: TCGA-BRCA.d47439d3-9c7a-4dea-838d-e9955842055b.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4756/10000] (9.25GB) Downloading: 78192f60-a160-41e0-b848-cbf13c1301d9.wxs.aliquot_ensemble_masked.maf.gz (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4757/10000] (9.25GB) Downloading: 3ffcb415-e185-47b4-8cab-b06c4206845e.mirbase21.isoforms.quantification.txt (0.35 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4758/10000] (9.25GB) Downloading: 4d70b2a9-7ca6-4784-9e9b-15562a679821.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4759/10000] (9.25GB) Downloading: TCGA-BRCA.ec923957-81ba-44b9-8e2c-15305f8829a5.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4760/10000] (9.25GB) Downloading: TCGA-A1-A0SH.1FB1255E-D9EC-4FE9-BE96-F81271FCCFB6.PDF (0.32 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4761/10000] (9.26GB) Downloading: TCGA-BH-A1EN-01A-21-A17I-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4762/10000] (9.26GB) Downloading: TCGA-BRCA.ec923957-81ba-44b9-8e2c-15305f8829a5.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4763/10000] (9.26GB) Downloading: EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6_A05_1244724.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4764/10000] (9.26GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_G06_667062.nocnv_grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4765/10000] (9.26GB) Downloading: 2cfc41ee-6c94-43a1-b234-14d2e96f6db3_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4766/10000] (9.27GB) Downloading: 62afbd74-0a4e-4dd1-8e27-c4d8f3c778e6_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4767/10000] (9.27GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A3XW.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4768/10000] (9.27GB) Downloading: fe6d927f-5f78-4abd-a5a9-f3f38e8f1a4a.methylation_array.sesame.level3betas.txt (12.31 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4769/10000] (9.28GB) Downloading: TCGA-BRCA.5b9509ca-fb9c-4e51-b7d4-9c04f5cc141f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4770/10000] (9.28GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_F05_667086.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4771/10000] (9.28GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A0FL.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4772/10000] (9.28GB) Downloading: TCGA-AN-A0FL-01Z-00-DX1.20A041C6-A306-4599-A7D1-65032A252AA9.svs (1006.89 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4773/10000] (10.27GB) Downloading: 11e64dba-16d5-4a05-ae1c-de5f2cd73b96.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4774/10000] (10.27GB) Downloading: TCGA-AN-A0FL-01A-01-TSA.a9270e98-40e9-45f5-935a-681708f170c9.svs (626.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4775/10000] (10.88GB) Downloading: TCGA-BRCA.a5ec69cb-1eeb-4a12-bdc6-e7f3b6eaa7df.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4776/10000] (10.88GB) Downloading: nationwidechildrens.org_clinical.TCGA-AN-A0FL.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4777/10000] (10.88GB) Downloading: nationwidechildrens.org_ssf.TCGA-AN-A0FL.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4778/10000] (10.88GB) Downloading: 11e64dba-16d5-4a05-ae1c-de5f2cd73b96.mirbase21.isoforms.quantification.txt (0.21 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4779/10000] (10.88GB) Downloading: 83834ecf-bc98-416a-98c0-824229e6cfe0.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4780/10000] (10.88GB) Downloading: TCGA-BRCA.fec7f250-896a-40c3-a6ed-82607bf7af4d.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4781/10000] (10.88GB) Downloading: TCGA-BRCA.3ab709a7-87e2-44e5-bce1-ca2a0fc0286e.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4782/10000] (10.88GB) Downloading: 3fd9c506-ed43-45db-bff4-6e968ac19564.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4783/10000] (10.88GB) Downloading: TCGA-E2-A14V-01Z-00-DX1.D6274B5E-644C-478C-817F-B8BB9262D6F4.svs (968.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4784/10000] (11.83GB) Downloading: TCGA-A2-A3XT-01A-21-A24A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4785/10000] (11.83GB) Downloading: TCGA-BRCA.83803fb6-49a3-46a2-a927-657c4733337a.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4786/10000] (11.83GB) Downloading: ffd5af39-59ff-4c10-b45f-123847eb0103.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4787/10000] (11.83GB) Downloading: RAMIE_p_6TCGA_250_232_4_236_N_GenomeWideSNP_6_G06_1245274.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4788/10000] (11.83GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09C.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4789/10000] (11.83GB) Downloading: nationwidechildrens.org_clinical_radiation_brca.txt (0.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4790/10000] (11.83GB) Downloading: TCGA-BRCA.d8e8db6d-4f38-4ef6-a77a-d3ea769cc78f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4791/10000] (11.84GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_G10_799898.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4792/10000] (11.84GB) Downloading: TCGA-BH-A0B6-01A-01-TSA.263AFB9B-2F32-4E0F-815A-9A45FF271800.svs (254.33 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4793/10000] (12.09GB) Downloading: 7d1d43ef-4bcb-40a2-84b4-040b02844551.methylation_array.sesame.level3betas.txt (0.73 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4794/10000] (12.09GB) Downloading: TCGA-D8-A27G-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4795/10000] (12.09GB) Downloading: TCGA-BRCA.4bc204b6-5ec6-4786-9504-209305c82371.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4796/10000] (12.09GB) Downloading: TCGA-BRCA.38f3fe40-a4aa-4f30-94a1-91e54c11c99b.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4797/10000] (12.09GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_D02_1343828.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4798/10000] (12.09GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_H04_735322.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4799/10000] (12.09GB) Downloading: f9c68e7b-13e7-4b2a-90c2-6187d3b02610.mirbase21.isoforms.quantification.txt (0.31 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4800/10000] (12.09GB) Downloading: TCGA-BRCA.84a2d172-c9f4-4ce9-8ee8-6ec6b5d4a747.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4801/10000] (12.09GB) Downloading: TCGA-C8-A12V.8ED8A37B-C885-4333-AC5D-EA73A5A81173.PDF (0.22 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4802/10000] (12.09GB) Downloading: a1d5d127-be2e-4173-b07e-539e0314fd33.methylation_array.sesame.level3betas.txt (12.54 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4803/10000] (12.10GB) Downloading: TCGA-C8-A12V-01A-01-TSA.e3f84baa-0829-4683-a26c-b50c7f732f4a.svs (240.77 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4804/10000] (12.34GB) Downloading: d51b0428-1d4d-45bc-bb61-e290845d6423.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4805/10000] (12.34GB) Downloading: TCGA-BRCA.4bc204b6-5ec6-4786-9504-209305c82371.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4806/10000] (12.34GB) Downloading: TCGA-BRCA.aee8a3d7-7392-4e87-8315-b4fb849705fe.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4807/10000] (12.34GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_F12_1343816.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4808/10000] (12.34GB) Downloading: ae4877c3-2ab0-424b-b32f-42ea18a48b51.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4809/10000] (12.34GB) Downloading: TCGA-BH-A0B6.06602AD0-AC4D-4674-B4B0-2D207C3E78DC.PDF (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4810/10000] (12.34GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_H04_735322.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4811/10000] (12.34GB) Downloading: TCGA-BRCA.aee8a3d7-7392-4e87-8315-b4fb849705fe.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4812/10000] (12.34GB) Downloading: 75e5a3c4-844d-4409-9fbb-6e0a383d4642.wgs.ASCAT.copy_number_variation.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4813/10000] (12.34GB) Downloading: TCGA-A2-A1G0.DA82E751-09C3-466E-A63A-38368D8A2C7C.PDF (0.45 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4814/10000] (12.34GB) Downloading: TCGA-BRCA.454e0016-63ac-4727-a1bd-0319b09d17a0.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4815/10000] (12.34GB) Downloading: TCGA-BRCA.84a2d172-c9f4-4ce9-8ee8-6ec6b5d4a747.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4816/10000] (12.34GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A1Y3.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4817/10000] (12.34GB) Downloading: TCGA-BH-A0B6-01A-21-A24A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4818/10000] (12.34GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_H02_787620.nocnv_grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4819/10000] (12.34GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0B6.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4820/10000] (12.34GB) Downloading: TCGA-D8-A1Y3-01Z-00-DX1.8AA5F695-A06C-4DEA-AD71-16254A48B218.svs (1199.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4821/10000] (13.52GB) Downloading: e6e72b0e-4244-4b0d-ba32-9f1f77dc941e.methylation_array.sesame.level3betas.txt (12.56 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4822/10000] (13.53GB) Downloading: d51b0428-1d4d-45bc-bb61-e290845d6423.mirbase21.isoforms.quantification.txt (0.43 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4823/10000] (13.53GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A12V.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4824/10000] (13.53GB) Downloading: cda8d0f6-6325-4333-98d3-2edc188de249.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4825/10000] (13.53GB) Downloading: TCGA-C8-A12V-01Z-00-DX1.84B29360-B87B-4648-A697-B6610336C2BB.svs (1257.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4826/10000] (14.76GB) Downloading: nationwidechildrens.org_ssf.TCGA-C8-A12V.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4827/10000] (14.76GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-D8-A1Y3.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4828/10000] (14.76GB) Downloading: TCGA-BRCA.454e0016-63ac-4727-a1bd-0319b09d17a0.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4829/10000] (14.76GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_H02_787620.grch38.seg.v2.txt (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4830/10000] (14.76GB) Downloading: 94fd6642-9ecb-49a8-a7f6-d74e7e152ad7.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4831/10000] (14.76GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A1Y3.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4832/10000] (14.76GB) Downloading: TCGA-BRCA.0da7828c-fa60-464e-bf84-43de16003663.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4833/10000] (14.76GB) Downloading: 75d14ed3-7ab5-47ae-b521-abf8a8f0c69d.methylation_array.sesame.level3betas.txt (12.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4834/10000] (14.77GB) Downloading: TCGA-A2-A0ET-01A-03-TSC.74515b85-25d8-4c5a-9fe8-027a78238b9a.svs (376.30 MB)... "
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.14 GB).\n",
+      "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "de28aa83373b44c8b795cce809dc7664",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Processing Files (0 / 0): |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
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+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "New Data Upload: |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
     }
    ],
    "source": [

data/gdc_data_organized/0807435a-e75e-4e04-8e45-ed0cd49a841a/COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_D03_667110.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,244 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	3301765	7857572	2950	-0.004
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	7858444	15956281	4166	-0.045
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	15960576	16328359	147	0.3923
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	16328513	22942356	3814	-0.0279
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	22944939	55606657	17131	-0.0478
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	55606713	88274240	21128	-0.0278
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	88274883	88275182	4	-1.1997
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	88276233	107395742	11070	-0.0244
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	107395883	111686404	2503	-0.061
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	111691119	119984772	5254	-0.0278
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	146716041	151630186	639	0.6976
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	151633929	154895579	1772	0.762
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	154902467	156831013	824	0.7035
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	156831449	157361097	308	0.7785
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	157361351	157361365	2	-0.4801
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	157361617	163546615	4189	0.7739
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	163546727	163551883	3	-0.4168
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	163554603	186055873	14819	0.7777
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	186059954	197686896	6730	0.8117
+8b4314b3-0f2a-4451-87ff-ad498c7a1ab9	1	197686941	200345490	1687	0.7807
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data/gdc_data_organized/0807435a-e75e-4e04-8e45-ed0cd49a841a/COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_E06_667172.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,225 @@
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+<bio:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/biospecimen/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/biospecimen/2.7/TCGA_BCR.Biospecimen.xsd" schemaVersion="2.7" xmlns:bio="http://tcga.nci/bcr/xml/biospecimen/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:bio_shared="http://tcga.nci/bcr/xml/biospecimen/shared/2.7">
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+        <admin:batch_number xsd_ver="1.17">56.91.0</admin:batch_number>
+        <admin:project_code xsd_ver="">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">1</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">7</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+    </admin:admin>
+    <bio:patient>
+        <admin:additional_studies/>
+        <shared:bcr_patient_barcode cde="2673794" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0807435a-e75e-4e04-8e45-ed0cd49a841a</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B6</shared:tissue_source_site>
+        <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A0IA</shared:patient_id>
+        <shared:gender cde="2200604" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+        <bio:days_to_index precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">0</bio:days_to_index>
+        <bio:bcr_canonical_check>
+            <bio:bcr_patient_canonical_status cde="" xsd_ver="2.6" procurement_status="Completed" owner="">Canonical</bio:bcr_patient_canonical_status>
+        </bio:bcr_canonical_check>
+        <bio:samples>
+            <bio:sample>
+                <admin:additional_studies/>
+                <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:sample_type_id>
+                <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
+                <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Primary Tumor</bio:sample_type>
+                <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">70</bio:initial_weight>
+                <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">true</bio:oct_embedded>
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+                <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">6664</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ef8c35b3-bdab-4a7e-b5ab-a0a99f4db803</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
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+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f051422c-cb96-4b79-b8ab-3f7f8dd6b8ef</bio:bcr_portion_uuid>
+                        <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                        <bio:analytes>
+                            <bio:analyte>
+                                <admin:additional_studies/>
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+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
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+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8e91b3ea-cb20-4f40-a251-a57d762db01d</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A032</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
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+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D-A032-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8d86bb8c-cc51-429a-aabd-4a33b200ce97</bio:bcr_aliquot_uuid>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A033</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
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+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D-A033-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">68ca279a-4b0b-47e4-959c-85e9094e3604</bio:bcr_aliquot_uuid>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A036</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D-A036-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8b4314b3-0f2a-4451-87ff-ad498c7a1ab9</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.13</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A044</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D-A044-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3d5b4054-e0e5-40e4-b772-629afdb8e0a8</bio:bcr_aliquot_uuid>
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+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.80</bio:quantity>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100478845</bio:biospecimen_barcode_bottom>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A045</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11D-A045-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">269851a0-323a-49ea-bb89-6e49b98d27e3</bio:bcr_aliquot_uuid>
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+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.20</bio:quantity>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
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+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
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+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.81</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">320bfd43-5779-46ed-93da-5b4dbea19637</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A034</bio:plate_id>
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+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11R-A034-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">80cfaf9d-f0aa-4a35-918a-2eaad05b3a5a</bio:bcr_aliquot_uuid>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
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+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11R-A035-13</bio:bcr_aliquot_barcode>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:rna>
+                                    <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.30</bio:ratio_28s_18s>
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+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
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+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
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+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E0E1E443-D442-47B6-8D0A-A41CEB123695</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A050</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11W-A050-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f7e5ada6-8f53-4765-a874-5ee9d258ad6a</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100470781</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A051</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11W-A051-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1d23b155-df74-4ab4-ad51-59c6a79ec7dc</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100470877</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7C024684-3BF5-444B-977C-B4CDDA47C5E7</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A048</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11X-A048-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">158638b7-6b88-4f60-ac4c-cfe4b50d0a4f</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100472509</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A049</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-11X-A049-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">14d6b6c9-ac9c-4f10-a2f7-5df12576da5a</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100472221</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G X</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-01-BSA</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6a397611-09c6-4511-bfa0-f423c3d35488</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-01-BSA.6a397611-09c6-4511-bfa0-f423c3d35488.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-01-TSA</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">77975eac-fd36-4fd6-915f-279f8ede5437</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A0IA-01A-01-TSA.77975eac-fd36-4fd6-915f-279f8ede5437.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                        </bio:slides>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">55F3F917-E441-4C10-A3E3-0645A4E8374E</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A0IA.55F3F917-E441-4C10-A3E3-0645A4E8374E.pdf</bio:pathology_report_file_name>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                    <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">8A868F0A-6CE2-46A7-AF0C-C5FC5D657D86</bio:ffpe_slide_uuid>
+                </bio:diagnostic_slides>
+            </bio:sample>
+            <bio:sample>
+                <admin:additional_studies/>
+                <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
+                <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
+                <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
+                <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
+                <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">6664</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">adb9716c-39ea-45c1-9148-d4b22f9f0da3</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">27</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">323a94f0-d249-4f7f-826f-2b86d9fb0c40</bio:bcr_portion_uuid>
+                        <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                        <bio:analytes>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.88</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">cc786776-7c37-4b54-b839-8ea94d17cb0d</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A031</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01D-A031-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4ea541e8-83a9-4d38-8d91-62329693ab5b</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.30</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099052601</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
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+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
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+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6099225e-8be5-4a60-9b09-76bd3c97775d</bio:bcr_aliquot_uuid>
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+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01D-A046-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e2aa51a2-e29a-494a-91b6-fd0da5f1e95c</bio:bcr_aliquot_uuid>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A047</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01D-A047-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3198ff37-5f9f-4ec2-83a6-5bacef6b6bfb</bio:bcr_aliquot_uuid>
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+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Pre-extracted DNA received by TSS</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">888D6F26-F545-4F15-BE5A-83E531CD07B7</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A053</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01W-A053-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8fbcfe49-3871-4d7e-85d8-03cbbeed90a8</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A055</bio:plate_id>
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+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01W-A055-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5b3fdff1-5930-419f-a5e4-46554ae2f80f</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
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+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5DDF5191-BEE0-4AC2-A270-5C0ABBEC41A9</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
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+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
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+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01X-A052-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">fb9e5e35-949b-4fef-896e-6ec93bc0008a</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
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+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100480573</bio:biospecimen_barcode_bottom>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A054</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A0IA-10A-01X-A054-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">304ee3bb-0c2f-4b70-bcd2-35d8bccc1643</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100480279</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G X</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides/>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                </bio:diagnostic_slides>
+            </bio:sample>
+        </bio:samples>
+    </bio:patient>
+</bio:tcga_bcr>

data/gdc_data_organized/0807435a-e75e-4e04-8e45-ed0cd49a841a/nationwidechildrens.org_clinical.TCGA-B6-A0IA.xml

@@ -0,0 +1,265 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<brca:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/brca/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/brca/2.7/TCGA_BCR.BRCA_Clinical.xsd" schemaVersion="2.7" xmlns:brca="http://tcga.nci/bcr/xml/clinical/brca/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:brca_shared="http://tcga.nci/bcr/xml/clinical/brca/shared/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:brca_nte="http://tcga.nci/bcr/xml/clinical/brca/shared/new_tumor_event/2.7/1.0" xmlns:nte="http://tcga.nci/bcr/xml/clinical/shared/new_tumor_event/2.7" xmlns:follow_up_v2.1="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/2.1" xmlns:follow_up_v4.0="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/4.0" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">87759AFE-A3E7-4A9B-ACCC-7C71F503B648</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">56.91.0</admin:batch_number>
+        <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+        <admin:patient_withdrawal>
+            <admin:withdrawn>false</admin:withdrawn>
+        </admin:patient_withdrawal>
+        <admin:program xsi:nil="true" xsd_ver="2.7"/>
+        <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
+    </admin:admin>
+    <brca:patient>
+        <admin:additional_studies/>
+        <clin_shared:tumor_tissue_site preferred_name="submitted_tumor_site" display_order="9999" cde="3427536" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252257">Breast</clin_shared:tumor_tissue_site>
+        <clin_shared:tumor_tissue_site_other preferred_name="site_of_primary_tumor_other" display_order="999" cde="2584114" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="252258" xsi:nil="true"/>
+        <shared:other_dx preferred_name="history_other_malignancy" display_order="14" cde="3382736" cde_ver="2.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243591">No</shared:other_dx>
+        <shared:gender preferred_name="gender" display_order="10" cde="2200604" cde_ver="3.000" xsd_ver="1.8" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243582">FEMALE</shared:gender>
+        <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243587">Alive</clin_shared:vital_status>
+        <clin_shared:days_to_birth precision="day" xsd_ver="1.12" tier="1" cde="3008233" owner="TSS" procurement_status="Completed" preferred_name="birth_days_to" display_order="9" cde_ver="1.000">-18748</clin_shared:days_to_birth>
+        <clin_shared:days_to_last_known_alive precision="day" xsd_ver="2.1" tier="2" cde="" owner="TSS" procurement_status="Not Available" preferred_name="" display_order="9999" cde_ver=""/>
+        <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+        <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">6719</clin_shared:days_to_last_followup>
+        <clin_shared:race_list>
+            <clin_shared:race preferred_name="race" display_order="12" cde="2192199" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243589">WHITE</clin_shared:race>
+        </clin_shared:race_list>
+        <shared:bcr_patient_barcode preferred_name="" display_order="9999" cde="2003301" cde_ver="" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false">TCGA-B6-A0IA</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">B6</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0IA</shared:patient_id>
+        <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">0807435a-e75e-4e04-8e45-ed0cd49a841a</shared:bcr_patient_uuid>
+        <shared:history_of_neoadjuvant_treatment preferred_name="history_neoadjuvant_treatment" display_order="15" cde="3382737" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243592">No</shared:history_of_neoadjuvant_treatment>
+        <clin_shared:informed_consent_verified preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false">YES</clin_shared:informed_consent_verified>
+        <clin_shared:icd_o_3_site preferred_name="" display_order="9999" cde="3226281" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_o_3_site>
+        <clin_shared:icd_o_3_histology preferred_name="" display_order="9999" cde="3226275" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">8523/3</clin_shared:icd_o_3_histology>
+        <clin_shared:icd_10 preferred_name="" display_order="9999" cde="3226287" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_10>
+        <clin_shared:days_to_initial_pathologic_diagnosis precision="day" xsd_ver="1.12" tier="1" cde="3131740" owner="TSS" procurement_status="Completed" preferred_name="initial_pathologic_dx_days_to" display_order="9999" cde_ver="1.000">0</clin_shared:days_to_initial_pathologic_diagnosis>
+        <clin_shared:age_at_initial_pathologic_diagnosis precision="day" xsd_ver="1.12" tier="1" cde="2006657" owner="TSS" procurement_status="Completed">51</clin_shared:age_at_initial_pathologic_diagnosis>
+        <clin_shared:year_of_initial_pathologic_diagnosis preferred_name="initial_pathologic_dx_year" display_order="34" cde="2896960" cde_ver="1.000" xsd_ver="1.12" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252264">1992</clin_shared:year_of_initial_pathologic_diagnosis>
+        <clin_shared:ethnicity preferred_name="ethnicity" display_order="13" cde="2192217" cde_ver="2.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243590">NOT HISPANIC OR LATINO</clin_shared:ethnicity>
+        <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243588">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+        <clin_shared:primary_lymph_node_presentation_assessment preferred_name="lymph_nodes_examined" display_order="47" cde="2200396" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <clin_shared:lymph_node_examined_count preferred_name="lymph_nodes_examined_count" display_order="48" cde="3" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252276">15</clin_shared:lymph_node_examined_count>
+        <brca_shared:er_detection_method_text preferred_name="er_positivity_method" display_order="63" cde="69" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252289">IHC</brca_shared:er_detection_method_text>
+        <brca_shared:pgr_detection_method_text preferred_name="pr_positivity_define_method" display_order="69" cde="785" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252294">IHC</brca_shared:pgr_detection_method_text>
+        <brca:anatomic_neoplasm_subdivisions>
+            <clin_shared:anatomic_neoplasm_subdivision preferred_name="anatomic_organ_subdivision" display_order="9999" cde="3108203" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252259">Right</clin_shared:anatomic_neoplasm_subdivision>
+        </brca:anatomic_neoplasm_subdivisions>
+        <brca_shared:her2_neu_chromosone_17_signal_ratio_value preferred_name="her2_cent17_ratio" display_order="79" cde="2497552" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252304"/>
+        <brca:axillary_lymph_node_stage_method_type preferred_name="axillary_staging_method" display_order="44" cde="2516112" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252273">Axillary lymph node dissection alone</brca:axillary_lymph_node_stage_method_type>
+        <brca:axillary_lymph_node_stage_other_method_descriptive_text preferred_name="axillary_staging_method_other" display_order="45" cde="3124496" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252274"/>
+        <brca:breast_carcinoma_surgical_procedure_name preferred_name="surgical_procedure_first" display_order="38" cde="2739580" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252267">Other</brca:breast_carcinoma_surgical_procedure_name>
+        <brca:breast_neoplasm_other_surgical_procedure_descriptive_text preferred_name="surgery_for_positive_margins_other" display_order="42" cde="3124493" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="252271" xsi:nil="true"/>
+        <brca:breast_carcinoma_primary_surgical_procedure_name preferred_name="surgery_for_positive_margins" display_order="41" cde="1218" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252270"/>
+        <brca:surgical_procedure_purpose_other_text preferred_name="first_surgical_procedure_other" display_order="39" cde="3020338" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252268">Excisional biopsy</brca:surgical_procedure_purpose_other_text>
+        <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252260">Other, specify</shared:histological_type>
+        <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252261">Ductal/Cribiform</shared:histological_type_other>
+        <clin_shared:menopause_status preferred_name="menopause_status" display_order="11" cde="2957270" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243586">Indeterminate (neither Pre or Postmenopausal)</clin_shared:menopause_status>
+        <brca_shared:breast_carcinoma_progesterone_receptor_status preferred_name="pr_status_by_ihc" display_order="64" cde="2957357" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252290">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
+        <brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator preferred_name="micromet_detection_by_ihc" display_order="46" cde="3086152" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252275">NO</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
+        <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252287"/>
+        <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252297"/>
+        <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252272"/>
+        <clin_shared:margin_status preferred_name="margin_status" display_order="40" cde="3114007" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252269">Negative</clin_shared:margin_status>
+        <clin_shared:initial_pathologic_diagnosis_method preferred_name="method_initial_path_dx" display_order="36" cde="2757941" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252265">Other method, specify:</clin_shared:initial_pathologic_diagnosis_method>
+        <clin_shared:init_pathology_dx_method_other preferred_name="method_initial_path_dx_other" display_order="37" cde="2757948" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252266">Biopsy, NOS</clin_shared:init_pathology_dx_method_other>
+        <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252300"/>
+        <brca_shared:breast_carcinoma_estrogen_receptor_status preferred_name="er_status_by_ihc" display_order="58" cde="2957359" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252285">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
+        <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Evaluated" restricted="false" source_system_identifier="252295"/>
+        <clin_shared:number_of_lymphnodes_positive_by_ihc preferred_name="lymph_nodes_examined_ihc_count" display_order="50" cde="3086383" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252278"/>
+        <clin_shared:number_of_lymphnodes_positive_by_he preferred_name="lymph_nodes_examined_he_count" display_order="49" cde="3086388" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252277">0</clin_shared:number_of_lymphnodes_positive_by_he>
+        <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252293"/>
+        <brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text preferred_name="er_positivity_scale_other" display_order="62" cde="3086851" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252288"/>
+        <brca_shared:her2_erbb_pos_finding_cell_percent_category preferred_name="her2_ihc_percent_positive" display_order="71" cde="3086980" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252296"/>
+        <brca_shared:pos_finding_her2_erbb2_other_measurement_scale_text preferred_name="her2_positivity_scale_other" display_order="73" cde="3087479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252298"/>
+        <brca_shared:her2_erbb_method_calculation_method_text preferred_name="her2_positivity_method_text" display_order="74" cde="3087487" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252299"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count preferred_name="her2_and_cent17_cells_count" display_order="78" cde="3087902" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252303"/>
+        <brca_shared:her2_and_centromere_17_positive_finding_other_measurement_scale_text preferred_name="her2_and_cent17_scale_other" display_order="80" cde="3087923" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252305"/>
+        <brca_shared:her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="her2_fish_method" display_order="81" cde="3087929" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252306"/>
+        <clin_shared:tissue_prospective_collection_indicator preferred_name="prospective_collection" display_order="4" cde="3088492" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243538">NO</clin_shared:tissue_prospective_collection_indicator>
+        <clin_shared:tissue_retrospective_collection_indicator preferred_name="retrospective_collection" display_order="5" cde="3088528" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243539">YES</clin_shared:tissue_retrospective_collection_indicator>
+        <brca_shared:fluorescence_in_situ_hybridization_diagnostic_procedure_chromosome_17_signal_result_range preferred_name="cent17_copy_number" display_order="77" cde="3104295" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252302"/>
+        <brca:first_nonlymph_node_metastasis_anatomic_sites>
+            <clin_shared:metastatic_site_at_diagnosis preferred_name="metastasis_site" display_order="56" cde="3124499" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252283"/>
+            <clin_shared:metastatic_site_at_diagnosis_other preferred_name="metastasis_site_other" display_order="57" cde="3124503" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252284"/>
+        </brca:first_nonlymph_node_metastasis_anatomic_sites>
+        <brca_shared:er_level_cell_percentage_category preferred_name="er_status_ihc_Percent_Positive" display_order="59" cde="3128341" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252286"/>
+        <brca_shared:progesterone_receptor_level_cell_percent_category preferred_name="pr_status_ihc_percent_positive" display_order="65" cde="3128342" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252291"/>
+        <brca:distant_metastasis_present_ind2 preferred_name="metastatic_tumor_indicator" display_order="999" cde="2194698" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252307"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252308"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252309"/>
+        <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252310"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252311"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252312"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252317"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252313"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252314"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252315"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252316"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252318"/>
+        <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252319"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252320"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252321"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252322"/>
+        <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252324"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252325"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252326"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252327"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252328"/>
+        <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252323"/>
+        <brca_shared:her2_neu_breast_carcinoma_copy_analysis_input_total_number preferred_name="her2_copy_number" display_order="76" cde="3133738" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252301"/>
+        <brca:breast_carcinoma_immunohistochemistry_progesterone_receptor_pos_finding_scale preferred_name="pr_positivity_scale_used" display_order="66" cde="3203083" cde_ver="1.000" xsd_ver="2.4.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="252292"/>
+        <shared_stage:stage_event system="AJCC">
+            <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1079845"/>
+            <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252282">Stage IIA</shared_stage:pathologic_stage>
+            <shared_stage:tnm_categories>
+                <shared_stage:clinical_categories>
+                    <shared_stage:clinical_T preferred_name="ajcc_tumor_clinical_ct" display_order="9999" cde="3440328" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <shared_stage:clinical_N preferred_name="ajcc_nodes_clinical_cn" display_order="9999" cde="3440330" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                    <shared_stage:clinical_M preferred_name="ajcc_metastasis_clinical_cm" display_order="9999" cde="3440331" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                </shared_stage:clinical_categories>
+                <shared_stage:pathologic_categories>
+                    <shared_stage:pathologic_T preferred_name="ajcc_tumor_pathologic_pt" display_order="52" cde="3045435" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252279">T2</shared_stage:pathologic_T>
+                    <shared_stage:pathologic_N preferred_name="ajcc_nodes_pathologic_pn" display_order="53" cde="3203106" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252280">N0 (i-)</shared_stage:pathologic_N>
+                    <shared_stage:pathologic_M preferred_name="ajcc_metastasis_pathologic_pm" display_order="54" cde="3045439" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="252281">M0</shared_stage:pathologic_M>
+                </shared_stage:pathologic_categories>
+            </shared_stage:tnm_categories>
+            <shared_stage:psa>
+                <shared_stage:psa_value preferred_name="psa_most_recent_results" display_order="9999" cde="3351903" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:days_to_psa precision="day" xsd_ver="2.6" tier="2" cde="3414608" owner="TSS" procurement_status="Not Applicable" preferred_name="days_to_psa_most_recent" display_order="9999" cde_ver="1.000"/>
+            </shared_stage:psa>
+            <shared_stage:gleason_grading>
+                <shared_stage:gleason_score preferred_name="gleason_score" display_order="9999" cde="2534619" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:primary_pattern preferred_name="gleason_pattern_primary" display_order="9999" cde="2534617" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:secondary_pattern preferred_name="gleason_pattern_secondary" display_order="9999" cde="2534618" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:tertiary_pattern preferred_name="gleason_pattern_tertiary" display_order="9999" cde="2783875" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:gleason_grading>
+            <shared_stage:ann_arbor>
+                <shared_stage:b_symptoms preferred_name="b_symptoms_present_indicator" display_order="9999" cde="2902402" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:extranodal_involvement preferred_name="extranodal_lymphomatous_involvement" display_order="9999" cde="3364582" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:ann_arbor>
+            <shared_stage:serum_markers preferred_name="" display_order="9999" cde="3901772" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:igcccg_stage preferred_name="" display_order="9999" cde="3901822" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:masaoka_stage preferred_name="" display_order="9999" cde="3952848" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+        </shared_stage:stage_event>
+        <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_nte:new_tumor_events>
+            <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        </brca_nte:new_tumor_events>
+        <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243536">2</clin_shared:day_of_form_completion>
+        <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243535">11</clin_shared:month_of_form_completion>
+        <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="243537">2010</clin_shared:year_of_form_completion>
+        <brca:follow_ups>
+            <follow_up_v2.1:follow_up version="2.1" sequence="1">
+                <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-B6-A0IA-F12610</clin_shared:bcr_followup_barcode>
+                <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">4D334E64-3DE2-4A7D-BEAC-5E9B8813CA01</clin_shared:bcr_followup_uuid>
+                <clin_shared:followup_case_report_form_submission_reason preferred_name="followup_reason" display_order="999" cde="3233305" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991490">Scheduled Follow-up Submission</clin_shared:followup_case_report_form_submission_reason>
+                <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991491">NO</clin_shared:radiation_therapy>
+                <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991492">YES</clin_shared:postoperative_rx_tx>
+                <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991493">Alive</clin_shared:vital_status>
+                <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">6719</clin_shared:days_to_last_followup>
+                <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+                <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991500">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+                <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991501">NO</nte:new_tumor_event_after_initial_treatment>
+                <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Applicable" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
+                <nte:new_neoplasm_event_type preferred_name="new_tumor_event_type" display_order="83" cde="3119721" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991505"/>
+                <nte:new_neoplasm_event_occurrence_anatomic_site preferred_name="new_tumor_event_site" display_order="84" cde="3108271" cde_ver="2.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991506"/>
+                <nte:new_neoplasm_occurrence_anatomic_site_text preferred_name="new_tumor_event_site_other" display_order="85" cde="3128033" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991507"/>
+                <nte:additional_surgery_locoregional_procedure preferred_name="new_tumor_event_surgery" display_order="999" cde="3008755" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991508"/>
+                <nte:days_to_additional_surgery_metastatic_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408682" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_met" display_order="9999" cde_ver="1.000"/>
+                <nte:additional_radiation_therapy preferred_name="new_tumor_event_radiation_tx" display_order="95" cde="3427615" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991512"/>
+                <nte:additional_pharmaceutical_therapy preferred_name="new_tumor_event_pharmaceutical_tx" display_order="96" cde="3427616" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991513"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991514"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991515"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_positive_finding_scale_type preferred_name="nte_er_positivity_scale_used" display_order="99" cde="3203082" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991516"/>
+                <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991517"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991518"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991519"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991520"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991521"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_progesterone_receptor_positive_finding_scale_type preferred_name="nte_pr_positivity_scale_used" display_order="105" cde="3203085" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991522"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991523"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991524"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991525"/>
+                <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991526"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991527"/>
+                <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991528"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991529"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991530"/>
+                <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991531"/>
+                <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991532"/>
+                <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991533"/>
+                <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991534"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991535"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991536"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="991537"/>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991488">1</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991487">6</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="991489">2011</clin_shared:year_of_form_completion>
+            </follow_up_v2.1:follow_up>
+            <follow_up_v4.0:follow_up version="4.0" sequence="2">
+                <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-B6-A0IA-F71513</clin_shared:bcr_followup_barcode>
+                <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">0F55E065-C77C-4851-8F2E-1E223AF5CE7C</clin_shared:bcr_followup_uuid>
+                <clin_shared:lost_follow_up preferred_name="followup_lost_to" display_order="4" cde="61333" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4127105">NO</clin_shared:lost_follow_up>
+                <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4127106">NO</clin_shared:radiation_therapy>
+                <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4127107">YES</clin_shared:postoperative_rx_tx>
+                <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4127108">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+                <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4127109">Alive</clin_shared:vital_status>
+                <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">8391</clin_shared:days_to_last_followup>
+                <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+                <brca_nte:new_tumor_events>
+                    <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="4128608">NO</nte:new_tumor_event_after_initial_treatment>
+                    <brca_nte:new_tumor_event>
+                        <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
+                        <nte:new_neoplasm_event_type preferred_name="new_tumor_event_type" display_order="83" cde="3119721" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128609"/>
+                        <nte:new_neoplasm_event_occurrence_anatomic_site preferred_name="new_tumor_event_site" display_order="84" cde="3108271" cde_ver="2.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128610"/>
+                        <nte:new_neoplasm_occurrence_anatomic_site_text preferred_name="new_tumor_event_site_other" display_order="85" cde="3128033" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128611"/>
+                        <nte:new_tumor_event_additional_surgery_procedure preferred_name="new_tumor_event_surgery" display_order="90" cde="3427611" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128616"/>
+                        <nte:days_to_new_tumor_event_additional_surgery_procedure precision="day" xsd_ver="2.5" tier="2" cde="3008335" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to" display_order="94" cde_ver="1.000"/>
+                        <nte:additional_radiation_therapy preferred_name="new_tumor_event_radiation_tx" display_order="95" cde="3427615" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128621"/>
+                        <nte:additional_pharmaceutical_therapy preferred_name="new_tumor_event_pharmaceutical_tx" display_order="96" cde="3427616" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128622"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128623"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128624"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_positive_finding_scale_type preferred_name="nte_er_positivity_scale_used" display_order="99" cde="3203082" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128625"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128626"/>
+                        <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128627"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128628"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128629"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128630"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_progesterone_receptor_positive_finding_scale_type preferred_name="nte_pr_positivity_scale_used" display_order="105" cde="3203085" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128631"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128632"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128633"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128634"/>
+                        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128635"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128636"/>
+                        <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128637"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128638"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128639"/>
+                        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128640"/>
+                        <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128641"/>
+                        <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128642"/>
+                        <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128643"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128644"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128645"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="4128646"/>
+                    </brca_nte:new_tumor_event>
+                </brca_nte:new_tumor_events>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">26</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">3</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2015</clin_shared:year_of_form_completion>
+            </follow_up_v4.0:follow_up>
+        </brca:follow_ups>
+        <rx:drugs/>
+        <rad:radiations/>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/2779fa01-ac93-4e80-a997-3385f72172c3/TCGA-BRCA.3ab709a7-87e2-44e5-bce1-ca2a0fc0286e.ascat3.allelic_specific.seg.txt

@@ -0,0 +1,54 @@
+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr1	61735	112706169	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr1	112709921	115763959	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr1	115764777	116343608	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr1	116344505	248930189	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr2	12784	242147305	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr3	18667	198169247	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr4	12281	190106768	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr5	15532	181363319	2	2	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr6	149661	170741917	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr7	43259	159334314	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr8	81254	41632237	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr8	41633621	145072769	4	3	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr9	46587	138200944	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr10	26823	133769379	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	198572	69039644	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	69048055	69096945	6	5	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	69097201	69722153	9	8	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	69724133	69884020	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	69884534	72019669	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	72028377	76112073	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	76121828	76733615	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr11	76736415	135074876	1	1	0
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr12	51460	133201603	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr13	18452809	114342922	2	1	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr14	18225647	21953454	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr14	21954753	22514241	6	4	2
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr14	22519044	106877229	3	2	1
+3ab709a7-87e2-44e5-bce1-ca2a0fc0286e	chr15	19811075	101928837	2	1	1
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+5b354ba0-d2f1-4ada-b203-fb4175afeacd	Y	13483009	56872112	3359	-2.2361

data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_B03_628532.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,67 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
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data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H05_628424.grch38.seg.v2.txt

@@ -0,0 +1,483 @@
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+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	19	35375899	43198881	3864	-0.0747
+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	19	43199352	43262860	23	-0.8449
+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	19	43263109	58586487	8492	-0.0635
+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	20	80664	1580276	1202	0.2022
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+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	21	13803967	46677045	23596	-0.0683
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+8bb0471f-9d25-4c27-9a4c-ecc00090a7da	22	18547989	20760313	1177	0.0023
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data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/TCGA-A8-A095-01A-01-TS1.6e35462c-2639-48ee-9503-d2689ebb0346.svs

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+oid sha256:a22ed6ebd438909f6181f9cad0e34ab8e800e0b947a03d47d13f71996407ca25
+size 536990663

data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/TCGA-A8-A095-01A-21-A13B-20_RPPA_data.tsv

@@ -0,0 +1,488 @@
+AGID	lab_id	catalog_number	set_id	peptide_target	protein_expression
+AGID00100	882	sc-628	Old	1433BETA	0.60836
+AGID00111	913	sc-23957	Old	1433EPSILON	0.19418
+AGID00101	883	sc-1019	Old	1433ZETA	-0.49883
+AGID00001	2	9452	Old	4EBP1	-0.81888
+AGID00002	3	9456	Old	4EBP1_pS65	-0.26082
+AGID00003	6	9459	Old	4EBP1_pT37T46	-0.073534
+AGID00443	8	9455	Old	4EBP1_pT70	-0.20597
+AGID00120	985	4937	Old	53BP1	-0.97359
+AGID00004	13	3661	Old	ACC_pS79	-0.99214
+AGID00005	14	1768-1/ab45174	Old	ACC1	-0.81741
+AGID00408	2372	3658	Set163	AceCS1	-0.823545386854048
+AGID00473	1182	5335	Old	ACETYLATUBULINLYS40	-2.0139
+AGID00404	2367	9189	Set163	ACSL1	-0.406684918147987
+AGID02144	2450	PA5-27081	Old	ACVRL1	0.093024
+AGID00186	1198	ab88574	Old	ADAR1	-0.43869
+AGID00146	1084	4691	Old	AKT	-0.55959
+AGID00028	230	9271	Old	AKT_pS473	0.33386
+AGID00170	1154	2965	Old	AKT_pT308	-0.071172
+AGID00316	1800	3063	Set163	Akt2	-0.280699876793093
+AGID00347	2009	8599	Set163	Akt2_pS474	0.500284560951983
+AGID02215	2577	ab195377	Set163	ALKBH5	-1.2546800885842
+AGID00498	924	CA1030	Old	ALPHACATENIN	NA
+AGID00287	1630	ABC80	Set163	Ambra1_pS52	0.30874927895381
+AGID00236	1351	ab129081	Set163	AMPK-a2_pS345	0.296900028384376
+AGID00006	39	2532	Old	AMPKALPHA	-0.64495
+AGID00007	40	2535	Old	AMPKALPHA_pT172	-0.6841
+AGID00193	1208	610066	Old	ANNEXIN1	-0.22481
+AGID00166	1142	610668	Old	ANNEXINVII	0.13866
+AGID00371	756	1852-1/ab52615	Old	AR	0.79008
+AGID00194	1217	4432	Old	ARAF	-0.32936
+AGID02191	2507	PA5-39728	Old	ARAF_pS299	0.13519
+AGID00260	1053	sc-32761	Old	ARID1A	0.29897
+AGID00264	1560	HPA029318	Old	ASNS	-0.43806
+AGID00276	1612	3415	Set163	Atg3	-0.0212449417149896
+AGID00309	1775	13507	Set163	Atg4B	0.526414604620244
+AGID00310	1776	12994	Set163	Atg5	-0.646114969718134
+AGID00277	1613	8558	Set163	Atg7	-0.183254878638597
+AGID00242	1363	2873	Old	ATM	-0.4569
+AGID02142	2447	13050	Set163	ATM_pS1981	0.419219977646005
+AGID00217	1289	ab14748	Set163	ATP5A	0.0660044779822888
+AGID02145	2451	PA5-43776	Set163	ATP5H	0.608230097733748
+AGID02150	2456	13934	Set163	ATR	0.163332086418618
+AGID00315	1795	ab178407	Set163	ATR_pS428	0.127778868888139
+AGID00268	1569	ab97508	Set163	ATRX	-1.43157751640857
+AGID00391	2332	14475	Set163	Aurora-A	-0.0683748786385974
+AGID00392	2333	2914	Set163	Aurora-ABC_pT288_pT232_pT198	0.234825131273407
+AGID02195	2512	MA5-27890	Set163	Aurora-B	0.073528815377208
+AGID00215	1271	8661	Old	AXL	-0.0055708
+AGID02143	2449	8457	Set163	b-Actin	-0.0860951443912087
+AGID00179	1170	9565	Set163	b-Catenin_pT41_S45	0.289350126430042
+AGID00301	1725	14058	Set163	B7-H3	0.522584206753896
+AGID00302	1726	14572	Set163	B7-H4	0.218839786649321
+AGID00008	63	9291	Old	BAD_pS112	-0.11282
+AGID00009	71	1542-1/ab32371	Old	BAK	0.92871
+AGID00192	1207	sc-28383	Old	BAP1C4	-0.44829
+AGID00010	73	2772	Old	BAX	0.0022261
+AGID00433	80	M0887	Old	BCL2	0.3669
+AGID00219	1299	PAB8528	Old	BCL2A1	0.62907
+AGID00012	84	1018-1	Old	BCLXL	-0.1911
+AGID00377	87	sc-10086	Old	BECLIN	0.53962
+AGID00011	75	9562	Old	BETACATENIN	-1.4789
+AGID00013	88	1008-1/ab32060	Old	BID	0.72704
+AGID00180	90	1036-1/ab32158	Old	BIM	0.41155
+AGID00221	1311	610978	Set163	BiP-GRP78	-0.193030434603212
+AGID00373	2194	07-507	Set163	BMK1-Erk5_pT218_Y220	-0.0155048449890986
+AGID00355	92	1647/ab33899	Old	BRAF	-0.80803
+AGID00014	94	2696	Old	BRAF_pS445	-0.63274
+AGID00445	761	9012	Old	BRCA2	0.27416
+AGID00266	1567	13440	Old	BRD4	-1.312
+AGID00168	1146	2865	Set163	c-Abl_pY412	0.552344389398108
+AGID00278	1615	3130	Set163	c-IAP2	0.0112900125806203
+AGID00345	1990	5649	Old	CA9	NA
+AGID00265	1565	2862	Old	CABL	-0.053546
+AGID00429	2407	2679	Set163	Calnexin	-0.257275132122505
+AGID00176	1165	9496	Set163	Caspase-8-cleaved	0.501870039509387
+AGID00623	111	9665	Old	CASPASE3	0.032931
+AGID00015	109	9491	Old	CASPASE7CLEAVEDD198	-0.17232
+AGID00118	951	9746	Old	CASPASE8	0.22994
+AGID00537	935	551246	Old	CASPASE9	NA
+AGID00016	114	3238	Old	CAVEOLIN1	0.52976
+AGID00358	2100	ab76000	Set163	CD134	0.75305368384395
+AGID00303	1737	826701	Set163	CD171	-0.0925849011658801
+AGID00410	125	1632-1/ab78237	Old	CD20	0.5406
+AGID00220	1308	ab28340	Old	CD26	-0.41955
+AGID00191	1206	610467	Set163	CD29	-0.0428252308959637
+AGID00017	127	M0823	Old	CD31	0.4693
+AGID00369	2174	ab108403	Set163	CD38	0.0895651321744989
+AGID00359	2104	ab133616	Set163	CD4	0.12958386359554
+AGID00411	1398	3570	Set163	CD44	-0.00727000000000047
+AGID00237	1352	M070101-2	Set163	CD45	0.181504956045808
+AGID00115	937	611016	Old	CD49B	0.6007
+AGID02171	2482	91882	Set163	CD86	-0.211164889313064
+AGID00329	1873	4688	Set163	cdc25C	-0.118289866811774
+AGID00227	1332	4651	Set163	Cdc42	0.337104903020053
+AGID00422	2396	3387	Set163	Cdc6	0.0348150063682891
+AGID00501	1007	9112	Old	CDK1	-0.059999
+AGID00293	1658	ab32384	Set163	CDK1_pT14	-1.01857487136055
+AGID00314	1783	4539	Old	CDK1_pY15	-0.13871
+AGID00423	2397	8064	Set163	CDT1	0.614909674879359
+AGID02101	2348	15102	Set163	cGAS	-0.157174874063826
+AGID00447	2410	13460	Set163	CHD1L	-0.513576708130482
+AGID00189	1203	2360	Old	CHK1	0.51356
+AGID00234	1348	ab79758	Old	CHK1_pS296	0.013848
+AGID00107	903	2348	Old	CHK1_pS345	0.57985
+AGID00018	146	3440	Old	CHK2	-0.83395
+AGID00019	147	2197	Old	CHK2_pT68	0.3706
+AGID00527	2078	4952	Old	CIAP	-0.015429
+AGID00350	2018	3793	Set163	CIITA	0.280815124896453
+AGID00434	155	9164	Old	CJUN_pS73	0.19576
+AGID00020	157	1522-1/ab32363	Old	CKIT	1.2837
+AGID00400	852	NB100-91714	Old	CLAUDIN7	-0.22546
+AGID00466	726	3127	Old	CMET	0.51789
+AGID00079	727	3129	Old	CMET_pY1235	0.41254
+AGID00167	161	9402	Old	CMYC	1.0618
+AGID00292	1656	11130-1-AP	Old	COG3	-1.2169
+AGID00021	171	sc-20649	Old	COLLAGENVI	2.8648
+AGID00141	1069	459230	Old	COMPLEXIISUBUNIT30	NA
+AGID00267	1568	3512	Set163	Connexin-43	0.0938048556087913
+AGID00269	1571	6434	Set163	Coup-TFII	0.373905122609067
+AGID00150	1116	4850	Set163	Cox-IV	-0.841665531583139
+AGID00195	1218	4842	Set163	Cox2	0.237295128639448
+AGID00188	803	05-739	Old	CRAF	-0.56592
+AGID00022	179	9427	Old	CRAF_pS338	0.4544
+AGID00023	181	9197	Set163	Creb	0.429084004077757
+AGID00393	2334	9198	Set163	CREB_pS133	-0.258052741395194
+AGID00365	2155	4980	Set163	CSK	0.00665508705061777
+AGID00367	2160	9201	Set163	CtIP	0.411889786649321
+AGID00536	2096	ab107198	Old	CTLA4	NA
+AGID00025	198	2936	Set163	Cyclin-D3	-0.0728849936317108
+AGID00024	192	1495-1/ab32053	Old	CYCLINB1	-1.2712
+AGID00382	194	sc-718	Old	CYCLIND1	0.68623
+AGID00437	199	sc-25303	Old	CYCLINE1	-0.75166
+AGID00449	202	1142-1	Old	CYCLINE2	1.2728
+AGID00209	1257	ab110324	Set163	Cyclophilin-F	-1.18826516331412
+AGID00247	1379	ab48389	Set163	D-a-Tubulin	0.648820116448722
+AGID00308	1770	GTX10524	Set163	DAPK1_pS308	0.0406850706230298
+AGID00304	1744	ab51601	Set163	DAPK2	0.412729900186814
+AGID00343	1980	6998	Set163	DDB-1	-0.423984944972781
+AGID00427	2402	5583	Set163	DDR1	-0.239350646567554
+AGID00428	2403	SAB4504671	Set163	DDR1_pY513	0.221395100982876
+AGID00532	1273	Bast Lab	Old	DIRAS3	0.44764
+AGID00104	891	ab76008	Old	DJ1	-0.20961
+AGID02146	2452	4658	Set163	DM-Histone-H3	0.554419736430817
+AGID00386	1397	ab32521	Set163	DM-K9-Histone-H3	0.425590090767619
+AGID00352	2030	14649	Set163	DNA-Ligase-IV	-0.0343001290986508
+AGID00407	2371	13609	Set163	DNA_POLG	-0.598484958697095
+AGID00399	2344	5032	Set163	DNMT1	-0.539505010960389
+AGID00409	2373	5391	Set163	DRP1	-0.856466446536943
+AGID00253	1406	5149	Old	DUSP4	-0.37981
+AGID00334	1936	ab76310	Set163	DUSP6	0.0744447901063925
+AGID00116	940	3218	Old	DVL3	-0.59274
+AGID00211	1261	sc-251	Old	E2F1	NA
+AGID00148	1099	3195	Old	ECADHERIN	-1.2575
+AGID00135	1060	2332	Old	EEF2	-1.9495
+AGID00136	1061	3692	Old	EEF2K	-0.4517
+AGID00152	1120	2232	Old	EGFR	0.034398
+AGID00450	217	2234	Old	EGFR_pY1068	0.16839
+AGID00026	221	1124-1/ab32578	Old	EGFR_pY1173	0.67838
+AGID00078	722	9742	Old	EIF4E	-0.24317
+AGID00328	1871	ab76256	Set163	eIF4E_pS209	0.35495480376139
+AGID00154	1124	2498	Old	EIF4G	-0.76333
+AGID00027	228	9181	Set163	Elk1_pS383	0.344830126430041
+AGID00235	1350	M061329-2	Set163	EMA	1.35321469459073
+AGID00394	2337	3810	Set163	Enolase-1	-0.172440111319428
+AGID00395	2338	8171	Set163	Enolase-2	-0.187359868024781
+AGID00196	1219	GTX629542	Old	ENY2	-1.0509
+AGID00438	1849	A302-024A	Set163	EphA2	0.283265124896453
+AGID00552	2422	6347	Set163	EphA2_pS897	-0.0151748713605518
+AGID00553	2423	12677	Set163	EphA2_pY588	0.152296628534948
+AGID00075	693	556347	Old	EPPK1	-0.59503
+AGID00335	238	RM-9101	Old	ERALPHA	1.1768
+AGID00029	241	1091-1/ab32396	Old	ERALPHA_pS118	0.18264
+AGID00240	247	MS-671	Old	ERCC1	0.019916
+AGID00239	1355	11331-1-AP	Old	ERCC5	-0.33172
+AGID00484	249	sc-154	Old	ERK2	-1.3074
+AGID00372	2193	3552	Set163	Erk5	-0.139604868726592
+AGID00405	2369	13826	Set163	ERRalpha	0
+AGID00187	1200	A303-501A	Old	ETS1	2.0012
+AGID00511	2492	2593	Set163	EVI1	0.072799520168947
+AGID00485	1284	4905	Old	EZH2	NA
+AGID00030	252	1700-1/ab40794	Set163	FAK	0.726365120044423
+AGID02151	2457	8556	Set163	FAK_pY397	0.303108516249745
+AGID00171	1156	3180	Old	FASN	-0.092571
+AGID00356	2085	500-P18/10775-082	Set163	FGF-basic	0.105540123206907
+AGID00031	262	1574-1/ab45688	Old	FIBRONECTIN	2.4383
+AGID00339	1959	4403	Set163	FN14	-0.0987898709706567
+AGID02152	2458	20459	Old	FOXM1	0.063109
+AGID00378	269	9467	Old	FOXO3A	0.60249
+AGID02197	2515	orb6051	Old	FOXO3A_pS318S321	-0.054291
+AGID02167	2475	PA5-64616	Set163	FRS2-alpha_pY196	0.296345133144905
+AGID02213	2575	ab124892	Set163	FTO	-0.705394872192329
+AGID02141	2446	12263	Old	G6PD	0.30286
+AGID00117	943	3239	Old	GAB2	-0.37852
+AGID00412	274	AM4300	Old	GAPDH	-2.9042
+AGID00086	764	558686	Old	GATA3	1.2289
+AGID00383	1578	4253	Old	GATA6	0.22005
+AGID00289	1634	12601-1-AP	Set163	GCLC	0.255230104076045
+AGID00305	1745	ab124827	Set163	GCLM	0.312185123787418
+AGID00212	1263	3305	Old	GCN5L2	-1.0156
+AGID00270	1579	3538	Set163	Gli1	-0.357365274772173
+AGID00263	1520	ab69838	Set163	Gli3	0.133843978916527
+AGID00548	2530	3660	Set163	Glucocorticoid-Receptor	-0.595459879288423
+AGID00387	1617	12793	Set163	Glutamate-D1-2	-0.8946460084682
+AGID00262	1491	ab156876	Set163	Glutaminase	0.15612506459265
+AGID00319	1807	4275	Set163	Granzyme-B	-0.388289971615625
+AGID00368	2169	ab183737	Set163	GRB7	0.28260434822518
+AGID00396	2339	3593	Set163	Grp75	-0.394789940112087
+AGID00174	1163	9315	Set163	GSK-3B	-1.02373574964787
+AGID00502	1082	9336	Old	GSK3_pS9	-0.73096
+AGID00033	284	sc-7291	Old	GSK3ALPHABETA	-0.72614
+AGID00034	285	9331	Old	GSK3ALPHABETA_pS21S9	-0.84214
+AGID00129	1035	3886	Old	GYS	NA
+AGID00130	1036	3891	Old	GYS_pS641	NA
+AGID01354	1342	9718	Set163	H2AX_pS139	0.300165084485973
+AGID00363	1409	MA1-2022	Set163	H2AX_pS140	-0.0565999369582673
+AGID00131	1038	MS-325-P1	Old	HER2	-0.36537
+AGID00142	299	06-229	Old	HER2_pY1248	0.49387
+AGID00110	911	sc-285	Old	HER3	0.86304
+AGID00080	728	4791	Old	HER3_pY1289	0.34361
+AGID00103	890	2573	Old	HEREGULIN	0.085487
+AGID00271	1582	11988	Set163	HES1	-0.164465108416875
+AGID00397	2340	2024	Set163	Hexokinase-I	-0.37637512013106
+AGID00442	1023	2867	Set163	Hexokinase-II	-2.17514643177292
+AGID00419	1402	610958	Old	HIF1ALPHA	NA
+AGID00205	1250	ab1791	Set163	Histone-H3	-0.587465048944852
+AGID00398	2341	3377	Set163	Histone-H3_pS10	0.0479899956678307
+AGID00332	1901	ab128959	Set163	HLA-DQA1	-0.13614624614823
+AGID00333	1902	14832-1-AP	Set163	HMHA1	-0.468175370010576
+AGID00035	321	2402	Set163	HSP27	0.220240069141427
+AGID00036	323	2401	Set163	HSP27_pS82	-0.468814882797481
+AGID00320	1808	12165	Set163	HSP60	-0.100760094164036
+AGID00037	325	4872	Old	HSP70	2.7256
+AGID00366	2158	86630	Set163	IDO	-0.137330365843029
+AGID00197	1221	3024	Old	IGF1R_pY1135Y1136	0.36393
+AGID00038	335	3922	Old	IGFBP2	0.21934
+AGID00090	793	611504	Set163	IGFBP3	-0.0926451962386105
+AGID00039	336	3027	Set163	IGFRb	-0.19348486928111
+AGID00336	1949	12153	Set163	IL-6	0.564599800373633
+AGID02221	2583	57145	Set163	IMP3	-0.065995015465846
+AGID02153	2459	14543	Old	INPP4B	0.95296
+AGID00272	1586	3025	Set163	IR-b	-0.825454910454053
+AGID00519	2519	4302	Set163	IRF-3	-0.553669624196225
+AGID00520	2520	4947	Set163	IRF-3_pS396	-0.197775412639117
+AGID00223	1316	sc-497	Old	IRF1	-0.38549
+AGID00092	802	06-248	Old	IRS1	0.7793
+AGID00040	371	4502	Set163	IRS2	-0.0340153371554063
+AGID00250	1394	sc-13157	Old	JAB1	0.038428
+AGID00256	1413	ab109536	Set163	Jagged1	0.271770654101774
+AGID00177	1166	3230	Old	JAK2	-0.21042
+AGID00758	377	4671	Old	JNK_pT183Y185	0.63985
+AGID02136	2439	PA5-28262	Old	JNK2	-0.33608
+AGID00307	1757	ab10484	Set163	KAP1	-0.541820382617187
+AGID00528	904	2180	Old	KU80	-1.3841
+AGID00375	2237	HPA028732	Set163	LAD1	-0.920569867331634
+AGID00290	1643	IHC-00439	Set163	Lasu1	-0.688089895923955
+AGID00279	1618	4108	Set163	LC3A-B	0.207589858701961
+AGID00042	397	2752	Old	LCK	0.41953
+AGID00119	976	3582	Old	LDHA	NA
+AGID00533	977	ab85319	Old	LDHB	NA
+AGID00529	1477	3050	Old	LKB1	0.010885
+AGID00244	1367	2568	Set163	LRP6_pS1490	0.302380106051514
+AGID00439	2424	2796	Set163	Lyn	0.0693300691414278
+AGID02154	2460	4370	Old	MAPK_pT202Y204	1.5152
+AGID00198	1222	5453	Set163	Mcl-1	-0.571505922102105
+AGID00288	1633	AB3314P	Set163	MCT4	-0.144575006524248
+AGID00175	1164	3521	Set163	MDM2_pS166	-0.218829870242852
+AGID00044	417	1235-1/ab32576	Old	MEK1	0.066042
+AGID00143	1076	9154	Old	MEK1_pS217S221	-0.15823
+AGID00201	1243	9125	Set163	MEK2	0.0581446547347732
+AGID00361	2118	ab51061	Set163	MelanA	0.257230106051515
+AGID00362	2119	ab137078	Set163	Melanoma-gp100	0.489435026469556
+AGID00337	1951	12711	Set163	MERIT40	-0.681720507799534
+AGID00338	1952	12110	Set163	MERIT40_pS29	-0.0431948682413894
+AGID02212	2574	ab195352	Set163	METTL3	-0.670014876212582
+AGID00225	1323	sc-20121	Set163	MIF	-0.17489487059809
+AGID00137	1062	WH0054206M1	Old	MIG6	-0.0054098
+AGID00403	2117	ab20663	Set163	MITF	0.0968397394961555
+AGID00503	1067	ab3298	Old	MITOCHONDRIA	NA
+AGID00321	1809	14739	Set163	Mitofusin-1	-0.609463663868697
+AGID00322	1810	11925	Set163	Mitofusin-2	-0.619284997859908
+AGID00389	2324	3515	Set163	MLH1	-0.211325015465846
+AGID00312	1780	14993	Set163	MLKL	0.632704975315298
+AGID00402	2359	MAB3328	Set163	MMP14	0.140725067642497
+AGID00045	435	4022	Set163	MMP2	1.10192226857745
+AGID00122	1005	2195	Set163	Mnk1	-0.239456085199552
+AGID00331	1899	sc-377312	Set163	MR1	0.919609943439194
+AGID00273	1589	ab103319	Set163	MRAP	0.119855133006275
+AGID00530	440	4847	Old	MRE11	0.68618
+AGID00390	905	2850	Old	MSH2	-0.59059
+AGID00138	1063	22030002	Old	MSH6	-0.66615
+AGID00299	1675	ab76148	Set163	MSI2	-0.0511798669157456
+AGID00232	1344	ab14705	Set163	MTCO1	-1.69187655182592
+AGID00046	444	2983	Old	MTOR	-0.72794
+AGID00047	446	2971	Old	MTOR_pS2448	-0.13437
+AGID00204	1247	H00009788-M01A	Set163	MTSS1	0.217089953559142
+AGID00401	1139	21370002	Old	MYH11	1.2425
+AGID00291	1647	3403	Old	MYOSINIIA	-0.38285
+AGID00173	1160	5026	Old	MYOSINIIA_pS1943	0.050112
+AGID00318	1803	4282	Set163	Myt1	-0.00959512609212484
+AGID00216	1274	5795-1/ab129189	Old	NAPSINA	NA
+AGID00418	452	4061	Old	NCADHERIN	1.1379
+AGID00156	1126	3217	Old	NDRG1_pT346	0.23145
+AGID02133	2436	PA5-45913	Set163	NDUFB4	0.34949513071889
+AGID00134	1046	22710002	Old	NF2	-1.1285
+AGID00048	457	3033	Old	NFKBP65_pS536	0.060549
+AGID02155	2461	3608	Old	NOTCH1	0.45481
+AGID00340	1969	4147	Set163	Notch1-cleaved	0.352609882823479
+AGID00087	767	sc-5593	Set163	Notch3	0.381035105072444
+AGID00258	1420	3187	Set163	NQO1	-0.262940056560806
+AGID00162	1136	sc-31	Old	NRAS	0.22852
+AGID00257	1419	12721	Old	NRF2	NA
+AGID00297	1669	2750	Set163	Oct-4	0.42919011935994
+AGID00420	466	1712-1/ab40803	Old	P16INK4A	-0.46541
+AGID00384	470	sc-6246	Old	P21	0.5898
+AGID00105	897	1591-1/ab32034	Old	P27	0.32743
+AGID00096	842	AF1555	Old	P27_pT157	0.22378
+AGID00099	878	ab64949	Old	P27_pT198	0.046205
+AGID00181	1175	9228	Set163	p38-a	0.0476840165543998
+AGID00098	479	9211	Old	P38_pT180Y182	0.46679
+AGID00049	478	9212	Old	P38MAPK	-0.11846
+AGID00151	1119	4695	Set163	p44-42-MAPK	-0.507429882061012
+AGID00050	481	9282	Old	P53	0.116
+AGID00490	1187	610833	Old	P62LCKLIGAND	-0.82744
+AGID00545	1415	ab53039	Old	P63	NA
+AGID00052	494	9205	Old	P70S6K_pT389	0.74445
+AGID00051	493	1494-1/ab32529	Old	P70S6K1	-1.1456
+AGID00085	759	9347	Old	P90RSK	-0.24899
+AGID00531	770	9344	Old	P90RSK_pT359S363	0.13395
+AGID00182	1178	9346	Set163	p90RSK_pT573	0.00253500636828902
+AGID00053	499	612024	Old	PAI1	0.64378
+AGID00224	1322	HPA035895	Set163	PAICS	-0.842514868726593
+AGID00323	1811	2602	Set163	PAK1	-0.779085297646025
+AGID02199	2517	PA5-69540	Set163	PAK4	-0.253649983364469
+AGID00245	1370	4336-BPC-100	Set163	PAR	0.3936346708851
+AGID00374	2209	66564	Set163	PARG	0.631834855608791
+AGID00370	1372	sc-7150	Old	PARP1	-0.89098
+AGID00468	501	9546	Old	PARPCLEAVED	0.45135
+AGID00274	1591	ab53715	Set163	Patched	0.263645094328663
+AGID00513	2486	60433	Set163	PAX6	0.429165026469556
+AGID00441	1621	9857	Set163	PAX8	-0.187021253071034
+AGID00054	504	2542	Old	PAXILLIN	-0.98727
+AGID00055	509	2130	Old	PCADHERIN	-0.13707
+AGID00248	511	ab29	Old	PCNA	0.19905
+AGID00413	2095	43248	Old	PDCD1	NA
+AGID00094	816	600-401-965	Old	PDCD4	-0.18169
+AGID00385	1225	3169	Set163	PDGFRB	0.55072011935994
+AGID00210	1258	ab110332	Set163	PDH	0.336888972582899
+AGID00324	1817	3205	Set163	PDHA1	0.295539453938754
+AGID00280	1622	3820	Set163	PDHK1	0.202835122609067
+AGID00056	515	3062	Old	PDK1	0.18103
+AGID00057	516	3061	Old	PDK1_pS241	-0.52418
+AGID00300	1234	sc-19090	Old	PDL1	-0.26551
+AGID00124	1017	2780	Old	PEA15	-0.17572
+AGID00125	1018	44-836G	Old	PEA15_pS116	0.97421
+AGID00440	2429	3192	Set163	PERK	-0.430495484449145
+AGID02207	2569	ab192876	Set163	PGM1	-0.0854955220177109
+AGID00281	1623	13428	Set163	PHGDH	-0.162675493737314
+AGID00425	2399	22789-1-AP	Set163	PHLPP	0.165205130095057
+AGID00226	1330	sc-376412	Set163	PI3K-p110-b	0.125935118658129
+AGID00093	808	4255	Old	PI3KP110ALPHA	-0.32582
+AGID00058	523	06-195	Old	PI3KP85	-0.18482
+AGID00296	1667	5675	Set163	PKA-a	-0.246820013204453
+AGID00259	1426	9375	Set163	PKC-a-b-II_pT638_T641	0.0788551259361737
+AGID00172	529	05-154	Old	PKCALPHA	-0.14636
+AGID00460	530	06-822	Old	PKCALPHA_pS657	-0.35198
+AGID00114	932	07-875	Old	PKCDELTA_pS664	0.38398
+AGID00163	1137	9371	Old	PKCPANBETAII_pS660	-0.76995
+AGID00126	1025	4053	Old	PKM2	NA
+AGID00512	2489	5690	Set163	PLC-gamma1	-0.871495704300462
+AGID02138	2441	GTX133463	Set163	PLC-gamma2_pY759	0.443029963401831
+AGID00084	754	4513	Set163	PLK1	-0.450994938526513
+AGID00203	1246	22510002	Set163	PMS2	-0.373854874063826
+AGID00207	1254	ab14734	Set163	Porin	0.164645132174498
+AGID00381	549	1483-1/ab32085	Old	PR	0.12277
+AGID00081	738	AHO1031	Set163	PRAS40	-0.00671486699372497
+AGID00082	739	44-1100G	Old	PRAS40_pT246	0.086835
+AGID00424	2398	OAAF05458	Set163	PRC1_pT481	0.257405107013256
+AGID00492	1205	HPA007730	Old	PRDX1	-0.30928
+AGID00190	1204	ab102739	Old	PREX1	0.37774
+AGID00061	566	9552	Old	PTEN	-0.81804
+AGID00364	2154	ab76942	Set163	PTPN12	-0.235265029398103
+AGID00218	1290	4976	Set163	Puma	-0.164339866777116
+AGID00200	1242	SAB2900066	Old	PYGB	NA
+AGID00535	1494	ab61013	Old	PYGL	NA
+AGID00202	1245	H00005837-M10	Old	PYGM	NA
+AGID00275	1607	3291	Set163	Pyk2_pY402	0.275389547513595
+AGID00145	1083	3539	Old	RAB11	0.84699
+AGID00169	1150	4314	Old	RAB25	-0.49374
+AGID00342	1979	24555	Set163	Rad23A	-0.928609953420512
+AGID00261	987	05-525	Old	RAD50	0.079183
+AGID00360	579	NA71	Old	RAD51	0.36769
+AGID00158	1128	2280	Old	RAPTOR	-0.14053
+AGID00059	552	9309	Old	RB	0.55923
+AGID00060	557	9308	Old	RB_pS807S811	-0.92163
+AGID00164	1138	21390002	Old	RBM15	-2.0037
+AGID00547	735	3221	Old	RET_pY905	NA
+AGID00097	847	MAB3426	Set163	Rheb	0.42120503769854
+AGID00159	1129	2114	Old	RICTOR	-0.76482
+AGID00160	1130	3806	Old	RICTOR_pT1135	0.83193
+AGID00282	1624	4926	Set163	RIP	-0.210769911693053
+AGID00283	1625	13526	Set163	RIP3	0.293274379208848
+AGID00416	1368	2208	Set163	RPA32	-0.366579897968739
+AGID00246	1375	A300-245A	Set163	RPA32_pS4_S8	-0.0811059710382724
+AGID00341	1978	3388	Set163	RRM1	0.309389911415797
+AGID00344	1981	PA5-27856	Set163	RRM2	-0.082441528978074
+AGID00554	2425	8408	Set163	RSK1	-0.996292721467239
+AGID00353	2031	13018	Set163	S100A4	0.172350121993899
+AGID00330	1874	2317	Old	S6	-2.1877
+AGID00062	600	2211	Old	S6_pS235S236	-0.36529
+AGID00063	601	2215	Old	S6_pS240S244	-0.77868
+AGID00157	1127	sc-58420	Old	SCD1	0.39771
+AGID00230	1339	11998	Set163	SDHA	0.0474851248964534
+AGID00294	1039	ab69836	Old	SETD2	0.38124
+AGID00161	1131	32-4500	Old	SF2	0.35475
+AGID02179	2495	3534	Set163	SFRP1	0.350129095963034
+AGID00431	2411	12103	Set163	SGK1	0.500674389398108
+AGID00430	2409	8156	Set163	SGK3	0.13765008577696
+AGID02168	2476	bs-3413R	Old	SHC_pY317	0.40697
+AGID00376	2241	3397	Set163	SHP2	0.288874873907875
+AGID00183	1180	3751	Old	SHP2_pY542	-0.014732
+AGID02208	2570	ab8120	Set163	SIRP-alpha	-0.452680536391847
+AGID00222	1133	sc-99002	Old	SLC1A5	-1.2845
+AGID00255	1411	sc-136891	Set163	Slfn11	0.36431503769854
+AGID00064	610	2954	Old	SMAC	-0.95852
+AGID00113	922	1649-1/ab33902	Old	SMAD1	0.30961
+AGID00091	796	1735-1/ab40854	Old	SMAD3	1.116
+AGID02160	2467	46535	Old	SMAD4	0.61248
+AGID00065	616	3895	Old	SNAIL	0.85647
+AGID00325	1818	4266	Set163	SOD1	0.0226636410074836
+AGID00380	1328	13141	Set163	SOD2	0.254999900186814
+AGID00298	1670	2748	Set163	Sox2	0.278754919655584
+AGID00066	621	05-184	Old	SRC	-0.062783
+AGID02157	2463	6943	Old	SRC_pY416	0.31522
+AGID00068	626	2105	Old	SRC_pY527	0.54509
+AGID00185	1197	4904	Set163	Stat3	-0.893158038139752
+AGID00388	637	9131	Old	STAT3_pY705	0.046188
+AGID00069	638	1289-1/ab32043	Old	STAT5ALPHA	-1.4586
+AGID00077	718	1972-1/ab52630	Old	STATHMIN	0.7401
+AGID00357	2099	13647	Set163	STING	0.0552701323564498
+AGID00128	1033	sc-1240	Old	SYK	-1.2488
+AGID00070	646	05-348	Set163	Tau	-0.0409798959239551
+AGID00327	777	2149	Old	TAZ	0.65251
+AGID00228	1333	7495	Set163	TFAM	-0.483951198173811
+AGID00165	1140	22500002	Old	TFRC	-2.2349
+AGID00149	1107	S1711/ab137573	Old	TIGAR	0.54435
+AGID00109	908	MS-224-P1	Old	TRANSGLUTAMINASE	-0.0092844
+AGID00406	2370	612344	Set163	TRAP1	-1.16248487406383
+AGID00559	2537	PA5-34561	Set163	TRIM24	-0.340612120370713
+AGID00306	1756	ab167154	Set163	TRIM25	-1.09768058543199
+AGID00426	2400	PA5-52193	Set163	TRIP13	-0.0426998673316345
+AGID00155	1125	4906	Old	TSC1	-0.44558
+AGID00144	1081	2044-1/ab76013	Old	TTF1	NA
+AGID00071	670	1613-1/ab32554	Old	TUBERIN	-1.2168
+AGID02194	2511	ab109403	Old	TUBERIN_pT1462	0.3727
+AGID00417	1842	ab173300	Set163	TUFM	-0.456234899017124
+AGID00238	1353	sc-81417	Set163	Twist	0.36553512690658
+AGID00436	1080	5585	Set163	Tyro3	0.276984587360884
+AGID00295	1662	5546	Set163	U-Histone-H2B	0.165869953559142
+AGID00214	1270	HPA005651	Set163	UBAC1	-0.229220008733654
+AGID00351	2020	sc-136145	Set163	UBQLN4	0.327355115677596
+AGID00213	1267	sc-271268	Set163	UGT1A	0.198150129029343
+AGID00284	1626	6888	Set163	ULK1_pS757	0.229537218540952
+AGID00208	1256	MS304/ab14745	Set163	UQCRC2	-0.0792948969376826
+AGID00313	1781	13115	Set163	UVRAG	0.184245122609068
+AGID00073	678	3112	Set163	VASP	-0.311525238035379
+AGID00184	1181	2502	Set163	VAV1	-0.768280765130333
+AGID00074	688	2479	Old	VEGFR2	-0.28994
+AGID00421	2394	68547	Set163	VHL	-0.0150148730934197
+AGID00231	1343	SAB4200080	Set163	Vinculin	-0.178885289952093
+AGID00317	1802	4936	Set163	Wee1	-0.538031078709965
+AGID00354	2058	4910	Set163	Wee1_pS642	0.34274487986894
+AGID00285	1627	12124	Set163	WIPI1	0.0678951070132564
+AGID00286	1628	8567	Set163	WIPI2	-0.141919866777116
+AGID02214	2576	ab195380	Set163	WTAP	-1.00994558045
+AGID00133	1044	sc-32136	Old	XBP1	0.48434
+AGID00076	699	2042	Set163	XIAP	0.0777645960252212
+AGID00241	1359	sc-56813	Set163	XPA	1.36558013197522
+AGID00349	1354	ab3299	Set163	XPF	0.368332502722268
+AGID02137	2440	PA5-29359	Old	XRCC1	0.073731
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data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/nationwidechildrens.org_biospecimen.TCGA-A8-A095.xml

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+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
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+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
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+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112369337</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.77</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f369781f-36cb-4ced-9fdb-f74ef3039a56</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A00Z</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11R-A00Z-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c943873c-e153-42bc-a8de-e1080b252e81</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050325</bio:biospecimen_barcode_bottom>
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+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A010</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11R-A010-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">35c83967-3afd-4a07-a0d7-8aecff6f0f50</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99051285</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:rna>
+                                    <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.90</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.50</bio:rinvalue>
+                                </bio:rna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1EB6E6E7-4116-4D82-9409-7F74CE5E94E1</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A019</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11W-A019-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d16f025a-4187-4632-b833-02a3ffa54210</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034677</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A020</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11W-A020-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">94d77a00-5648-4440-b655-db3d5441de85</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035541</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9A12CC27-9532-4549-B475-7342422D3D9E</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A023</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11X-A023-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ba13e935-0ab7-4e86-94e8-933b7bdeac4c</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059925</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A024</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-11X-A024-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">77a2177a-4f3b-42e7-9ac1-f48890ee6e59</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034389</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">65</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">75</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">32</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-01-BS1</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4a8ab901-ac44-4973-8507-03d54f82e067</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A095-01A-01-BS1.4a8ab901-ac44-4973-8507-03d54f82e067.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">70</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">3</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-01A-01-TS1</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6e35462c-2639-48ee-9503-d2689ebb0346</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A095-01A-01-TS1.6e35462c-2639-48ee-9503-d2689ebb0346.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                        </bio:slides>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">41A41A7F-E4DD-4D3A-B97D-B4657CA211E1</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A095.41A41A7F-E4DD-4D3A-B97D-B4657CA211E1.pdf</bio:pathology_report_file_name>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                    <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">97072E53-7323-4836-9D58-22B7C346A7CE</bio:ffpe_slide_uuid>
+                </bio:diagnostic_slides>
+            </bio:sample>
+            <bio:sample>
+                <admin:additional_studies/>
+                <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
+                <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
+                <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
+                <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
+                <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
+                <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:days_to_collection precision="month" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">1153</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">12189ce3-8af1-4aee-8c17-c6fc5292232f</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8e101f6c-cd53-4ebe-81e6-07b345443965</bio:bcr_portion_uuid>
+                        <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                        <bio:analytes>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.91</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ae56e89e-c73d-43da-8465-6d34031a0f4f</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A012</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D-A012-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5b354ba0-d2f1-4ada-b203-fb4175afeacd</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050229</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A017</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D-A017-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">50f118ff-cee3-4c51-942a-fc61b161c985</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059816</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A018</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D-A018-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">19007942-ef2c-44cd-85db-6c176ee90109</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099051189</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A069</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">31</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D-A069-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8d843f7a-a26a-4a43-929b-9f11582cf204</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099028575</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A88Z</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01D-A88Z-36</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1E812BE3-2401-4263-836A-2672845F7BF0</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">7.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112369338</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E0B33636-B27D-4E03-A985-E4C93EFFF066</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A021</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01W-A021-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9dafa22c-39df-467b-920b-a1e42c820671</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035925</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A022</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01W-A022-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d30c802b-19a9-45a7-acf4-0eb74b5f8dd2</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099037557</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">76072D7C-00E8-444A-93D6-9BD146D0D24F</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A025</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01X-A025-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5cdf91dc-78f4-4a08-8352-b114d5c31916</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034869</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A026</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A095-10A-01X-A026-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6ef8e64b-829e-49b8-845d-50840400b23a</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099036309</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides/>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                </bio:diagnostic_slides>
+            </bio:sample>
+        </bio:samples>
+    </bio:patient>
+</bio:tcga_bcr>

data/gdc_data_organized/29df128d-ace2-40cf-88ee-3f6f2170f159/nationwidechildrens.org_clinical.TCGA-A8-A095.xml

@@ -0,0 +1,356 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<brca:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/brca/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/brca/2.7/TCGA_BCR.BRCA_Clinical.xsd" schemaVersion="2.7" xmlns:brca="http://tcga.nci/bcr/xml/clinical/brca/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:brca_shared="http://tcga.nci/bcr/xml/clinical/brca/shared/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:brca_nte="http://tcga.nci/bcr/xml/clinical/brca/shared/new_tumor_event/2.7/1.0" xmlns:nte="http://tcga.nci/bcr/xml/clinical/shared/new_tumor_event/2.7" xmlns:follow_up_v4.0="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/4.0" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">C29288E9-3E0F-42CE-B233-719EBB0F6EFC</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">47.98.0</admin:batch_number>
+        <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+        <admin:patient_withdrawal>
+            <admin:withdrawn>false</admin:withdrawn>
+        </admin:patient_withdrawal>
+        <admin:program xsi:nil="true" xsd_ver="2.7"/>
+        <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
+    </admin:admin>
+    <brca:patient>
+        <admin:additional_studies/>
+        <clin_shared:tumor_tissue_site preferred_name="submitted_tumor_site" display_order="9999" cde="3427536" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184676">Breast</clin_shared:tumor_tissue_site>
+        <clin_shared:tumor_tissue_site_other preferred_name="site_of_primary_tumor_other" display_order="999" cde="2584114" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="184677" xsi:nil="true"/>
+        <shared:other_dx preferred_name="history_other_malignancy" display_order="14" cde="3382736" cde_ver="2.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184665">No</shared:other_dx>
+        <shared:gender preferred_name="gender" display_order="10" cde="2200604" cde_ver="3.000" xsd_ver="1.8" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184656">FEMALE</shared:gender>
+        <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184661">Alive</clin_shared:vital_status>
+        <clin_shared:days_to_birth precision="month" xsd_ver="1.12" tier="1" cde="3008233" owner="TSS" procurement_status="Completed" preferred_name="birth_days_to" display_order="9" cde_ver="1.000">-16742</clin_shared:days_to_birth>
+        <clin_shared:days_to_last_known_alive precision="day" xsd_ver="2.1" tier="2" cde="" owner="TSS" procurement_status="Not Available" preferred_name="" display_order="9999" cde_ver=""/>
+        <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+        <clin_shared:days_to_last_followup precision="month" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">1277</clin_shared:days_to_last_followup>
+        <clin_shared:race_list>
+            <clin_shared:race preferred_name="race" display_order="12" cde="2192199" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184663"/>
+        </clin_shared:race_list>
+        <shared:bcr_patient_barcode preferred_name="" display_order="9999" cde="2003301" cde_ver="" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A8</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A095</shared:patient_id>
+        <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">29df128d-ace2-40cf-88ee-3f6f2170f159</shared:bcr_patient_uuid>
+        <shared:history_of_neoadjuvant_treatment preferred_name="history_neoadjuvant_treatment" display_order="15" cde="3382737" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184666">No</shared:history_of_neoadjuvant_treatment>
+        <clin_shared:informed_consent_verified preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false">YES</clin_shared:informed_consent_verified>
+        <clin_shared:icd_o_3_site preferred_name="" display_order="9999" cde="3226281" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_o_3_site>
+        <clin_shared:icd_o_3_histology preferred_name="" display_order="9999" cde="3226275" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">8500/3</clin_shared:icd_o_3_histology>
+        <clin_shared:icd_10 preferred_name="" display_order="9999" cde="3226287" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_10>
+        <clin_shared:days_to_initial_pathologic_diagnosis precision="month" xsd_ver="1.12" tier="1" cde="3131740" owner="TSS" procurement_status="Completed" preferred_name="initial_pathologic_dx_days_to" display_order="9999" cde_ver="1.000">0</clin_shared:days_to_initial_pathologic_diagnosis>
+        <clin_shared:age_at_initial_pathologic_diagnosis precision="month" xsd_ver="1.12" tier="1" cde="2006657" owner="TSS" procurement_status="Completed">45</clin_shared:age_at_initial_pathologic_diagnosis>
+        <clin_shared:year_of_initial_pathologic_diagnosis preferred_name="initial_pathologic_dx_year" display_order="34" cde="2896960" cde_ver="1.000" xsd_ver="1.12" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184683">2007</clin_shared:year_of_initial_pathologic_diagnosis>
+        <clin_shared:ethnicity preferred_name="ethnicity" display_order="13" cde="2192217" cde_ver="2.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184664"/>
+        <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184662">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+        <clin_shared:primary_lymph_node_presentation_assessment preferred_name="lymph_nodes_examined" display_order="47" cde="2200396" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <clin_shared:lymph_node_examined_count preferred_name="lymph_nodes_examined_count" display_order="48" cde="3" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184695"/>
+        <brca_shared:er_detection_method_text preferred_name="er_positivity_method" display_order="63" cde="69" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184708"/>
+        <brca_shared:pgr_detection_method_text preferred_name="pr_positivity_define_method" display_order="69" cde="785" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184713"/>
+        <brca:anatomic_neoplasm_subdivisions>
+            <clin_shared:anatomic_neoplasm_subdivision preferred_name="anatomic_organ_subdivision" display_order="9999" cde="3108203" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184678">Left</clin_shared:anatomic_neoplasm_subdivision>
+        </brca:anatomic_neoplasm_subdivisions>
+        <brca_shared:her2_neu_chromosone_17_signal_ratio_value preferred_name="her2_cent17_ratio" display_order="79" cde="2497552" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184723"/>
+        <brca:axillary_lymph_node_stage_method_type preferred_name="axillary_staging_method" display_order="44" cde="2516112" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184692"/>
+        <brca:axillary_lymph_node_stage_other_method_descriptive_text preferred_name="axillary_staging_method_other" display_order="45" cde="3124496" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184693"/>
+        <brca:breast_carcinoma_surgical_procedure_name preferred_name="surgical_procedure_first" display_order="38" cde="2739580" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184686">Other</brca:breast_carcinoma_surgical_procedure_name>
+        <brca:breast_neoplasm_other_surgical_procedure_descriptive_text preferred_name="surgery_for_positive_margins_other" display_order="42" cde="3124493" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="184690" xsi:nil="true"/>
+        <brca:breast_carcinoma_primary_surgical_procedure_name preferred_name="surgery_for_positive_margins" display_order="41" cde="1218" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184689"/>
+        <brca:surgical_procedure_purpose_other_text preferred_name="first_surgical_procedure_other" display_order="39" cde="3020338" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184687">Surgical Resection</brca:surgical_procedure_purpose_other_text>
+        <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184679">Infiltrating Ductal Carcinoma</shared:histological_type>
+        <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="184680" xsi:nil="true"/>
+        <clin_shared:menopause_status preferred_name="menopause_status" display_order="11" cde="2957270" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184660">Pre (&lt;6 months since LMP AND no prior bilateral ovariectomy AND not on estrogen replacement)</clin_shared:menopause_status>
+        <brca_shared:breast_carcinoma_progesterone_receptor_status preferred_name="pr_status_by_ihc" display_order="64" cde="2957357" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184709">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
+        <brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator preferred_name="micromet_detection_by_ihc" display_order="46" cde="3086152" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184694"/>
+        <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184706"/>
+        <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184716">1+</brca_shared:her2_immunohistochemistry_level_result>
+        <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184691"/>
+        <clin_shared:margin_status preferred_name="margin_status" display_order="40" cde="3114007" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184688">Negative</clin_shared:margin_status>
+        <clin_shared:initial_pathologic_diagnosis_method preferred_name="method_initial_path_dx" display_order="36" cde="2757941" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184684"/>
+        <clin_shared:init_pathology_dx_method_other preferred_name="method_initial_path_dx_other" display_order="37" cde="2757948" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="184685" xsi:nil="true"/>
+        <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184719">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
+        <brca_shared:breast_carcinoma_estrogen_receptor_status preferred_name="er_status_by_ihc" display_order="58" cde="2957359" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184704">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
+        <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184714">Negative</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
+        <clin_shared:number_of_lymphnodes_positive_by_ihc preferred_name="lymph_nodes_examined_ihc_count" display_order="50" cde="3086383" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184697"/>
+        <clin_shared:number_of_lymphnodes_positive_by_he preferred_name="lymph_nodes_examined_he_count" display_order="49" cde="3086388" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184696"/>
+        <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184712"/>
+        <brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text preferred_name="er_positivity_scale_other" display_order="62" cde="3086851" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184707"/>
+        <brca_shared:her2_erbb_pos_finding_cell_percent_category preferred_name="her2_ihc_percent_positive" display_order="71" cde="3086980" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184715"/>
+        <brca_shared:pos_finding_her2_erbb2_other_measurement_scale_text preferred_name="her2_positivity_scale_other" display_order="73" cde="3087479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184717"/>
+        <brca_shared:her2_erbb_method_calculation_method_text preferred_name="her2_positivity_method_text" display_order="74" cde="3087487" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184718"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count preferred_name="her2_and_cent17_cells_count" display_order="78" cde="3087902" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184722"/>
+        <brca_shared:her2_and_centromere_17_positive_finding_other_measurement_scale_text preferred_name="her2_and_cent17_scale_other" display_order="80" cde="3087923" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184724"/>
+        <brca_shared:her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="her2_fish_method" display_order="81" cde="3087929" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184725"/>
+        <clin_shared:tissue_prospective_collection_indicator preferred_name="prospective_collection" display_order="4" cde="3088492" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184654">NO</clin_shared:tissue_prospective_collection_indicator>
+        <clin_shared:tissue_retrospective_collection_indicator preferred_name="retrospective_collection" display_order="5" cde="3088528" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184655">YES</clin_shared:tissue_retrospective_collection_indicator>
+        <brca_shared:fluorescence_in_situ_hybridization_diagnostic_procedure_chromosome_17_signal_result_range preferred_name="cent17_copy_number" display_order="77" cde="3104295" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184721"/>
+        <brca:first_nonlymph_node_metastasis_anatomic_sites>
+            <clin_shared:metastatic_site_at_diagnosis preferred_name="metastasis_site" display_order="56" cde="3124499" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184702"/>
+            <clin_shared:metastatic_site_at_diagnosis_other preferred_name="metastasis_site_other" display_order="57" cde="3124503" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184703"/>
+        </brca:first_nonlymph_node_metastasis_anatomic_sites>
+        <brca_shared:er_level_cell_percentage_category preferred_name="er_status_ihc_Percent_Positive" display_order="59" cde="3128341" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184705"/>
+        <brca_shared:progesterone_receptor_level_cell_percent_category preferred_name="pr_status_ihc_percent_positive" display_order="65" cde="3128342" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184710"/>
+        <brca:distant_metastasis_present_ind2 preferred_name="metastatic_tumor_indicator" display_order="999" cde="2194698" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184726"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184727"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184728"/>
+        <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184729"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184730"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184731"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184736"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184732"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184733"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184734"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184735"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184737"/>
+        <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184738"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184739"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184740"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184741"/>
+        <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184743"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184744"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184745"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184746"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184747"/>
+        <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184742"/>
+        <brca_shared:her2_neu_breast_carcinoma_copy_analysis_input_total_number preferred_name="her2_copy_number" display_order="76" cde="3133738" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184720"/>
+        <brca:breast_carcinoma_immunohistochemistry_progesterone_receptor_pos_finding_scale preferred_name="pr_positivity_scale_used" display_order="66" cde="3203083" cde_ver="1.000" xsd_ver="2.4.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="184711"/>
+        <shared_stage:stage_event system="AJCC">
+            <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1079961">6th</shared_stage:system_version>
+            <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184701">Stage I</shared_stage:pathologic_stage>
+            <shared_stage:tnm_categories>
+                <shared_stage:clinical_categories>
+                    <shared_stage:clinical_T preferred_name="ajcc_tumor_clinical_ct" display_order="9999" cde="3440328" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <shared_stage:clinical_N preferred_name="ajcc_nodes_clinical_cn" display_order="9999" cde="3440330" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                    <shared_stage:clinical_M preferred_name="ajcc_metastasis_clinical_cm" display_order="9999" cde="3440331" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                </shared_stage:clinical_categories>
+                <shared_stage:pathologic_categories>
+                    <shared_stage:pathologic_T preferred_name="ajcc_tumor_pathologic_pt" display_order="52" cde="3045435" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184698">T1c</shared_stage:pathologic_T>
+                    <shared_stage:pathologic_N preferred_name="ajcc_nodes_pathologic_pn" display_order="53" cde="3203106" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184699">N0</shared_stage:pathologic_N>
+                    <shared_stage:pathologic_M preferred_name="ajcc_metastasis_pathologic_pm" display_order="54" cde="3045439" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184700">M0</shared_stage:pathologic_M>
+                </shared_stage:pathologic_categories>
+            </shared_stage:tnm_categories>
+            <shared_stage:psa>
+                <shared_stage:psa_value preferred_name="psa_most_recent_results" display_order="9999" cde="3351903" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:days_to_psa precision="day" xsd_ver="2.6" tier="2" cde="3414608" owner="TSS" procurement_status="Not Applicable" preferred_name="days_to_psa_most_recent" display_order="9999" cde_ver="1.000"/>
+            </shared_stage:psa>
+            <shared_stage:gleason_grading>
+                <shared_stage:gleason_score preferred_name="gleason_score" display_order="9999" cde="2534619" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:primary_pattern preferred_name="gleason_pattern_primary" display_order="9999" cde="2534617" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:secondary_pattern preferred_name="gleason_pattern_secondary" display_order="9999" cde="2534618" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:tertiary_pattern preferred_name="gleason_pattern_tertiary" display_order="9999" cde="2783875" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:gleason_grading>
+            <shared_stage:ann_arbor>
+                <shared_stage:b_symptoms preferred_name="b_symptoms_present_indicator" display_order="9999" cde="2902402" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:extranodal_involvement preferred_name="extranodal_lymphomatous_involvement" display_order="9999" cde="3364582" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:ann_arbor>
+            <shared_stage:serum_markers preferred_name="" display_order="9999" cde="3901772" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:igcccg_stage preferred_name="" display_order="9999" cde="3901822" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:masaoka_stage preferred_name="" display_order="9999" cde="3952848" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+        </shared_stage:stage_event>
+        <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_nte:new_tumor_events>
+            <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        </brca_nte:new_tumor_events>
+        <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184652">27</clin_shared:day_of_form_completion>
+        <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184651">5</clin_shared:month_of_form_completion>
+        <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="184653">2011</clin_shared:year_of_form_completion>
+        <brca:follow_ups>
+            <follow_up_v4.0:follow_up version="4.0" sequence="1">
+                <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-F40554</clin_shared:bcr_followup_barcode>
+                <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">6CCE328F-29A6-4589-B6C4-32FBE8EBA27E</clin_shared:bcr_followup_uuid>
+                <clin_shared:lost_follow_up preferred_name="followup_lost_to" display_order="4" cde="61333" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417872">NO</clin_shared:lost_follow_up>
+                <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417873">YES</clin_shared:radiation_therapy>
+                <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417874">YES</clin_shared:postoperative_rx_tx>
+                <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417875">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+                <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417876">Alive</clin_shared:vital_status>
+                <clin_shared:days_to_last_followup precision="month" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">1277</clin_shared:days_to_last_followup>
+                <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+                <brca_nte:new_tumor_events>
+                    <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2417885">NO</nte:new_tumor_event_after_initial_treatment>
+                    <brca_nte:new_tumor_event>
+                        <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
+                        <nte:new_neoplasm_event_type preferred_name="new_tumor_event_type" display_order="83" cde="3119721" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417886"/>
+                        <nte:new_neoplasm_event_occurrence_anatomic_site preferred_name="new_tumor_event_site" display_order="84" cde="3108271" cde_ver="2.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417887"/>
+                        <nte:new_neoplasm_occurrence_anatomic_site_text preferred_name="new_tumor_event_site_other" display_order="85" cde="3128033" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417888"/>
+                        <nte:new_tumor_event_additional_surgery_procedure preferred_name="new_tumor_event_surgery" display_order="90" cde="3427611" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417893"/>
+                        <nte:days_to_new_tumor_event_additional_surgery_procedure precision="day" xsd_ver="2.5" tier="2" cde="3008335" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to" display_order="94" cde_ver="1.000"/>
+                        <nte:additional_radiation_therapy preferred_name="new_tumor_event_radiation_tx" display_order="95" cde="3427615" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417898"/>
+                        <nte:additional_pharmaceutical_therapy preferred_name="new_tumor_event_pharmaceutical_tx" display_order="96" cde="3427616" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417899"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417900"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417901"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_positive_finding_scale_type preferred_name="nte_er_positivity_scale_used" display_order="99" cde="3203082" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417902"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417903"/>
+                        <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417904"/>
+                        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417905"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417906"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417907"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_progesterone_receptor_positive_finding_scale_type preferred_name="nte_pr_positivity_scale_used" display_order="105" cde="3203085" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417908"/>
+                        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417909"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417910"/>
+                        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417911"/>
+                        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417912"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417913"/>
+                        <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417914"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417915"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417916"/>
+                        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417917"/>
+                        <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417918"/>
+                        <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417919"/>
+                        <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417920"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417921"/>
+                        <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417922"/>
+                        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2417923"/>
+                    </brca_nte:new_tumor_event>
+                </brca_nte:new_tumor_events>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">23</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2013</clin_shared:year_of_form_completion>
+            </follow_up_v4.0:follow_up>
+        </brca:follow_ups>
+        <rx:drugs>
+            <rx:drug>
+                <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257652">NO</rx:tx_on_clinical_trial>
+                <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-D37811</rx:bcr_drug_barcode>
+                <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">57584D49-5DD8-4991-A154-50BB92C2FB5A</rx:bcr_drug_uuid>
+                <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">0</rx:days_to_drug_therapy_start>
+                <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">120</rx:days_to_drug_therapy_end>
+                <rx:therapy_types>
+                    <rx:therapy_type preferred_name="pharmaceutical_therapy_type" display_order="7" cde="2793530" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257655">Chemotherapy</rx:therapy_type>
+                    <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:therapy_types>
+                <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257653">5-Fluorouracil</rx:drug_name>
+                <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257654">n/a</rx:clinical_trail_drug_classification>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <rx:route_of_administrations>
+                    <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:route_of_administrations>
+                <rx:therapy_ongoing preferred_name="pharmaceutical_tx_ongoing_indicator" display_order="12" cde="3103479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257660">NO</rx:therapy_ongoing>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257665">Complete Response</clin_shared:measure_of_response>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
+            </rx:drug>
+            <rx:drug>
+                <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257669">NO</rx:tx_on_clinical_trial>
+                <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-D37812</rx:bcr_drug_barcode>
+                <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">4968DB45-29C7-41D8-BC0A-204367F2EB4E</rx:bcr_drug_uuid>
+                <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">0</rx:days_to_drug_therapy_start>
+                <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">120</rx:days_to_drug_therapy_end>
+                <rx:therapy_types>
+                    <rx:therapy_type preferred_name="pharmaceutical_therapy_type" display_order="7" cde="2793530" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257672">Chemotherapy</rx:therapy_type>
+                    <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:therapy_types>
+                <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257670">Doxorubicin</rx:drug_name>
+                <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257671">n/a</rx:clinical_trail_drug_classification>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <rx:route_of_administrations>
+                    <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:route_of_administrations>
+                <rx:therapy_ongoing preferred_name="pharmaceutical_tx_ongoing_indicator" display_order="12" cde="3103479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257677">NO</rx:therapy_ongoing>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257682">Complete Response</clin_shared:measure_of_response>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
+            </rx:drug>
+            <rx:drug>
+                <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257686">NO</rx:tx_on_clinical_trial>
+                <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-D37813</rx:bcr_drug_barcode>
+                <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">023B7F41-CB22-43B7-81EE-6DC8B72DD4F3</rx:bcr_drug_uuid>
+                <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">0</rx:days_to_drug_therapy_start>
+                <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">120</rx:days_to_drug_therapy_end>
+                <rx:therapy_types>
+                    <rx:therapy_type preferred_name="pharmaceutical_therapy_type" display_order="7" cde="2793530" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257689">Chemotherapy</rx:therapy_type>
+                    <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:therapy_types>
+                <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257687">Cyclophosphamide</rx:drug_name>
+                <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257688">n/a</rx:clinical_trail_drug_classification>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <rx:route_of_administrations>
+                    <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:route_of_administrations>
+                <rx:therapy_ongoing preferred_name="pharmaceutical_tx_ongoing_indicator" display_order="12" cde="3103479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257694">NO</rx:therapy_ongoing>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257699">Complete Response</clin_shared:measure_of_response>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
+            </rx:drug>
+            <rx:drug>
+                <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257703">NO</rx:tx_on_clinical_trial>
+                <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-D37814</rx:bcr_drug_barcode>
+                <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">DD6C452A-B9DD-48FF-B9C3-2D1DCC1F1143</rx:bcr_drug_uuid>
+                <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">181</rx:days_to_drug_therapy_start>
+                <rx:days_to_drug_therapy_end precision="day" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Not Available" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000"/>
+                <rx:therapy_types>
+                    <rx:therapy_type preferred_name="pharmaceutical_therapy_type" display_order="7" cde="2793530" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257706">Hormone Therapy</rx:therapy_type>
+                    <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:therapy_types>
+                <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257704">Tamoxifen</rx:drug_name>
+                <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257705">n/a</rx:clinical_trail_drug_classification>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <rx:route_of_administrations>
+                    <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                </rx:route_of_administrations>
+                <rx:therapy_ongoing preferred_name="pharmaceutical_tx_ongoing_indicator" display_order="12" cde="3103479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2257711">YES</rx:therapy_ongoing>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="2257716" xsi:nil="true"/>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
+            </rx:drug>
+        </rx:drugs>
+        <rad:radiations>
+            <rad:radiation>
+                <rad:bcr_radiation_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A095-R38169</rad:bcr_radiation_barcode>
+                <rad:bcr_radiation_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">424F7885-0277-4F10-91D2-8BB221F37C57</rad:bcr_radiation_uuid>
+                <rad:days_to_radiation_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3008313" owner="TSS" procurement_status="Completed" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000">120</rad:days_to_radiation_therapy_start>
+                <rad:days_to_radiation_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3008333" owner="TSS" procurement_status="Completed" preferred_name="radiation_therapy_ended_days_to" display_order="17" cde_ver="1.000">181</rad:days_to_radiation_therapy_end>
+                <rad:radiation_type preferred_name="radiation_therapy_type" display_order="4" cde="2842944" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273435">External</rad:radiation_type>
+                <rad:radiation_type_notes preferred_name="radiation_type_other" display_order="999" cde="2195477" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <rad:radiation_dosage preferred_name="radiation_total_dose" display_order="6" cde="2721441" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2273437"/>
+                <rad:units preferred_name="radiation_adjuvant_units" display_order="7" cde="61446" cde_ver="3.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273438">Gy</rad:units>
+                <rad:numfractions preferred_name="radiation_adjuvant_fractions_total" display_order="8" cde="61465" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2273439"/>
+                <rad:anatomic_treatment_site preferred_name="radiation_therapy_site" display_order="5" cde="2793522" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273436">Primary Tumor Field</rad:anatomic_treatment_site>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rad:radiation_treatment_ongoing preferred_name="radiation_therapy_ongoing_indicator" display_order="13" cde="2842745" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273444">NO</rad:radiation_treatment_ongoing>
+                <rad:course_number preferred_name="course_number" display_order="999" cde="2732184" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273449">Complete Response</clin_shared:measure_of_response>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">11</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
+            </rad:radiation>
+        </rad:radiations>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/2e538802-2a31-4774-89a8-c6e4381a887d/TCGA-A2-A1G0.DA82E751-09C3-466E-A63A-38368D8A2C7C.PDF

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data/gdc_data_organized/2e538802-2a31-4774-89a8-c6e4381a887d/TCGA-BRCA.454e0016-63ac-4727-a1bd-0319b09d17a0.ascat2.allelic_specific.seg.txt

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+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr1	62920	195868209	6	3	3
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr1	195875140	195905777	0	0	0
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr1	195906930	248930189	6	3	3
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr2	12784	54013398	4	2	2
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr2	54015722	54480707	8	6	2
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr2	54480724	88834118	4	2	2
+454e0016-63ac-4727-a1bd-0319b09d17a0	chr2	88836539	89069842	17	17	0
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data/gdc_data_organized/3144f1fb-4342-4079-bfe8-940da4bfd88e/ffd5af39-59ff-4c10-b45f-123847eb0103.mirbase21.mirnas.quantification.txt

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+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	15462	9472.598875	N
+hsa-let-7a-2	15242	9337.818656	N
+hsa-let-7a-3	15239	9335.980744	N
+hsa-let-7b	43042	26369.137290	N
+hsa-let-7c	6161	3774.458781	N
+hsa-let-7d	591	362.068680	N
+hsa-let-7e	1635	1001.662085	N
+hsa-let-7f-1	5772	3536.142847	N
+hsa-let-7f-2	6007	3680.112627	N
+hsa-let-7g	669	409.854394	N
+hsa-let-7i	836	512.164834	N
+hsa-mir-1-1	0	0.000000	N
+hsa-mir-1-2	2	1.225275	N
+hsa-mir-100	4333	2654.557685	Y
+hsa-mir-101-1	5423	3322.332408	N
+hsa-mir-101-2	5346	3275.159332	N
+hsa-mir-103a-1	15287	9365.387337	Y
+hsa-mir-103a-2	15394	9430.939535	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	0	0.000000	N
+hsa-mir-105-2	0	0.000000	N
+hsa-mir-106a	4	2.450549	Y
+hsa-mir-106b	801	490.722526	N
+hsa-mir-107	55	33.695055	Y
+hsa-mir-10a	47041	28819.074097	N
+hsa-mir-10b	148574	91021.983266	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	6	3.675824	N
+hsa-mir-1181	0	0.000000	N
+hsa-mir-1182	0	0.000000	N
+hsa-mir-1183	0	0.000000	N
+hsa-mir-1184-1	0	0.000000	N
+hsa-mir-1184-2	0	0.000000	N
+hsa-mir-1184-3	0	0.000000	N
+hsa-mir-1185-1	0	0.000000	N
+hsa-mir-1185-2	0	0.000000	N
+hsa-mir-1193	0	0.000000	N
+hsa-mir-1197	0	0.000000	N
+hsa-mir-1199	0	0.000000	N
+hsa-mir-1200	0	0.000000	N
+hsa-mir-1202	0	0.000000	N
+hsa-mir-1203	0	0.000000	N
+hsa-mir-1204	0	0.000000	N
+hsa-mir-1205	0	0.000000	N
+hsa-mir-1206	0	0.000000	N
+hsa-mir-1207	0	0.000000	N
+hsa-mir-1208	0	0.000000	N
+hsa-mir-122	0	0.000000	N
+hsa-mir-1224	0	0.000000	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	1	0.612637	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	2	1.225275	N
+hsa-mir-1229	1	0.612637	N
+hsa-mir-1231	0	0.000000	N
+hsa-mir-1233-1	0	0.000000	N
+hsa-mir-1233-2	0	0.000000	N
+hsa-mir-1234	0	0.000000	N
+hsa-mir-1236	0	0.000000	N
+hsa-mir-1237	0	0.000000	N
+hsa-mir-1238	0	0.000000	N
+hsa-mir-124-1	1	0.612637	N
+hsa-mir-124-2	0	0.000000	N
+hsa-mir-124-3	0	0.000000	N
+hsa-mir-1243	0	0.000000	N
+hsa-mir-1244-1	0	0.000000	N
+hsa-mir-1244-2	0	0.000000	N
+hsa-mir-1244-3	0	0.000000	N
+hsa-mir-1244-4	0	0.000000	N
+hsa-mir-1245a	7	4.288462	N
+hsa-mir-1245b	0	0.000000	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	6	3.675824	N
+hsa-mir-1248	5	3.063187	N
+hsa-mir-1249	6	3.675824	N
+hsa-mir-1250	0	0.000000	N
+hsa-mir-1251	1	0.612637	N
+hsa-mir-1252	0	0.000000	N
+hsa-mir-1253	0	0.000000	N
+hsa-mir-1254-1	1	0.612637	N
+hsa-mir-1254-2	0	0.000000	N
+hsa-mir-1255a	1	0.612637	N
+hsa-mir-1255b-1	0	0.000000	N
+hsa-mir-1255b-2	0	0.000000	N
+hsa-mir-1256	0	0.000000	N
+hsa-mir-1257	0	0.000000	N
+hsa-mir-1258	1	0.612637	N
+hsa-mir-125a	1749	1071.502744	N
+hsa-mir-125b-1	848	519.516482	N
+hsa-mir-125b-2	865	529.931317	N
+hsa-mir-126	4569	2799.140102	N
+hsa-mir-1260a	0	0.000000	N
+hsa-mir-1260b	0	0.000000	N
+hsa-mir-1261	0	0.000000	N
+hsa-mir-1262	0	0.000000	N
+hsa-mir-1263	0	0.000000	N
+hsa-mir-1264	0	0.000000	N
+hsa-mir-1265	0	0.000000	N
+hsa-mir-1266	26	15.928571	N
+hsa-mir-1267	0	0.000000	N
+hsa-mir-1268a	0	0.000000	N
+hsa-mir-1268b	0	0.000000	N
+hsa-mir-1269a	5	3.063187	N
+hsa-mir-1269b	1	0.612637	N
+hsa-mir-127	2040	1249.780216	N
+hsa-mir-1270	1	0.612637	N
+hsa-mir-1271	9	5.513736	N
+hsa-mir-1272	0	0.000000	N
+hsa-mir-1273a	0	0.000000	N
+hsa-mir-1273c	0	0.000000	N
+hsa-mir-1273d	0	0.000000	N
+hsa-mir-1273e	0	0.000000	N
+hsa-mir-1273f	0	0.000000	N
+hsa-mir-1273g	0	0.000000	N
+hsa-mir-1273h	0	0.000000	N
+hsa-mir-1275	1	0.612637	N
+hsa-mir-1276	0	0.000000	N
+hsa-mir-1277	3	1.837912	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	77	47.173077	N
+hsa-mir-128-2	43	26.343407	N
+hsa-mir-1281	0	0.000000	N
+hsa-mir-1282	0	0.000000	N
+hsa-mir-1283-1	0	0.000000	N
+hsa-mir-1283-2	0	0.000000	N
+hsa-mir-1284	1	0.612637	N
+hsa-mir-1285-1	0	0.000000	N
+hsa-mir-1285-2	0	0.000000	N
+hsa-mir-1286	0	0.000000	N
+hsa-mir-1287	36	22.054945	N
+hsa-mir-1288	0	0.000000	N
+hsa-mir-1289-1	0	0.000000	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	0	0.000000	N
+hsa-mir-129-2	1	0.612637	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	2	1.225275	N
+hsa-mir-1292	2	1.225275	N
+hsa-mir-1293	2	1.225275	N
+hsa-mir-1294	0	0.000000	N
+hsa-mir-1295a	1	0.612637	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	8	4.901099	N
+hsa-mir-1297	0	0.000000	N
+hsa-mir-1298	0	0.000000	N
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+hsa-mir-1304	2	1.225275	N
+hsa-mir-1305	0	0.000000	N
+hsa-mir-1306	10	6.126374	N
+hsa-mir-1307	1588	972.868129	N
+hsa-mir-130a	152	93.120879	N
+hsa-mir-130b	37	22.667582	N
+hsa-mir-132	107	65.552198	N
+hsa-mir-1321	0	0.000000	N
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+hsa-mir-1323	0	0.000000	N
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+hsa-mir-133a-1	1	0.612637	N
+hsa-mir-133a-2	2	1.225275	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	877	537.282966	N
+hsa-mir-1343	0	0.000000	N
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+hsa-mir-136	143	87.607143	N
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+hsa-mir-138-2	0	0.000000	N
+hsa-mir-139	88	53.912088	N
+hsa-mir-140	741	453.964284	N
+hsa-mir-141	2176	1333.098897	N
+hsa-mir-142	3897	2387.447796	N
+hsa-mir-143	39251	24046.629055	N
+hsa-mir-144	29	17.766483	N
+hsa-mir-145	2086	1277.961535	N
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+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	180	110.274725	N
+hsa-mir-146b	1386	849.115382	N
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+hsa-mir-147b	1	0.612637	N
+hsa-mir-148a	48646	29802.357061	N
+hsa-mir-148b	163	99.859890	N
+hsa-mir-149	260	159.285714	N
+hsa-mir-150	1230	753.543954	N
+hsa-mir-151a	2486	1523.016479	N
+hsa-mir-151b	0	0.000000	N
+hsa-mir-152	491	300.804944	N
+hsa-mir-153-1	1	0.612637	N
+hsa-mir-153-2	19	11.640110	N
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+hsa-mir-155	300	183.791208	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	163	99.859890	N
+hsa-mir-15b	123	75.354395	N
+hsa-mir-16-1	261	159.898351	N
+hsa-mir-16-2	235	143.969780	N
+hsa-mir-17	793	485.821427	Y
+hsa-mir-181a-1	1955	1197.706041	N
+hsa-mir-181a-2	2463	1508.925820	N
+hsa-mir-181b-1	449	275.074175	N
+hsa-mir-181b-2	379	232.189560	N
+hsa-mir-181c	91	55.750000	N
+hsa-mir-181d	15	9.189560	N
+hsa-mir-182	62856	38507.933960	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	25518	15633.280177	N
+hsa-mir-184	39	23.892857	N
+hsa-mir-185	62	37.983516	N
+hsa-mir-186	303	185.629120	N
+hsa-mir-187	84	51.461538	N
+hsa-mir-188	3	1.837912	N
+hsa-mir-18a	18	11.027472	N
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+hsa-mir-190a	7	4.288462	N
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+hsa-mir-191	684	419.043955	N
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+hsa-mir-192	740	453.351647	Y
+hsa-mir-193a	431	264.046703	N
+hsa-mir-193b	128	78.417582	N
+hsa-mir-194-1	94	57.587912	N
+hsa-mir-194-2	86	52.686813	N
+hsa-mir-195	66	40.434066	N
+hsa-mir-196a-1	1220	747.417580	N
+hsa-mir-196a-2	1360	833.186811	N
+hsa-mir-196b	708	433.747252	N
+hsa-mir-197	251	153.771978	N
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+hsa-mir-199a-2	13617	8342.282944	Y
+hsa-mir-199b	17252	10569.219751	Y
+hsa-mir-19a	41	25.118132	N
+hsa-mir-19b-1	105	64.326923	N
+hsa-mir-19b-2	84	51.461538	N
+hsa-mir-200a	533	326.535713	N
+hsa-mir-200b	362	221.774725	N
+hsa-mir-200c	9442	5784.521962	N
+hsa-mir-202	2	1.225275	N
+hsa-mir-203a	3102	1900.401094	N
+hsa-mir-203b	3	1.837912	N
+hsa-mir-204	2	1.225275	N
+hsa-mir-205	2266	1388.236260	N
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+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	360	220.549450	N
+hsa-mir-20b	17	10.414835	N
+hsa-mir-21	708964	434337.833972	N
+hsa-mir-210	2875	1761.332413	N
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+hsa-mir-2110	1	0.612637	N
+hsa-mir-2113	0	0.000000	N
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+hsa-mir-2117	0	0.000000	N
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+hsa-mir-214	94	57.587912	N
+hsa-mir-215	7	4.288462	Y
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+hsa-mir-218-1	29	17.766483	N
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+hsa-mir-219b	0	0.000000	N
+hsa-mir-22	110445	67662.733331	N
+hsa-mir-221	119	72.903846	N
+hsa-mir-222	55	33.695055	N
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+hsa-mir-23a	4522	2770.346146	Y
+hsa-mir-23b	867	531.156592	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	701	429.458790	N
+hsa-mir-24-2	759	464.991757	N
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+hsa-mir-26a-1	828	507.263735	N
+hsa-mir-26a-2	849	520.129119	N
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+hsa-mir-27b	676	414.142856	Y
+hsa-mir-28	5216	3195.516475	N
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+hsa-mir-29a	3920	2401.538455	N
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+hsa-mir-29b-2	218	133.554945	N
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+hsa-mir-30b	355	217.486263	Y
+hsa-mir-30c-1	346	211.972527	N
+hsa-mir-30c-2	361	221.162087	Y
+hsa-mir-30d	5010	3069.313178	N
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+hsa-mir-33b	9	5.513736	N
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+hsa-mir-3619	2	1.225275	N
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+hsa-mir-3651	2	1.225275	N
+hsa-mir-3652	1	0.612637	N
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+hsa-mir-3677	20	12.252747	N
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+hsa-mir-424	407	249.343406	N
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+hsa-mir-4708	0	0.000000	N
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+hsa-mir-4742	2	1.225275	N
+hsa-mir-4743	0	0.000000	N
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+hsa-mir-4746	9	5.513736	N
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+hsa-mir-4759	0	0.000000	N
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+hsa-mir-4761	0	0.000000	N
+hsa-mir-4762	1	0.612637	N
+hsa-mir-4763	1	0.612637	N
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+hsa-mir-4775	1	0.612637	N
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+hsa-mir-484	86	52.686813	N
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+hsa-mir-486-1	17	10.414835	N
+hsa-mir-486-2	27	16.541209	N
+hsa-mir-487a	3	1.837912	N
+hsa-mir-487b	12	7.351648	N
+hsa-mir-488	0	0.000000	N
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+hsa-mir-490	0	0.000000	N
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+hsa-mir-492	0	0.000000	N
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+hsa-mir-494	5	3.063187	N
+hsa-mir-495	10	6.126374	N
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+hsa-mir-498	0	0.000000	N
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+hsa-mir-499b	0	0.000000	N
+hsa-mir-5000	1	0.612637	N
+hsa-mir-5001	1	0.612637	N
+hsa-mir-5002	2	1.225275	N
+hsa-mir-5003	1	0.612637	N
+hsa-mir-5004	0	0.000000	N
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+hsa-mir-500a	207	126.815934	Y
+hsa-mir-500b	1	0.612637	Y
+hsa-mir-501	72	44.109890	N
+hsa-mir-5010	1	0.612637	N
+hsa-mir-5011	0	0.000000	N
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+hsa-mir-503	41	25.118132	N
+hsa-mir-504	0	0.000000	N
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+hsa-mir-509-2	4	2.450549	N
+hsa-mir-509-3	2	1.225275	N
+hsa-mir-5090	0	0.000000	N
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+hsa-mir-514a-3	0	0.000000	N
+hsa-mir-514b	1	0.612637	N
+hsa-mir-515-1	0	0.000000	N
+hsa-mir-515-2	0	0.000000	N
+hsa-mir-516a-1	2	1.225275	N
+hsa-mir-516a-2	2	1.225275	N
+hsa-mir-516b-1	0	0.000000	N
+hsa-mir-516b-2	0	0.000000	N
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+hsa-mir-519a-2	1	0.612637	Y
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+hsa-mir-520b	1	0.612637	Y
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+hsa-mir-527	0	0.000000	N
+hsa-mir-532	866	530.543955	N
+hsa-mir-539	70	42.884615	N
+hsa-mir-541	1	0.612637	N
+hsa-mir-542	771	472.343405	N
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+hsa-mir-550a-3	0	0.000000	N
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+hsa-mir-5587	0	0.000000	N
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+hsa-mir-5699	2	1.225275	N
+hsa-mir-570	0	0.000000	N
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+hsa-mir-5787	0	0.000000	N
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+hsa-mir-580	0	0.000000	N
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+hsa-mir-582	272	166.637362	N
+hsa-mir-583	0	0.000000	N
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+hsa-mir-598	11	6.739011	N
+hsa-mir-599	0	0.000000	N
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+hsa-mir-6079	0	0.000000	N
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+hsa-mir-6088	0	0.000000	N
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+hsa-mir-610	0	0.000000	N
+hsa-mir-611	0	0.000000	N
+hsa-mir-612	2	1.225275	N
+hsa-mir-6124	0	0.000000	N
+hsa-mir-6125	0	0.000000	N
+hsa-mir-6126	0	0.000000	N
+hsa-mir-6127	0	0.000000	N
+hsa-mir-6128	0	0.000000	N
+hsa-mir-6129	0	0.000000	N
+hsa-mir-613	0	0.000000	N
+hsa-mir-6130	0	0.000000	N
+hsa-mir-6131	0	0.000000	N
+hsa-mir-6132	0	0.000000	N
+hsa-mir-6133	0	0.000000	N
+hsa-mir-6134	0	0.000000	N
+hsa-mir-614	0	0.000000	N
+hsa-mir-615	27	16.541209	N
+hsa-mir-616	8	4.901099	N
+hsa-mir-6165	0	0.000000	N
+hsa-mir-617	0	0.000000	N
+hsa-mir-618	4	2.450549	N
+hsa-mir-619	0	0.000000	N
+hsa-mir-620	0	0.000000	N
+hsa-mir-621	0	0.000000	N
+hsa-mir-622	0	0.000000	N
+hsa-mir-623	0	0.000000	N
+hsa-mir-624	0	0.000000	N
+hsa-mir-625	257	157.447802	N
+hsa-mir-626	0	0.000000	N
+hsa-mir-627	2	1.225275	N
+hsa-mir-628	13	7.964286	N
+hsa-mir-629	386	236.478021	N
+hsa-mir-630	0	0.000000	N
+hsa-mir-631	0	0.000000	N
+hsa-mir-632	0	0.000000	N
+hsa-mir-633	0	0.000000	N
+hsa-mir-634	0	0.000000	N
+hsa-mir-635	0	0.000000	N
+hsa-mir-636	0	0.000000	N
+hsa-mir-637	0	0.000000	N
+hsa-mir-638	0	0.000000	N
+hsa-mir-639	0	0.000000	N
+hsa-mir-640	0	0.000000	N
+hsa-mir-641	0	0.000000	N
+hsa-mir-642a	12	7.351648	N
+hsa-mir-642b	0	0.000000	N
+hsa-mir-643	0	0.000000	N
+hsa-mir-644a	0	0.000000	N
+hsa-mir-645	0	0.000000	N
+hsa-mir-646	0	0.000000	N
+hsa-mir-647	0	0.000000	N
+hsa-mir-648	0	0.000000	N
+hsa-mir-649	0	0.000000	N
+hsa-mir-6499	0	0.000000	N
+hsa-mir-650	0	0.000000	N
+hsa-mir-6500	0	0.000000	N
+hsa-mir-6501	3	1.837912	N
+hsa-mir-6502	0	0.000000	N
+hsa-mir-6503	0	0.000000	N
+hsa-mir-6504	0	0.000000	N
+hsa-mir-6505	1	0.612637	N
+hsa-mir-6506	0	0.000000	N
+hsa-mir-6507	0	0.000000	N
+hsa-mir-6508	0	0.000000	N
+hsa-mir-6509	0	0.000000	N
+hsa-mir-651	6	3.675824	N
+hsa-mir-6510	3	1.837912	N
+hsa-mir-6511a-1	0	0.000000	N
+hsa-mir-6511a-2	0	0.000000	N
+hsa-mir-6511a-3	0	0.000000	N
+hsa-mir-6511a-4	0	0.000000	N
+hsa-mir-6511b-1	1	0.612637	N
+hsa-mir-6511b-2	0	0.000000	N
+hsa-mir-6512	0	0.000000	N
+hsa-mir-6513	0	0.000000	N
+hsa-mir-6514	0	0.000000	N
+hsa-mir-6515	0	0.000000	N
+hsa-mir-6516	0	0.000000	N
+hsa-mir-652	31	18.991758	N
+hsa-mir-653	32	19.604396	N
+hsa-mir-654	24	14.703297	N
+hsa-mir-655	5	3.063187	N
+hsa-mir-656	2	1.225275	N
+hsa-mir-657	0	0.000000	N
+hsa-mir-658	0	0.000000	N
+hsa-mir-659	2	1.225275	N
+hsa-mir-660	56	34.307692	N
+hsa-mir-661	0	0.000000	N
+hsa-mir-662	0	0.000000	N
+hsa-mir-663a	0	0.000000	N
+hsa-mir-663b	0	0.000000	N
+hsa-mir-664a	37	22.667582	N
+hsa-mir-664b	2	1.225275	N
+hsa-mir-665	0	0.000000	N
+hsa-mir-668	1	0.612637	N
+hsa-mir-670	0	0.000000	N
+hsa-mir-671	11	6.739011	N
+hsa-mir-6715a	0	0.000000	N
+hsa-mir-6715b	0	0.000000	N
+hsa-mir-6716	0	0.000000	N
+hsa-mir-6717	0	0.000000	N
+hsa-mir-6718	1	0.612637	N
+hsa-mir-6719	0	0.000000	N
+hsa-mir-6720	0	0.000000	N
+hsa-mir-6721	0	0.000000	N
+hsa-mir-6722	0	0.000000	N
+hsa-mir-6723	0	0.000000	N
+hsa-mir-6724-1	0	0.000000	N
+hsa-mir-6724-2	0	0.000000	N
+hsa-mir-6724-3	0	0.000000	N
+hsa-mir-6724-4	0	0.000000	N
+hsa-mir-6726	0	0.000000	N
+hsa-mir-6727	0	0.000000	N
+hsa-mir-6728	0	0.000000	N
+hsa-mir-6729	0	0.000000	N
+hsa-mir-6730	1	0.612637	N
+hsa-mir-6731	0	0.000000	N
+hsa-mir-6732	0	0.000000	N
+hsa-mir-6733	0	0.000000	N
+hsa-mir-6734	1	0.612637	N
+hsa-mir-6735	0	0.000000	N
+hsa-mir-6736	0	0.000000	N
+hsa-mir-6737	0	0.000000	N
+hsa-mir-6738	0	0.000000	N
+hsa-mir-6739	0	0.000000	N
+hsa-mir-6740	0	0.000000	N
+hsa-mir-6741	1	0.612637	N
+hsa-mir-6742	0	0.000000	N
+hsa-mir-6743	0	0.000000	N
+hsa-mir-6744	0	0.000000	N
+hsa-mir-6745	0	0.000000	N
+hsa-mir-6746	0	0.000000	N
+hsa-mir-6747	0	0.000000	N
+hsa-mir-6748	0	0.000000	N
+hsa-mir-6749	0	0.000000	N
+hsa-mir-675	151	92.508242	N
+hsa-mir-6750	0	0.000000	N
+hsa-mir-6751	0	0.000000	N
+hsa-mir-6752	0	0.000000	N
+hsa-mir-6753	1	0.612637	N
+hsa-mir-6754	0	0.000000	N
+hsa-mir-6755	3	1.837912	N
+hsa-mir-6756	0	0.000000	N
+hsa-mir-6757	2	1.225275	N
+hsa-mir-6758	0	0.000000	N
+hsa-mir-6759	0	0.000000	N
+hsa-mir-676	0	0.000000	N
+hsa-mir-6760	0	0.000000	N
+hsa-mir-6761	2	1.225275	N
+hsa-mir-6762	1	0.612637	N
+hsa-mir-6763	0	0.000000	N
+hsa-mir-6764	0	0.000000	N
+hsa-mir-6765	0	0.000000	N
+hsa-mir-6766	0	0.000000	N
+hsa-mir-6767	0	0.000000	N
+hsa-mir-6768	0	0.000000	N
+hsa-mir-6769a	0	0.000000	N
+hsa-mir-6769b	0	0.000000	N
+hsa-mir-6770-1	0	0.000000	N
+hsa-mir-6770-2	0	0.000000	N
+hsa-mir-6770-3	0	0.000000	N
+hsa-mir-6771	0	0.000000	N
+hsa-mir-6772	0	0.000000	N
+hsa-mir-6773	0	0.000000	N
+hsa-mir-6774	1	0.612637	N
+hsa-mir-6775	0	0.000000	N
+hsa-mir-6776	0	0.000000	N
+hsa-mir-6777	0	0.000000	N
+hsa-mir-6778	0	0.000000	N
+hsa-mir-6779	0	0.000000	N
+hsa-mir-6780a	0	0.000000	N
+hsa-mir-6780b	0	0.000000	N
+hsa-mir-6781	0	0.000000	N
+hsa-mir-6782	0	0.000000	N
+hsa-mir-6783	0	0.000000	N
+hsa-mir-6784	0	0.000000	N
+hsa-mir-6785	0	0.000000	N
+hsa-mir-6786	0	0.000000	N
+hsa-mir-6787	0	0.000000	N
+hsa-mir-6788	0	0.000000	N
+hsa-mir-6789	0	0.000000	N
+hsa-mir-6790	0	0.000000	N
+hsa-mir-6791	0	0.000000	N
+hsa-mir-6792	0	0.000000	N
+hsa-mir-6793	1	0.612637	N
+hsa-mir-6794	0	0.000000	N
+hsa-mir-6795	0	0.000000	N
+hsa-mir-6796	0	0.000000	N
+hsa-mir-6797	0	0.000000	N
+hsa-mir-6798	0	0.000000	N
+hsa-mir-6799	0	0.000000	N
+hsa-mir-6800	0	0.000000	N
+hsa-mir-6801	0	0.000000	N
+hsa-mir-6802	1	0.612637	N
+hsa-mir-6803	1	0.612637	N
+hsa-mir-6804	0	0.000000	N
+hsa-mir-6805	0	0.000000	N
+hsa-mir-6806	2	1.225275	N
+hsa-mir-6807	0	0.000000	N
+hsa-mir-6808	1	0.612637	N
+hsa-mir-6809	0	0.000000	N
+hsa-mir-6810	1	0.612637	N
+hsa-mir-6811	0	0.000000	N
+hsa-mir-6812	0	0.000000	N
+hsa-mir-6813	0	0.000000	N
+hsa-mir-6814	0	0.000000	N
+hsa-mir-6815	1	0.612637	N
+hsa-mir-6816	0	0.000000	N
+hsa-mir-6817	0	0.000000	N
+hsa-mir-6818	0	0.000000	N
+hsa-mir-6819	0	0.000000	N
+hsa-mir-6820	0	0.000000	N
+hsa-mir-6821	0	0.000000	N
+hsa-mir-6822	0	0.000000	N
+hsa-mir-6823	0	0.000000	N
+hsa-mir-6824	0	0.000000	N
+hsa-mir-6825	0	0.000000	N
+hsa-mir-6826	0	0.000000	N
+hsa-mir-6827	0	0.000000	N
+hsa-mir-6828	0	0.000000	N
+hsa-mir-6829	0	0.000000	N
+hsa-mir-6830	0	0.000000	N
+hsa-mir-6831	0	0.000000	N
+hsa-mir-6832	0	0.000000	N
+hsa-mir-6833	0	0.000000	N
+hsa-mir-6834	0	0.000000	N
+hsa-mir-6835	0	0.000000	N
+hsa-mir-6836	0	0.000000	N
+hsa-mir-6837	1	0.612637	N
+hsa-mir-6838	0	0.000000	N
+hsa-mir-6839	0	0.000000	N
+hsa-mir-6840	0	0.000000	N
+hsa-mir-6841	0	0.000000	N
+hsa-mir-6842	1	0.612637	N
+hsa-mir-6843	0	0.000000	N
+hsa-mir-6844	0	0.000000	N
+hsa-mir-6845	0	0.000000	N
+hsa-mir-6846	0	0.000000	N
+hsa-mir-6847	0	0.000000	N
+hsa-mir-6848	0	0.000000	N
+hsa-mir-6849	0	0.000000	N
+hsa-mir-6850	0	0.000000	N
+hsa-mir-6851	0	0.000000	N
+hsa-mir-6852	1	0.612637	N
+hsa-mir-6853	0	0.000000	N
+hsa-mir-6854	3	1.837912	N
+hsa-mir-6855	0	0.000000	N
+hsa-mir-6856	0	0.000000	N
+hsa-mir-6857	1	0.612637	N
+hsa-mir-6858	0	0.000000	N
+hsa-mir-6859-1	0	0.000000	N
+hsa-mir-6859-2	0	0.000000	N
+hsa-mir-6859-3	0	0.000000	N
+hsa-mir-6859-4	0	0.000000	N
+hsa-mir-6860	4	2.450549	N
+hsa-mir-6861	0	0.000000	N
+hsa-mir-6862-1	0	0.000000	N
+hsa-mir-6862-2	0	0.000000	N
+hsa-mir-6863	0	0.000000	N
+hsa-mir-6864	0	0.000000	N
+hsa-mir-6865	0	0.000000	N
+hsa-mir-6866	0	0.000000	N
+hsa-mir-6867	0	0.000000	N
+hsa-mir-6868	0	0.000000	N
+hsa-mir-6869	0	0.000000	N
+hsa-mir-6870	0	0.000000	N
+hsa-mir-6871	0	0.000000	N
+hsa-mir-6872	0	0.000000	N
+hsa-mir-6873	0	0.000000	N
+hsa-mir-6874	0	0.000000	N
+hsa-mir-6875	0	0.000000	N
+hsa-mir-6876	0	0.000000	N
+hsa-mir-6877	0	0.000000	N
+hsa-mir-6878	0	0.000000	N
+hsa-mir-6879	0	0.000000	N
+hsa-mir-6880	0	0.000000	N
+hsa-mir-6881	0	0.000000	N
+hsa-mir-6882	0	0.000000	N
+hsa-mir-6883	0	0.000000	N
+hsa-mir-6884	0	0.000000	N
+hsa-mir-6885	1	0.612637	N
+hsa-mir-6886	0	0.000000	N
+hsa-mir-6887	1	0.612637	N
+hsa-mir-6888	0	0.000000	N
+hsa-mir-6889	0	0.000000	N
+hsa-mir-6890	0	0.000000	N
+hsa-mir-6891	0	0.000000	N
+hsa-mir-6892	2	1.225275	N
+hsa-mir-6893	0	0.000000	N
+hsa-mir-6894	1	0.612637	N
+hsa-mir-6895	1	0.612637	N
+hsa-mir-7-1	25	15.315934	N
+hsa-mir-7-2	0	0.000000	N
+hsa-mir-7-3	0	0.000000	N
+hsa-mir-708	189	115.788461	N
+hsa-mir-7106	0	0.000000	N
+hsa-mir-7107	0	0.000000	N
+hsa-mir-7108	0	0.000000	N
+hsa-mir-7109	0	0.000000	N
+hsa-mir-711	0	0.000000	N
+hsa-mir-7110	0	0.000000	N
+hsa-mir-7111	0	0.000000	N
+hsa-mir-7112	1	0.612637	N
+hsa-mir-7113	0	0.000000	N
+hsa-mir-7114	0	0.000000	N
+hsa-mir-7150	0	0.000000	N
+hsa-mir-7151	0	0.000000	N
+hsa-mir-7152	0	0.000000	N
+hsa-mir-7153	0	0.000000	N
+hsa-mir-7154	0	0.000000	N
+hsa-mir-7155	1	0.612637	N
+hsa-mir-7156	0	0.000000	N
+hsa-mir-7157	0	0.000000	N
+hsa-mir-7158	1	0.612637	N
+hsa-mir-7159	0	0.000000	N
+hsa-mir-7160	0	0.000000	N
+hsa-mir-7161	0	0.000000	N
+hsa-mir-7162	0	0.000000	N
+hsa-mir-718	0	0.000000	N
+hsa-mir-744	41	25.118132	N
+hsa-mir-7515	0	0.000000	N
+hsa-mir-758	46	28.181319	N
+hsa-mir-759	0	0.000000	N
+hsa-mir-760	1	0.612637	N
+hsa-mir-761	0	0.000000	N
+hsa-mir-762	0	0.000000	N
+hsa-mir-764	0	0.000000	N
+hsa-mir-7641-1	0	0.000000	N
+hsa-mir-7641-2	0	0.000000	N
+hsa-mir-765	0	0.000000	N
+hsa-mir-766	10	6.126374	N
+hsa-mir-767	4	2.450549	N
+hsa-mir-769	25	15.315934	N
+hsa-mir-770	0	0.000000	N
+hsa-mir-7702	1	0.612637	N
+hsa-mir-7703	0	0.000000	N
+hsa-mir-7704	0	0.000000	N
+hsa-mir-7705	3	1.837912	N
+hsa-mir-7706	2	1.225275	N
+hsa-mir-7843	0	0.000000	N
+hsa-mir-7844	1	0.612637	N
+hsa-mir-7845	1	0.612637	N
+hsa-mir-7846	0	0.000000	N
+hsa-mir-7847	0	0.000000	N
+hsa-mir-7848	0	0.000000	N
+hsa-mir-7849	0	0.000000	N
+hsa-mir-7850	0	0.000000	N
+hsa-mir-7851	0	0.000000	N
+hsa-mir-7852	0	0.000000	N
+hsa-mir-7853	0	0.000000	N
+hsa-mir-7854	0	0.000000	N
+hsa-mir-7855	0	0.000000	N
+hsa-mir-7856	0	0.000000	N
+hsa-mir-7973-1	0	0.000000	N
+hsa-mir-7973-2	0	0.000000	N
+hsa-mir-7974	1	0.612637	N
+hsa-mir-7975	0	0.000000	N
+hsa-mir-7976	0	0.000000	N
+hsa-mir-7977	0	0.000000	N
+hsa-mir-7978	0	0.000000	N
+hsa-mir-802	0	0.000000	N
+hsa-mir-8052	0	0.000000	N
+hsa-mir-8053	0	0.000000	N
+hsa-mir-8054	0	0.000000	N
+hsa-mir-8055	0	0.000000	N
+hsa-mir-8056	0	0.000000	N
+hsa-mir-8057	0	0.000000	N
+hsa-mir-8058	0	0.000000	N
+hsa-mir-8059	0	0.000000	N
+hsa-mir-8060	0	0.000000	N
+hsa-mir-8061	0	0.000000	N
+hsa-mir-8062	0	0.000000	N
+hsa-mir-8063	0	0.000000	N
+hsa-mir-8064	0	0.000000	N
+hsa-mir-8065	0	0.000000	N
+hsa-mir-8066	0	0.000000	N
+hsa-mir-8067	0	0.000000	N
+hsa-mir-8068	0	0.000000	N
+hsa-mir-8069-1	0	0.000000	N
+hsa-mir-8069-2	0	0.000000	N
+hsa-mir-8070	0	0.000000	N
+hsa-mir-8071-1	0	0.000000	N
+hsa-mir-8071-2	0	0.000000	N
+hsa-mir-8072	0	0.000000	N
+hsa-mir-8073	0	0.000000	N
+hsa-mir-8074	0	0.000000	N
+hsa-mir-8075	0	0.000000	N
+hsa-mir-8076	0	0.000000	N
+hsa-mir-8077	0	0.000000	N
+hsa-mir-8078	0	0.000000	N
+hsa-mir-8079	0	0.000000	N
+hsa-mir-8080	0	0.000000	N
+hsa-mir-8081	0	0.000000	N
+hsa-mir-8082	0	0.000000	N
+hsa-mir-8083	0	0.000000	N
+hsa-mir-8084	0	0.000000	N
+hsa-mir-8085	0	0.000000	N
+hsa-mir-8086	0	0.000000	N
+hsa-mir-8087	0	0.000000	N
+hsa-mir-8088	0	0.000000	N
+hsa-mir-8089	0	0.000000	N
+hsa-mir-8485	0	0.000000	N
+hsa-mir-873	0	0.000000	N
+hsa-mir-874	59	36.145604	N
+hsa-mir-875	0	0.000000	N
+hsa-mir-876	0	0.000000	N
+hsa-mir-877	1	0.612637	N
+hsa-mir-885	1	0.612637	N
+hsa-mir-887	6	3.675824	N
+hsa-mir-888	0	0.000000	N
+hsa-mir-889	20	12.252747	N
+hsa-mir-890	0	0.000000	N
+hsa-mir-891a	1	0.612637	N
+hsa-mir-891b	0	0.000000	N
+hsa-mir-892a	0	0.000000	N
+hsa-mir-892b	0	0.000000	N
+hsa-mir-892c	0	0.000000	N
+hsa-mir-9-1	434	265.884615	N
+hsa-mir-9-2	457	279.975274	N
+hsa-mir-9-3	451	276.299450	N
+hsa-mir-920	0	0.000000	N
+hsa-mir-921	0	0.000000	N
+hsa-mir-922	0	0.000000	N
+hsa-mir-924	0	0.000000	N
+hsa-mir-92a-1	5184	3175.912079	N
+hsa-mir-92a-2	4893	2997.634607	N
+hsa-mir-92b	284	173.989011	N
+hsa-mir-93	7535	4616.222515	N
+hsa-mir-933	0	0.000000	N
+hsa-mir-934	2	1.225275	N
+hsa-mir-935	2	1.225275	N
+hsa-mir-936	0	0.000000	N
+hsa-mir-937	2	1.225275	N
+hsa-mir-938	0	0.000000	N
+hsa-mir-939	2	1.225275	N
+hsa-mir-940	9	5.513736	N
+hsa-mir-941-1	0	0.000000	N
+hsa-mir-941-2	0	0.000000	N
+hsa-mir-941-3	0	0.000000	N
+hsa-mir-941-4	0	0.000000	N
+hsa-mir-941-5	0	0.000000	N
+hsa-mir-942	7	4.288462	N
+hsa-mir-943	0	0.000000	N
+hsa-mir-944	2	1.225275	N
+hsa-mir-95	3	1.837912	N
+hsa-mir-9500	0	0.000000	N
+hsa-mir-96	53	32.469780	N
+hsa-mir-98	91	55.750000	N
+hsa-mir-99a	1283	786.013734	Y
+hsa-mir-99b	64111	39276.793848	N

data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/8204d38d-337a-4cba-9482-c84b6e0134b5.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	37965	12245.719482	N
+hsa-let-7a-2	37603	12128.955345	Y
+hsa-let-7a-3	37984	12251.847986	N
+hsa-let-7b	159303	51383.638893	N
+hsa-let-7c	3864	1246.344266	Y
+hsa-let-7d	1322	426.414886	N
+hsa-let-7e	2570	828.960860	N
+hsa-let-7f-1	6720	2167.555246	N
+hsa-let-7f-2	6871	2216.260729	N
+hsa-let-7g	632	203.853410	N
+hsa-let-7i	1365	440.284659	N
+hsa-mir-1-1	0	0.000000	N
+hsa-mir-1-2	3	0.967659	N
+hsa-mir-100	9747	3143.922765	N
+hsa-mir-101-1	17619	5683.058911	N
+hsa-mir-101-2	17791	5738.538003	N
+hsa-mir-103a-1	38290	12350.549162	Y
+hsa-mir-103a-2	38321	12360.548301	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	2	0.645106	N
+hsa-mir-105-2	2	0.645106	N
+hsa-mir-106a	47	15.159985	Y
+hsa-mir-106b	1667	537.695624	N
+hsa-mir-107	286	92.250119	Y
+hsa-mir-10a	41425	13361.752391	N
+hsa-mir-10b	98437	31751.136273	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	146	47.092718	N
+hsa-mir-1181	3	0.967659	N
+hsa-mir-1182	0	0.000000	N
+hsa-mir-1183	0	0.000000	N
+hsa-mir-1184-1	0	0.000000	N
+hsa-mir-1184-2	0	0.000000	N
+hsa-mir-1184-3	0	0.000000	N
+hsa-mir-1185-1	1	0.322553	N
+hsa-mir-1185-2	0	0.000000	N
+hsa-mir-1193	0	0.000000	N
+hsa-mir-1197	0	0.000000	N
+hsa-mir-1199	0	0.000000	N
+hsa-mir-1200	0	0.000000	N
+hsa-mir-1202	0	0.000000	N
+hsa-mir-1203	0	0.000000	N
+hsa-mir-1204	0	0.000000	N
+hsa-mir-1205	0	0.000000	N
+hsa-mir-1206	0	0.000000	N
+hsa-mir-1207	0	0.000000	N
+hsa-mir-1208	0	0.000000	N
+hsa-mir-122	0	0.000000	N
+hsa-mir-1224	1	0.322553	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	2	0.645106	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	2	0.645106	N
+hsa-mir-1229	0	0.000000	N
+hsa-mir-1231	0	0.000000	N
+hsa-mir-1233-1	0	0.000000	N
+hsa-mir-1233-2	0	0.000000	N
+hsa-mir-1234	1	0.322553	N
+hsa-mir-1236	0	0.000000	N
+hsa-mir-1237	0	0.000000	N
+hsa-mir-1238	0	0.000000	N
+hsa-mir-124-1	0	0.000000	N
+hsa-mir-124-2	0	0.000000	N
+hsa-mir-124-3	0	0.000000	N
+hsa-mir-1243	0	0.000000	N
+hsa-mir-1244-1	0	0.000000	N
+hsa-mir-1244-2	0	0.000000	N
+hsa-mir-1244-3	0	0.000000	N
+hsa-mir-1244-4	0	0.000000	N
+hsa-mir-1245a	7	2.257870	N
+hsa-mir-1245b	0	0.000000	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	5	1.612764	N
+hsa-mir-1248	0	0.000000	N
+hsa-mir-1249	4	1.290211	N
+hsa-mir-1250	0	0.000000	N
+hsa-mir-1251	0	0.000000	N
+hsa-mir-1252	0	0.000000	N
+hsa-mir-1253	0	0.000000	N
+hsa-mir-1254-1	2	0.645106	N
+hsa-mir-1254-2	0	0.000000	N
+hsa-mir-1255a	3	0.967659	N
+hsa-mir-1255b-1	0	0.000000	N
+hsa-mir-1255b-2	0	0.000000	N
+hsa-mir-1256	0	0.000000	N
+hsa-mir-1257	0	0.000000	N
+hsa-mir-1258	1	0.322553	N
+hsa-mir-125a	4346	1401.814747	N
+hsa-mir-125b-1	1383	446.090611	N
+hsa-mir-125b-2	1459	470.604629	N
+hsa-mir-126	2276	734.130318	N
+hsa-mir-1260a	0	0.000000	N
+hsa-mir-1260b	0	0.000000	N
+hsa-mir-1261	0	0.000000	N
+hsa-mir-1262	1	0.322553	N
+hsa-mir-1263	0	0.000000	N
+hsa-mir-1264	0	0.000000	N
+hsa-mir-1265	0	0.000000	N
+hsa-mir-1266	31	9.999139	N
+hsa-mir-1267	1	0.322553	N
+hsa-mir-1268a	0	0.000000	N
+hsa-mir-1268b	0	0.000000	N
+hsa-mir-1269a	4	1.290211	N
+hsa-mir-1269b	0	0.000000	N
+hsa-mir-127	3563	1149.255854	N
+hsa-mir-1270	2	0.645106	N
+hsa-mir-1271	16	5.160846	N
+hsa-mir-1272	0	0.000000	N
+hsa-mir-1273a	0	0.000000	N
+hsa-mir-1273c	0	0.000000	N
+hsa-mir-1273d	0	0.000000	N
+hsa-mir-1273e	0	0.000000	N
+hsa-mir-1273f	0	0.000000	N
+hsa-mir-1273g	0	0.000000	N
+hsa-mir-1273h	0	0.000000	N
+hsa-mir-1275	0	0.000000	N
+hsa-mir-1276	0	0.000000	N
+hsa-mir-1277	3	0.967659	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	381	122.892641	N
+hsa-mir-128-2	297	95.798201	N
+hsa-mir-1281	0	0.000000	N
+hsa-mir-1282	0	0.000000	N
+hsa-mir-1283-1	0	0.000000	N
+hsa-mir-1283-2	0	0.000000	N
+hsa-mir-1284	3	0.967659	N
+hsa-mir-1285-1	0	0.000000	N
+hsa-mir-1285-2	0	0.000000	N
+hsa-mir-1286	0	0.000000	N
+hsa-mir-1287	114	36.771026	N
+hsa-mir-1288	3	0.967659	N
+hsa-mir-1289-1	0	0.000000	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	2	0.645106	N
+hsa-mir-129-2	7	2.257870	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	1	0.322553	N
+hsa-mir-1292	1	0.322553	N
+hsa-mir-1293	0	0.000000	N
+hsa-mir-1294	2	0.645106	N
+hsa-mir-1295a	1	0.322553	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	4	1.290211	N
+hsa-mir-1297	0	0.000000	N
+hsa-mir-1298	0	0.000000	N
+hsa-mir-1299	0	0.000000	N
+hsa-mir-1301	11	3.548082	N
+hsa-mir-1302-1	0	0.000000	N
+hsa-mir-1302-10	0	0.000000	N
+hsa-mir-1302-11	0	0.000000	N
+hsa-mir-1302-2	0	0.000000	N
+hsa-mir-1302-3	0	0.000000	N
+hsa-mir-1302-4	0	0.000000	N
+hsa-mir-1302-5	0	0.000000	N
+hsa-mir-1302-6	0	0.000000	N
+hsa-mir-1302-7	0	0.000000	N
+hsa-mir-1302-8	0	0.000000	N
+hsa-mir-1302-9	0	0.000000	N
+hsa-mir-1303	0	0.000000	N
+hsa-mir-1304	3	0.967659	N
+hsa-mir-1305	1	0.322553	N
+hsa-mir-1306	19	6.128504	N
+hsa-mir-1307	3948	1273.438707	N
+hsa-mir-130a	77	24.836571	N
+hsa-mir-130b	52	16.772749	N
+hsa-mir-132	650	209.659362	N
+hsa-mir-1321	0	0.000000	N
+hsa-mir-1322	0	0.000000	N
+hsa-mir-1323	0	0.000000	N
+hsa-mir-1324	0	0.000000	N
+hsa-mir-133a-1	0	0.000000	N
+hsa-mir-133a-2	0	0.000000	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	857	276.427804	N
+hsa-mir-1343	3	0.967659	N
+hsa-mir-135a-1	0	0.000000	N
+hsa-mir-135a-2	0	0.000000	N
+hsa-mir-135b	3	0.967659	N
+hsa-mir-136	152	49.028035	N
+hsa-mir-137	0	0.000000	N
+hsa-mir-138-1	0	0.000000	N
+hsa-mir-138-2	1	0.322553	N
+hsa-mir-139	77	24.836571	N
+hsa-mir-140	1983	639.622329	N
+hsa-mir-141	4209	1357.625005	N
+hsa-mir-142	2406	776.062191	N
+hsa-mir-143	103069	33245.201139	N
+hsa-mir-144	255	82.250980	N
+hsa-mir-145	1637	528.019038	N
+hsa-mir-1468	14	4.515740	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	161	51.931011	N
+hsa-mir-146b	800	258.042291	N
+hsa-mir-1470	0	0.000000	N
+hsa-mir-1471	0	0.000000	N
+hsa-mir-147a	0	0.000000	N
+hsa-mir-147b	0	0.000000	N
+hsa-mir-148a	155884	50280.830651	N
+hsa-mir-148b	550	177.404075	N
+hsa-mir-149	130	41.931872	N
+hsa-mir-150	269	86.766720	N
+hsa-mir-151a	5832	1881.128303	N
+hsa-mir-151b	7	2.257870	N
+hsa-mir-152	1086	350.292410	N
+hsa-mir-153-1	0	0.000000	N
+hsa-mir-153-2	79	25.481676	N
+hsa-mir-1537	3	0.967659	N
+hsa-mir-1538	4	1.290211	N
+hsa-mir-1539	0	0.000000	N
+hsa-mir-154	20	6.451057	N
+hsa-mir-155	162	52.253564	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	487	157.083245	N
+hsa-mir-15b	61	19.675725	N
+hsa-mir-16-1	476	153.535163	N
+hsa-mir-16-2	485	156.438139	N
+hsa-mir-17	1720	554.790926	Y
+hsa-mir-181a-1	8157	2631.063712	N
+hsa-mir-181a-2	9987	3221.335453	N
+hsa-mir-181b-1	1175	378.999615	N
+hsa-mir-181b-2	1143	368.677924	N
+hsa-mir-181c	861	277.718016	N
+hsa-mir-181d	211	68.058654	N
+hsa-mir-182	59083	19057.390863	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	22386	7220.668413	N
+hsa-mir-184	1330	428.995309	N
+hsa-mir-185	217	69.993971	N
+hsa-mir-186	451	145.471342	N
+hsa-mir-187	14	4.515740	N
+hsa-mir-188	5	1.612764	N
+hsa-mir-18a	11	3.548082	N
+hsa-mir-18b	2	0.645106	N
+hsa-mir-1908	0	0.000000	N
+hsa-mir-1909	0	0.000000	N
+hsa-mir-190a	11	3.548082	N
+hsa-mir-190b	98	31.610181	N
+hsa-mir-191	1292	416.738300	N
+hsa-mir-1910	0	0.000000	N
+hsa-mir-1911	0	0.000000	N
+hsa-mir-1912	0	0.000000	N
+hsa-mir-1913	0	0.000000	N
+hsa-mir-1914	0	0.000000	N
+hsa-mir-1915	0	0.000000	N
+hsa-mir-192	1256	405.126397	Y
+hsa-mir-193a	4955	1598.249441	N
+hsa-mir-193b	249	80.315663	N
+hsa-mir-194-1	283	91.282461	N
+hsa-mir-194-2	305	98.378624	N
+hsa-mir-195	63	20.320830	N
+hsa-mir-196a-1	857	276.427804	N
+hsa-mir-196a-2	929	299.651611	N
+hsa-mir-196b	615	198.370011	N
+hsa-mir-197	364	117.409242	N
+hsa-mir-1972-1	0	0.000000	N
+hsa-mir-1972-2	0	0.000000	N
+hsa-mir-1973	0	0.000000	N
+hsa-mir-1976	47	15.159985	N
+hsa-mir-198	0	0.000000	N
+hsa-mir-199a-1	9206	2969.421666	Y
+hsa-mir-199a-2	14416	4649.922087	Y
+hsa-mir-199b	17071	5506.299941	Y
+hsa-mir-19a	33	10.644245	N
+hsa-mir-19b-1	81	26.126782	N
+hsa-mir-19b-2	68	21.933595	N
+hsa-mir-200a	3888	1254.085535	N
+hsa-mir-200b	2162	697.359292	N
+hsa-mir-200c	26565	8568.616832	N
+hsa-mir-202	1	0.322553	N
+hsa-mir-203a	10608	3421.640781	N
+hsa-mir-203b	59	19.030619	N
+hsa-mir-204	0	0.000000	N
+hsa-mir-205	674	217.400630	N
+hsa-mir-2052	0	0.000000	N
+hsa-mir-2053	0	0.000000	N
+hsa-mir-2054	0	0.000000	N
+hsa-mir-206	0	0.000000	N
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+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	789	254.494210	N
+hsa-mir-20b	417	134.504544	N
+hsa-mir-21	1027848	331535.316152	N
+hsa-mir-210	2387	769.933686	N
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+hsa-mir-2110	7	2.257870	N
+hsa-mir-2113	0	0.000000	N
+hsa-mir-2114	0	0.000000	N
+hsa-mir-2115	4	1.290211	N
+hsa-mir-2116	11	3.548082	N
+hsa-mir-2117	1	0.322553	N
+hsa-mir-212	10	3.225529	N
+hsa-mir-214	48	15.482537	N
+hsa-mir-215	15	4.838293	Y
+hsa-mir-216a	2	0.645106	N
+hsa-mir-216b	0	0.000000	N
+hsa-mir-217	47	15.159985	N
+hsa-mir-218-1	53	17.095302	N
+hsa-mir-218-2	46	14.837432	N
+hsa-mir-219a-1	9	2.902976	N
+hsa-mir-219a-2	0	0.000000	N
+hsa-mir-219b	1	0.322553	N
+hsa-mir-22	480626	155027.292811	N
+hsa-mir-221	244	78.702899	N
+hsa-mir-222	107	34.513156	N
+hsa-mir-223	83	26.771888	N
+hsa-mir-224	29	9.354033	N
+hsa-mir-2276	1	0.322553	N
+hsa-mir-2277	6	1.935317	N
+hsa-mir-2278	0	0.000000	N
+hsa-mir-2355	69	22.256148	N
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+hsa-mir-23a	15724	5071.821233	Y
+hsa-mir-23b	2739	883.472294	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	1375	443.510188	N
+hsa-mir-24-2	1409	454.476985	N
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+hsa-mir-25	14135	4559.284733	N
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+hsa-mir-2682	0	0.000000	N
+hsa-mir-26a-1	2140	690.263129	N
+hsa-mir-26a-2	2108	679.941437	N
+hsa-mir-26b	584	188.370873	N
+hsa-mir-27a	2107	679.618884	Y
+hsa-mir-27b	1630	525.761168	Y
+hsa-mir-28	15347	4950.218804	N
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+hsa-mir-297	0	0.000000	N
+hsa-mir-298	0	0.000000	N
+hsa-mir-299	4	1.290211	N
+hsa-mir-29a	4537	1463.422344	N
+hsa-mir-29b-1	393	126.763276	Y
+hsa-mir-29b-2	653	210.627020	Y
+hsa-mir-29c	6291	2029.180067	Y
+hsa-mir-300	0	0.000000	N
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+hsa-mir-302f	0	0.000000	N
+hsa-mir-3064	0	0.000000	N
+hsa-mir-3065	25	8.063822	N
+hsa-mir-3074	8	2.580423	N
+hsa-mir-30a	107491	34671.529904	Y
+hsa-mir-30b	174	56.124198	Y
+hsa-mir-30c-1	303	97.733518	Y
+hsa-mir-30c-2	522	168.372595	Y
+hsa-mir-30d	23181	7477.097940	N
+hsa-mir-30e	23330	7525.158317	Y
+hsa-mir-31	1	0.322553	N
+hsa-mir-3115	0	0.000000	N
+hsa-mir-3116-1	0	0.000000	N
+hsa-mir-3116-2	0	0.000000	N
+hsa-mir-3117	2	0.645106	N
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+hsa-mir-3118-3	0	0.000000	N
+hsa-mir-3118-4	0	0.000000	N
+hsa-mir-3119-1	0	0.000000	N
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+hsa-mir-3129	0	0.000000	N
+hsa-mir-3130-1	5	1.612764	N
+hsa-mir-3130-2	8	2.580423	N
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+hsa-mir-3134	0	0.000000	N
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+hsa-mir-3137	0	0.000000	N
+hsa-mir-3138	0	0.000000	N
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+hsa-mir-3140	0	0.000000	N
+hsa-mir-3141	0	0.000000	N
+hsa-mir-3142	0	0.000000	N
+hsa-mir-3143	0	0.000000	N
+hsa-mir-3144	0	0.000000	N
+hsa-mir-3145	1	0.322553	N
+hsa-mir-3146	0	0.000000	N
+hsa-mir-3147	0	0.000000	N
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+hsa-mir-3149	0	0.000000	N
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+hsa-mir-3152	0	0.000000	N
+hsa-mir-3153	0	0.000000	N
+hsa-mir-3154	0	0.000000	N
+hsa-mir-3155a	0	0.000000	N
+hsa-mir-3155b	0	0.000000	N
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+hsa-mir-3156-2	0	0.000000	N
+hsa-mir-3156-3	0	0.000000	N
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+hsa-mir-3158-1	0	0.000000	N
+hsa-mir-3158-2	0	0.000000	N
+hsa-mir-3159	0	0.000000	N
+hsa-mir-3160-1	0	0.000000	N
+hsa-mir-3160-2	0	0.000000	N
+hsa-mir-3161	0	0.000000	N
+hsa-mir-3162	0	0.000000	N
+hsa-mir-3163	0	0.000000	N
+hsa-mir-3164	0	0.000000	N
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+hsa-mir-3166	0	0.000000	N
+hsa-mir-3167	0	0.000000	N
+hsa-mir-3168	0	0.000000	N
+hsa-mir-3169	0	0.000000	N
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+hsa-mir-338	512	165.147066	N
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+hsa-mir-374c	0	0.000000	N
+hsa-mir-375	137233	44264.897185	N
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+hsa-mir-376a-2	4	1.290211	N
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+hsa-mir-378a	496	159.986221	N
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+hsa-mir-450b	25	8.063822	N
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+hsa-mir-451a	508	163.856855	N
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+hsa-mir-4522	1	0.322553	N
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+hsa-mir-455	589	189.983637	N
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+hsa-mir-4728	3	0.967659	N
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+hsa-mir-4731	0	0.000000	N
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+hsa-mir-4739	0	0.000000	N
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+hsa-mir-4743	0	0.000000	N
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+hsa-mir-4746	7	2.257870	N
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+hsa-mir-4762	1	0.322553	N
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+hsa-mir-4764	0	0.000000	N
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+hsa-mir-548u	0	0.000000	N
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+hsa-mir-550a-1	0	0.000000	N
+hsa-mir-550a-2	1	0.322553	N
+hsa-mir-550a-3	0	0.000000	N
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+hsa-mir-7162	0	0.000000	N
+hsa-mir-718	0	0.000000	N
+hsa-mir-744	212	68.381207	N
+hsa-mir-7515	0	0.000000	N
+hsa-mir-758	64	20.643383	N
+hsa-mir-759	0	0.000000	N
+hsa-mir-760	10	3.225529	N
+hsa-mir-761	0	0.000000	N
+hsa-mir-762	0	0.000000	N
+hsa-mir-764	0	0.000000	N
+hsa-mir-7641-1	0	0.000000	N
+hsa-mir-7641-2	0	0.000000	N
+hsa-mir-765	0	0.000000	N
+hsa-mir-766	30	9.676586	N
+hsa-mir-767	2	0.645106	N
+hsa-mir-769	72	23.223806	N
+hsa-mir-770	2	0.645106	N
+hsa-mir-7702	0	0.000000	N
+hsa-mir-7703	0	0.000000	N
+hsa-mir-7704	0	0.000000	N
+hsa-mir-7705	3	0.967659	N
+hsa-mir-7706	24	7.741269	N
+hsa-mir-7843	0	0.000000	N
+hsa-mir-7844	0	0.000000	N
+hsa-mir-7845	0	0.000000	N
+hsa-mir-7846	0	0.000000	N
+hsa-mir-7847	0	0.000000	N
+hsa-mir-7848	0	0.000000	N
+hsa-mir-7849	0	0.000000	N
+hsa-mir-7850	0	0.000000	N
+hsa-mir-7851	0	0.000000	N
+hsa-mir-7852	0	0.000000	N
+hsa-mir-7853	0	0.000000	N
+hsa-mir-7854	0	0.000000	N
+hsa-mir-7855	0	0.000000	N
+hsa-mir-7856	0	0.000000	N
+hsa-mir-7973-1	0	0.000000	N
+hsa-mir-7973-2	0	0.000000	N
+hsa-mir-7974	0	0.000000	N
+hsa-mir-7975	0	0.000000	N
+hsa-mir-7976	0	0.000000	N
+hsa-mir-7977	0	0.000000	N
+hsa-mir-7978	0	0.000000	N
+hsa-mir-802	0	0.000000	N
+hsa-mir-8052	0	0.000000	N
+hsa-mir-8053	0	0.000000	N
+hsa-mir-8054	0	0.000000	N
+hsa-mir-8055	0	0.000000	N
+hsa-mir-8056	0	0.000000	N
+hsa-mir-8057	0	0.000000	N
+hsa-mir-8058	0	0.000000	N
+hsa-mir-8059	0	0.000000	N
+hsa-mir-8060	0	0.000000	N
+hsa-mir-8061	0	0.000000	N
+hsa-mir-8062	0	0.000000	N
+hsa-mir-8063	0	0.000000	N
+hsa-mir-8064	0	0.000000	N
+hsa-mir-8065	0	0.000000	N
+hsa-mir-8066	0	0.000000	N
+hsa-mir-8067	0	0.000000	N
+hsa-mir-8068	0	0.000000	N
+hsa-mir-8069-1	0	0.000000	N
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+hsa-mir-8070	0	0.000000	N
+hsa-mir-8071-1	0	0.000000	N
+hsa-mir-8071-2	0	0.000000	N
+hsa-mir-8072	0	0.000000	N
+hsa-mir-8073	0	0.000000	N
+hsa-mir-8074	0	0.000000	N
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+hsa-mir-8076	0	0.000000	N
+hsa-mir-8077	0	0.000000	N
+hsa-mir-8078	0	0.000000	N
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+hsa-mir-873	0	0.000000	N
+hsa-mir-874	160	51.608458	N
+hsa-mir-875	0	0.000000	N
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+hsa-mir-877	0	0.000000	N
+hsa-mir-885	0	0.000000	N
+hsa-mir-887	27	8.708927	N
+hsa-mir-888	0	0.000000	N
+hsa-mir-889	94	30.319969	N
+hsa-mir-890	0	0.000000	N
+hsa-mir-891a	2	0.645106	N
+hsa-mir-891b	0	0.000000	N
+hsa-mir-892a	0	0.000000	N
+hsa-mir-892b	0	0.000000	N
+hsa-mir-892c	0	0.000000	N
+hsa-mir-9-1	134	43.222084	N
+hsa-mir-9-2	143	46.125060	N
+hsa-mir-9-3	147	47.415271	N
+hsa-mir-920	0	0.000000	N
+hsa-mir-921	0	0.000000	N
+hsa-mir-922	0	0.000000	N
+hsa-mir-924	0	0.000000	N
+hsa-mir-92a-1	12746	4111.258804	N
+hsa-mir-92a-2	11486	3704.842196	N
+hsa-mir-92b	710	229.012533	N
+hsa-mir-93	25949	8369.924268	N
+hsa-mir-933	0	0.000000	N
+hsa-mir-934	1	0.322553	N
+hsa-mir-935	0	0.000000	N
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+hsa-mir-937	10	3.225529	N
+hsa-mir-938	0	0.000000	N
+hsa-mir-939	4	1.290211	N
+hsa-mir-940	1	0.322553	N
+hsa-mir-941-1	0	0.000000	N
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+hsa-mir-941-4	0	0.000000	N
+hsa-mir-941-5	0	0.000000	N
+hsa-mir-942	15	4.838293	N
+hsa-mir-943	0	0.000000	N
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+hsa-mir-95	5	1.612764	N
+hsa-mir-9500	0	0.000000	N
+hsa-mir-96	60	19.353172	N
+hsa-mir-98	126	40.641661	N
+hsa-mir-99a	1373	442.865082	N
+hsa-mir-99b	86714	27969.849048	N

data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_F03_741528.grch38.seg.v2.txt

@@ -0,0 +1,570 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
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+e96765f9-45a3-446f-924a-45202dd4b7db	1	3040102	7360844	2929	0.0045
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+e96765f9-45a3-446f-924a-45202dd4b7db	1	10307286	10321714	20	0.5066
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+e96765f9-45a3-446f-924a-45202dd4b7db	18	59985948	59997792	41	0.5866
+e96765f9-45a3-446f-924a-45202dd4b7db	18	60001293	64372879	3111	-0.0379
+e96765f9-45a3-446f-924a-45202dd4b7db	18	64376126	71282852	4908	-0.0745
+e96765f9-45a3-446f-924a-45202dd4b7db	18	71286635	73639271	1841	-0.156
+e96765f9-45a3-446f-924a-45202dd4b7db	18	73639748	80257174	4807	-0.0177
+e96765f9-45a3-446f-924a-45202dd4b7db	19	90910	19707671	8487	0.0062
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+e96765f9-45a3-446f-924a-45202dd4b7db	19	36356476	42711176	3218	0.0032
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+e96765f9-45a3-446f-924a-45202dd4b7db	21	22651292	22651593	3	-1.7721
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data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_F03_741528.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,83 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
+e96765f9-45a3-446f-924a-45202dd4b7db	1	3301765	7360844	2642	0.0049
+e96765f9-45a3-446f-924a-45202dd4b7db	1	7362491	7365004	2	-1.8263
+e96765f9-45a3-446f-924a-45202dd4b7db	1	7365357	55636149	25561	0.0001
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+e96765f9-45a3-446f-924a-45202dd4b7db	1	149907993	184649888	21764	0.3979
+e96765f9-45a3-446f-924a-45202dd4b7db	1	184650779	199489775	8643	0.3736
+e96765f9-45a3-446f-924a-45202dd4b7db	1	199490817	247650984	31240	0.4035
+e96765f9-45a3-446f-924a-45202dd4b7db	2	480597	141019156	73954	-0.0301
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+e96765f9-45a3-446f-924a-45202dd4b7db	3	25855663	36209948	6165	-0.045
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+e96765f9-45a3-446f-924a-45202dd4b7db	3	74199993	99424442	10778	-0.049
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+e96765f9-45a3-446f-924a-45202dd4b7db	10	366509	47265449	28400	-0.0214
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+e96765f9-45a3-446f-924a-45202dd4b7db	13	18874255	32497158	8371	-0.0211
+e96765f9-45a3-446f-924a-45202dd4b7db	13	32500789	110321711	46610	-0.0455
+e96765f9-45a3-446f-924a-45202dd4b7db	13	110323103	114226675	1989	-0.0233
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+e96765f9-45a3-446f-924a-45202dd4b7db	15	23437561	77905451	30710	-0.0173
+e96765f9-45a3-446f-924a-45202dd4b7db	15	77908416	101344124	14069	0.4114
+e96765f9-45a3-446f-924a-45202dd4b7db	16	603333	46470502	14036	-0.0011
+e96765f9-45a3-446f-924a-45202dd4b7db	16	46473753	49395200	1534	-0.6257
+e96765f9-45a3-446f-924a-45202dd4b7db	16	49395347	49395714	2	-3.9661
+e96765f9-45a3-446f-924a-45202dd4b7db	16	49396318	89317317	25440	-0.6691
+e96765f9-45a3-446f-924a-45202dd4b7db	17	1074619	82959812	37281	-0.0046
+e96765f9-45a3-446f-924a-45202dd4b7db	18	326691	64712910	35617	-0.0265
+e96765f9-45a3-446f-924a-45202dd4b7db	18	64713569	70742047	3181	-0.0709
+e96765f9-45a3-446f-924a-45202dd4b7db	18	70744854	79349796	4150	-0.0326
+e96765f9-45a3-446f-924a-45202dd4b7db	19	283868	58370362	24148	-0.0027
+e96765f9-45a3-446f-924a-45202dd4b7db	20	472817	63588502	37546	-0.0079
+e96765f9-45a3-446f-924a-45202dd4b7db	21	13974127	46262057	20588	-0.0279
+e96765f9-45a3-446f-924a-45202dd4b7db	22	16934932	48940621	17078	-0.0032
+e96765f9-45a3-446f-924a-45202dd4b7db	X	3236359	37850312	15456	0.0163
+e96765f9-45a3-446f-924a-45202dd4b7db	X	37851496	37852498	2	-1.5768
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+e96765f9-45a3-446f-924a-45202dd4b7db	X	74556252	93169030	7089	-0.0146
+e96765f9-45a3-446f-924a-45202dd4b7db	X	93170688	111112563	8000	0.0145
+e96765f9-45a3-446f-924a-45202dd4b7db	X	111113377	111118281	12	-0.7604
+e96765f9-45a3-446f-924a-45202dd4b7db	X	111118562	155677414	20384	0.0151

data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/TCGA-E2-A15L-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt

@@ -0,0 +1,434 @@
+GDC_Aliquot_ID	Chromosome	Start	End	Num_Probes	Segment_Mean
+TCGA-E2-A15L-01A-11D-A895-36	chr1	17001	771000	16	-0.441677
+TCGA-E2-A15L-01A-11D-A895-36	chr1	777001	12884000	11863	0.002004
+TCGA-E2-A15L-01A-11D-A895-36	chr1	12884001	13059000	12	-0.801409
+TCGA-E2-A15L-01A-11D-A895-36	chr1	13104001	16027000	2738	0.006239
+TCGA-E2-A15L-01A-11D-A895-36	chr1	16027001	16044000	16	0.541627
+TCGA-E2-A15L-01A-11D-A895-36	chr1	16044001	16534000	488	0.010520
+TCGA-E2-A15L-01A-11D-A895-36	chr1	16534001	16632000	66	0.168464
+TCGA-E2-A15L-01A-11D-A895-36	chr1	16632001	16884000	113	0.064385
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+TCGA-E2-A15L-01A-11D-A895-36	chr18	17065001	80263000	58904	-0.013641
+TCGA-E2-A15L-01A-11D-A895-36	chr19	89001	24330000	23850	0.002202
+TCGA-E2-A15L-01A-11D-A895-36	chr19	24330001	24415000	83	0.412537
+TCGA-E2-A15L-01A-11D-A895-36	chr19	24415001	27347000	118	-0.001031
+TCGA-E2-A15L-01A-11D-A895-36	chr19	27347001	27400000	53	0.251411
+TCGA-E2-A15L-01A-11D-A895-36	chr19	27400001	41186000	13607	-0.004037
+TCGA-E2-A15L-01A-11D-A895-36	chr19	41186001	41194000	8	-0.115170
+TCGA-E2-A15L-01A-11D-A895-36	chr19	41194001	54746000	13336	0.004675
+TCGA-E2-A15L-01A-11D-A895-36	chr19	54746001	54780000	31	-0.930517
+TCGA-E2-A15L-01A-11D-A895-36	chr19	54781001	58591000	3758	0.003415
+TCGA-E2-A15L-01A-11D-A895-36	chr20	60001	48473000	45103	-0.000530
+TCGA-E2-A15L-01A-11D-A895-36	chr20	48473001	48480000	7	-0.161280
+TCGA-E2-A15L-01A-11D-A895-36	chr20	48480001	64334000	15734	-0.000427
+TCGA-E2-A15L-01A-11D-A895-36	chr21	5103001	6376000	56	0.196752
+TCGA-E2-A15L-01A-11D-A895-36	chr21	6376001	7288000	45	-0.298088
+TCGA-E2-A15L-01A-11D-A895-36	chr21	7289001	7293000	4	2.360109
+TCGA-E2-A15L-01A-11D-A895-36	chr21	7293001	8023000	90	-0.106965
+TCGA-E2-A15L-01A-11D-A895-36	chr21	8036001	8043000	6	-2.425900
+TCGA-E2-A15L-01A-11D-A895-36	chr21	8044001	8988000	79	-0.116311
+TCGA-E2-A15L-01A-11D-A895-36	chr21	8988001	9249000	60	0.085663
+TCGA-E2-A15L-01A-11D-A895-36	chr21	9297001	9356000	5	-1.242134
+TCGA-E2-A15L-01A-11D-A895-36	chr21	9361001	10012000	296	0.123870
+TCGA-E2-A15L-01A-11D-A895-36	chr21	10012001	10460000	197	-0.109289
+TCGA-E2-A15L-01A-11D-A895-36	chr21	10460001	10673000	194	0.046003
+TCGA-E2-A15L-01A-11D-A895-36	chr21	10673001	12983000	159	0.230763
+TCGA-E2-A15L-01A-11D-A895-36	chr21	12983001	13037000	53	-0.043536
+TCGA-E2-A15L-01A-11D-A895-36	chr21	13037001	13175000	86	-0.667214
+TCGA-E2-A15L-01A-11D-A895-36	chr21	13189001	46682000	32421	-0.013031
+TCGA-E2-A15L-01A-11D-A895-36	chr22	10661001	10709000	21	0.693553
+TCGA-E2-A15L-01A-11D-A895-36	chr22	10710001	48985000	32069	-0.005429
+TCGA-E2-A15L-01A-11D-A895-36	chr22	48985001	48999000	8	-29.746059
+TCGA-E2-A15L-01A-11D-A895-36	chr22	48999001	50796000	1759	0.000047
+TCGA-E2-A15L-01A-11D-A895-36	chrX	251001	464000	187	0.421710
+TCGA-E2-A15L-01A-11D-A895-36	chrX	464001	5813000	2046	0.439318
+TCGA-E2-A15L-01A-11D-A895-36	chrX	9404001	9410000	4	1.634773
+TCGA-E2-A15L-01A-11D-A895-36	chrX	9411001	141006000	55	1.000290
+TCGA-E2-A15L-01A-11D-A895-36	chrX	141050001	155734000	41	0.436959
+TCGA-E2-A15L-01A-11D-A895-36	chrX	155734001	155970000	235	0.415611
+TCGA-E2-A15L-01A-11D-A895-36	chrX	155970001	156026000	40	0.457990
+TCGA-E2-A15L-01A-11D-A895-36	chrY	6534001	10658000	12	-0.880598
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10660001	10678000	10	-5.169242
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10678001	10693000	4	-3.865997
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10755001	10861000	10	-1.545343
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10863001	10867000	2	-0.911025
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10869001	10922000	4	-2.578135
+TCGA-E2-A15L-01A-11D-A895-36	chrY	10926001	11278000	29	-0.552796
+TCGA-E2-A15L-01A-11D-A895-36	chrY	11289001	11319000	20	-0.015429
+TCGA-E2-A15L-01A-11D-A895-36	chrY	11319001	11321000	2	-2.202477
+TCGA-E2-A15L-01A-11D-A895-36	chrY	11324001	11415000	33	-0.724422
+TCGA-E2-A15L-01A-11D-A895-36	chrY	11531001	11556000	4	-9.926202
+TCGA-E2-A15L-01A-11D-A895-36	chrY	11643001	26640000	18	-0.812629
+TCGA-E2-A15L-01A-11D-A895-36	chrY	26661001	56708000	4	-5.737114
+TCGA-E2-A15L-01A-11D-A895-36	chrY	56821001	56887000	66	-0.212960
+TCGA-E2-A15L-01A-11D-A895-36	chrM	1	16569	17	-0.562997

data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/TCGA-E2-A15L-01A-21-A13E-20_RPPA_data.tsv

@@ -0,0 +1,488 @@
+AGID	lab_id	catalog_number	set_id	peptide_target	protein_expression
+AGID00100	882	sc-628	Old	1433BETA	0.01087
+AGID00111	913	sc-23957	Old	1433EPSILON	0.17233
+AGID00101	883	sc-1019	Old	1433ZETA	-0.15933
+AGID00001	2	9452	Old	4EBP1	0.23345
+AGID00002	3	9456	Old	4EBP1_pS65	-0.16248
+AGID00003	6	9459	Old	4EBP1_pT37T46	-0.61421
+AGID00443	8	9455	Old	4EBP1_pT70	-0.16853
+AGID00120	985	4937	Old	53BP1	0.11843
+AGID00004	13	3661	Old	ACC_pS79	0.059757
+AGID00005	14	1768-1/ab45174	Old	ACC1	0.34768
+AGID00408	2372	3658	Set163	AceCS1	-0.22004
+AGID00473	1182	5335	Old	ACETYLATUBULINLYS40	-0.17247
+AGID00404	2367	9189	Set163	ACSL1	0.1503105
+AGID02144	2450	PA5-27081	Old	ACVRL1	0.063621
+AGID00186	1198	ab88574	Old	ADAR1	-0.11309
+AGID00146	1084	4691	Old	AKT	0.4658
+AGID00028	230	9271	Old	AKT_pS473	-0.50917
+AGID00170	1154	2965	Old	AKT_pT308	-0.73402
+AGID00316	1800	3063	Set163	Akt2	0.2067955
+AGID00347	2009	8599	Set163	Akt2_pS474	-0.1828901
+AGID02215	2577	ab195377	Set163	ALKBH5	0.4418653
+AGID00498	924	CA1030	Old	ALPHACATENIN	NA
+AGID00287	1630	ABC80	Set163	Ambra1_pS52	-0.1388954
+AGID00236	1351	ab129081	Set163	AMPK-a2_pS345	-0.1039546
+AGID00006	39	2532	Old	AMPKALPHA	0.23114
+AGID00007	40	2535	Old	AMPKALPHA_pT172	0.50693
+AGID00193	1208	610066	Old	ANNEXIN1	-0.5207
+AGID00166	1142	610668	Old	ANNEXINVII	0.21647
+AGID00371	756	1852-1/ab52615	Old	AR	1.4023
+AGID00194	1217	4432	Old	ARAF	0.2807
+AGID02191	2507	PA5-39728	Old	ARAF_pS299	0.053221
+AGID00260	1053	sc-32761	Old	ARID1A	0.63755
+AGID00264	1560	HPA029318	Old	ASNS	-0.49734
+AGID00276	1612	3415	Set163	Atg3	-0.1917296
+AGID00309	1775	13507	Set163	Atg4B	-0.14301
+AGID00310	1776	12994	Set163	Atg5	0.3799404
+AGID00277	1613	8558	Set163	Atg7	0.3824205
+AGID00242	1363	2873	Old	ATM	0.5029
+AGID02142	2447	13050	Set163	ATM_pS1981	-0.02030465
+AGID00217	1289	ab14748	Set163	ATP5A	-0.3864302
+AGID02145	2451	PA5-43776	Set163	ATP5H	0.1528655
+AGID02150	2456	13934	Set163	ATR	0.08412746
+AGID00315	1795	ab178407	Set163	ATR_pS428	-0.5401658
+AGID00268	1569	ab97508	Set163	ATRX	0.5693479
+AGID00391	2332	14475	Set163	Aurora-A	0.1073105
+AGID00392	2333	2914	Set163	Aurora-ABC_pT288_pT232_pT198	-0.1628795
+AGID02195	2512	MA5-27890	Set163	Aurora-B	-0.08642581
+AGID00215	1271	8661	Old	AXL	0.12706
+AGID02143	2449	8457	Set163	b-Actin	0.1873802
+AGID00179	1170	9565	Set163	b-Catenin_pT41_S45	-0.1597745
+AGID00301	1725	14058	Set163	B7-H3	-0.5478004
+AGID00302	1726	14572	Set163	B7-H4	-0.2344248
+AGID00008	63	9291	Old	BAD_pS112	0.19479
+AGID00009	71	1542-1/ab32371	Old	BAK	-0.32198
+AGID00192	1207	sc-28383	Old	BAP1C4	0.21982
+AGID00010	73	2772	Old	BAX	-0.1281
+AGID00433	80	M0887	Old	BCL2	0.78003
+AGID00219	1299	PAB8528	Old	BCL2A1	0.12934
+AGID00012	84	1018-1	Old	BCLXL	-0.37482
+AGID00377	87	sc-10086	Old	BECLIN	-0.043275
+AGID00011	75	9562	Old	BETACATENIN	-1.9261
+AGID00013	88	1008-1/ab32060	Old	BID	0.079588
+AGID00180	90	1036-1/ab32158	Old	BIM	0.61004
+AGID00221	1311	610978	Set163	BiP-GRP78	0.1324849
+AGID00373	2194	07-507	Set163	BMK1-Erk5_pT218_Y220	-0.05175947
+AGID00355	92	1647/ab33899	Old	BRAF	0.28017
+AGID00014	94	2696	Old	BRAF_pS445	0.1934
+AGID00445	761	9012	Old	BRCA2	0.2005
+AGID00266	1567	13440	Old	BRD4	0.051869
+AGID00168	1146	2865	Set163	c-Abl_pY412	-0.008560241
+AGID00278	1615	3130	Set163	c-IAP2	-0.1913446
+AGID00345	1990	5649	Old	CA9	NA
+AGID00265	1565	2862	Old	CABL	-0.10507
+AGID00429	2407	2679	Set163	Calnexin	0.2921602
+AGID00176	1165	9496	Set163	Caspase-8-cleaved	0.1676354
+AGID00623	111	9665	Old	CASPASE3	-0.25485
+AGID00015	109	9491	Old	CASPASE7CLEAVEDD198	-0.82299
+AGID00118	951	9746	Old	CASPASE8	0.028933
+AGID00537	935	551246	Old	CASPASE9	NA
+AGID00016	114	3238	Old	CAVEOLIN1	-0.059956
+AGID00358	2100	ab76000	Set163	CD134	0.04005905
+AGID00303	1737	826701	Set163	CD171	-0.2886595
+AGID00410	125	1632-1/ab78237	Old	CD20	-0.1289
+AGID00220	1308	ab28340	Old	CD26	0.041814
+AGID00191	1206	610467	Set163	CD29	0.05909014
+AGID00017	127	M0823	Old	CD31	0.032716
+AGID00369	2174	ab108403	Set163	CD38	0.0349605
+AGID00359	2104	ab133616	Set163	CD4	-0.1181708
+AGID00411	1398	3570	Set163	CD44	-0.3060246
+AGID00237	1352	M070101-2	Set163	CD45	-0.1240397
+AGID00115	937	611016	Old	CD49B	-0.43096
+AGID02171	2482	91882	Set163	CD86	-0.2202895
+AGID00329	1873	4688	Set163	cdc25C	0.3599355
+AGID00227	1332	4651	Set163	Cdc42	0.1426303
+AGID00422	2396	3387	Set163	Cdc6	0.1404704
+AGID00501	1007	9112	Old	CDK1	0.059284
+AGID00293	1658	ab32384	Set163	CDK1_pT14	0.3614505
+AGID00314	1783	4539	Old	CDK1_pY15	-0.041523
+AGID00423	2397	8064	Set163	CDT1	0.08346504
+AGID02101	2348	15102	Set163	cGAS	0.009280496
+AGID00447	2410	13460	Set163	CHD1L	0.07349866
+AGID00189	1203	2360	Old	CHK1	-0.091712
+AGID00234	1348	ab79758	Old	CHK1_pS296	0.046944
+AGID00107	903	2348	Old	CHK1_pS345	-0.35643
+AGID00018	146	3440	Old	CHK2	0.14987
+AGID00019	147	2197	Old	CHK2_pT68	-0.18652
+AGID00527	2078	4952	Old	CIAP	-0.052965
+AGID00350	2018	3793	Set163	CIITA	-0.06639951
+AGID00434	155	9164	Old	CJUN_pS73	-0.17699
+AGID00020	157	1522-1/ab32363	Old	CKIT	0.019672
+AGID00400	852	NB100-91714	Old	CLAUDIN7	0.19762
+AGID00466	726	3127	Old	CMET	-0.093319
+AGID00079	727	3129	Old	CMET_pY1235	-0.17706
+AGID00167	161	9402	Old	CMYC	-0.26258
+AGID00292	1656	11130-1-AP	Old	COG3	0.37378
+AGID00021	171	sc-20649	Old	COLLAGENVI	0.89753
+AGID00141	1069	459230	Old	COMPLEXIISUBUNIT30	NA
+AGID00267	1568	3512	Set163	Connexin-43	0.8530402
+AGID00269	1571	6434	Set163	Coup-TFII	0.3715105
+AGID00150	1116	4850	Set163	Cox-IV	-0.1475902
+AGID00195	1218	4842	Set163	Cox2	-0.2606595
+AGID00188	803	05-739	Old	CRAF	0.35933
+AGID00022	179	9427	Old	CRAF_pS338	-0.093681
+AGID00023	181	9197	Set163	Creb	0.1101094
+AGID00393	2334	9198	Set163	CREB_pS133	0.3488626
+AGID00365	2155	4980	Set163	CSK	0.1730605
+AGID00367	2160	9201	Set163	CtIP	0.03886516
+AGID00536	2096	ab107198	Old	CTLA4	NA
+AGID00025	198	2936	Set163	Cyclin-D3	-0.1926796
+AGID00024	192	1495-1/ab32053	Old	CYCLINB1	0.58548
+AGID00382	194	sc-718	Old	CYCLIND1	0.029398
+AGID00437	199	sc-25303	Old	CYCLINE1	-0.71462
+AGID00449	202	1142-1	Old	CYCLINE2	-0.35029
+AGID00209	1257	ab110324	Set163	Cyclophilin-F	-0.2614398
+AGID00247	1379	ab48389	Set163	D-a-Tubulin	-0.4004145
+AGID00308	1770	GTX10524	Set163	DAPK1_pS308	-0.2176196
+AGID00304	1744	ab51601	Set163	DAPK2	-0.2014147
+AGID00343	1980	6998	Set163	DDB-1	0.01559043
+AGID00427	2402	5583	Set163	DDR1	-0.2445353
+AGID00428	2403	SAB4504671	Set163	DDR1_pY513	-0.3252595
+AGID00532	1273	Bast Lab	Old	DIRAS3	0.10789
+AGID00104	891	ab76008	Old	DJ1	0.47897
+AGID02146	2452	4658	Set163	DM-Histone-H3	0.2223651
+AGID00386	1397	ab32521	Set163	DM-K9-Histone-H3	-0.03833454
+AGID00352	2030	14649	Set163	DNA-Ligase-IV	0.03482524
+AGID00407	2371	13609	Set163	DNA_POLG	0.07069041
+AGID00399	2344	5032	Set163	DNMT1	0.4104404
+AGID00409	2373	5391	Set163	DRP1	0.009858923
+AGID00253	1406	5149	Old	DUSP4	2.364
+AGID00334	1936	ab76310	Set163	DUSP6	0.2052902
+AGID00116	940	3218	Old	DVL3	-0.21713
+AGID00211	1261	sc-251	Old	E2F1	NA
+AGID00148	1099	3195	Old	ECADHERIN	-2.7697
+AGID00135	1060	2332	Old	EEF2	-0.43202
+AGID00136	1061	3692	Old	EEF2K	0.5756
+AGID00152	1120	2232	Old	EGFR	-0.53576
+AGID00450	217	2234	Old	EGFR_pY1068	0.097134
+AGID00026	221	1124-1/ab32578	Old	EGFR_pY1173	-0.061675
+AGID00078	722	9742	Old	EIF4E	0.31645
+AGID00328	1871	ab76256	Set163	eIF4E_pS209	0.2142202
+AGID00154	1124	2498	Old	EIF4G	-0.097941
+AGID00027	228	9181	Set163	Elk1_pS383	0.1119655
+AGID00235	1350	M061329-2	Set163	EMA	1.81894
+AGID00394	2337	3810	Set163	Enolase-1	-0.1251347
+AGID00395	2338	8171	Set163	Enolase-2	0.0133155
+AGID00196	1219	GTX629542	Old	ENY2	-0.07917
+AGID00438	1849	A302-024A	Set163	EphA2	-0.02195951
+AGID00552	2422	6347	Set163	EphA2_pS897	-0.3246095
+AGID00553	2423	12677	Set163	EphA2_pY588	-0.247598
+AGID00075	693	556347	Old	EPPK1	0.59663
+AGID00335	238	RM-9101	Old	ERALPHA	2.8403
+AGID00029	241	1091-1/ab32396	Old	ERALPHA_pS118	0.022482
+AGID00240	247	MS-671	Old	ERCC1	-0.25144
+AGID00239	1355	11331-1-AP	Old	ERCC5	-0.32793
+AGID00484	249	sc-154	Old	ERK2	-0.17415
+AGID00372	2193	3552	Set163	Erk5	0.3787305
+AGID00405	2369	13826	Set163	ERRalpha	0.2008454
+AGID00187	1200	A303-501A	Old	ETS1	-0.50031
+AGID00511	2492	2593	Set163	EVI1	0.3185049
+AGID00485	1284	4905	Old	EZH2	NA
+AGID00030	252	1700-1/ab40794	Set163	FAK	0.1955905
+AGID02151	2457	8556	Set163	FAK_pY397	-0.3350661
+AGID00171	1156	3180	Old	FASN	0.71146
+AGID00356	2085	500-P18/10775-082	Set163	FGF-basic	0.1292555
+AGID00031	262	1574-1/ab45688	Old	FIBRONECTIN	1.0686
+AGID00339	1959	4403	Set163	FN14	-0.3301745
+AGID02152	2458	20459	Old	FOXM1	-0.0099512
+AGID00378	269	9467	Old	FOXO3A	0.19149
+AGID02197	2515	orb6051	Old	FOXO3A_pS318S321	-0.072298
+AGID02167	2475	PA5-64616	Set163	FRS2-alpha_pY196	-0.0720095
+AGID02213	2575	ab124892	Set163	FTO	-0.0370895
+AGID02141	2446	12263	Old	G6PD	-0.22869
+AGID00117	943	3239	Old	GAB2	-0.24379
+AGID00412	274	AM4300	Old	GAPDH	-1.6171
+AGID00086	764	558686	Old	GATA3	2.8119
+AGID00383	1578	4253	Old	GATA6	0.10844
+AGID00289	1634	12601-1-AP	Set163	GCLC	-0.2876245
+AGID00305	1745	ab124827	Set163	GCLM	-0.09284951
+AGID00212	1263	3305	Old	GCN5L2	0.26723
+AGID00270	1579	3538	Set163	Gli1	-0.8461499
+AGID00263	1520	ab69838	Set163	Gli3	-0.1555407
+AGID00548	2530	3660	Set163	Glucocorticoid-Receptor	0.6107055
+AGID00387	1617	12793	Set163	Glutamate-D1-2	0.3613194
+AGID00262	1491	ab156876	Set163	Glutaminase	-0.1816196
+AGID00319	1807	4275	Set163	Granzyme-B	0.4825654
+AGID00368	2169	ab183737	Set163	GRB7	-0.5316703
+AGID00396	2339	3593	Set163	Grp75	0.1053854
+AGID00174	1163	9315	Set163	GSK-3B	0.4023696
+AGID00502	1082	9336	Old	GSK3_pS9	-0.49473
+AGID00033	284	sc-7291	Old	GSK3ALPHABETA	-0.042494
+AGID00034	285	9331	Old	GSK3ALPHABETA_pS21S9	-0.46129
+AGID00129	1035	3886	Old	GYS	NA
+AGID00130	1036	3891	Old	GYS_pS641	NA
+AGID01354	1342	9718	Set163	H2AX_pS139	-0.1223495
+AGID00363	1409	MA1-2022	Set163	H2AX_pS140	-0.2310546
+AGID00131	1038	MS-325-P1	Old	HER2	0.41037
+AGID00142	299	06-229	Old	HER2_pY1248	0.23667
+AGID00110	911	sc-285	Old	HER3	0.10162
+AGID00080	728	4791	Old	HER3_pY1289	-0.01141
+AGID00103	890	2573	Old	HEREGULIN	-0.040771
+AGID00271	1582	11988	Set163	HES1	0.6531803
+AGID00397	2340	2024	Set163	Hexokinase-I	-0.05536975
+AGID00442	1023	2867	Set163	Hexokinase-II	-0.01217106
+AGID00419	1402	610958	Old	HIF1ALPHA	NA
+AGID00205	1250	ab1791	Set163	Histone-H3	0.9271403
+AGID00398	2341	3377	Set163	Histone-H3_pS10	0.06628537
+AGID00332	1901	ab128959	Set163	HLA-DQA1	-0.5808109
+AGID00333	1902	14832-1-AP	Set163	HMHA1	0
+AGID00035	321	2402	Set163	HSP27	-0.4754546
+AGID00036	323	2401	Set163	HSP27_pS82	-0.3042095
+AGID00320	1808	12165	Set163	HSP60	-0.1793147
+AGID00037	325	4872	Old	HSP70	0.065513
+AGID00366	2158	86630	Set163	IDO	-0.363245
+AGID00197	1221	3024	Old	IGF1R_pY1135Y1136	0.14229
+AGID00038	335	3922	Old	IGFBP2	0.32692
+AGID00090	793	611504	Set163	IGFBP3	-0.8024898
+AGID00039	336	3027	Set163	IGFRb	0.5786705
+AGID00336	1949	12153	Set163	IL-6	-0.05469483
+AGID02221	2583	57145	Set163	IMP3	0.07374035
+AGID02153	2459	14543	Old	INPP4B	2.1317
+AGID00272	1586	3025	Set163	IR-b	0.4312405
+AGID00519	2519	4302	Set163	IRF-3	-0.1912143
+AGID00520	2520	4947	Set163	IRF-3_pS396	-0.35711
+AGID00223	1316	sc-497	Old	IRF1	-0.2641
+AGID00092	802	06-248	Old	IRS1	0.10817
+AGID00040	371	4502	Set163	IRS2	-0.28556
+AGID00250	1394	sc-13157	Old	JAB1	0.060622
+AGID00256	1413	ab109536	Set163	Jagged1	-0.210444
+AGID00177	1166	3230	Old	JAK2	-0.24669
+AGID00758	377	4671	Old	JNK_pT183Y185	0.069589
+AGID02136	2439	PA5-28262	Old	JNK2	0.46937
+AGID00307	1757	ab10484	Set163	KAP1	0.239365
+AGID00528	904	2180	Old	KU80	-0.041912
+AGID00375	2237	HPA028732	Set163	LAD1	-0.1712245
+AGID00290	1643	IHC-00439	Set163	Lasu1	0.05672547
+AGID00279	1618	4108	Set163	LC3A-B	-0.1027548
+AGID00042	397	2752	Old	LCK	-0.27349
+AGID00119	976	3582	Old	LDHA	NA
+AGID00533	977	ab85319	Old	LDHB	NA
+AGID00529	1477	3050	Old	LKB1	0.14582
+AGID00244	1367	2568	Set163	LRP6_pS1490	-0.4518145
+AGID00439	2424	2796	Set163	Lyn	-0.08709456
+AGID02154	2460	4370	Old	MAPK_pT202Y204	0.44417
+AGID00198	1222	5453	Set163	Mcl-1	0.2132994
+AGID00288	1633	AB3314P	Set163	MCT4	-0.4946996
+AGID00175	1164	3521	Set163	MDM2_pS166	-0.0183145
+AGID00044	417	1235-1/ab32576	Old	MEK1	-0.072698
+AGID00143	1076	9154	Old	MEK1_pS217S221	-0.24895
+AGID00201	1243	9125	Set163	MEK2	-0.05167998
+AGID00361	2118	ab51061	Set163	MelanA	-0.1286345
+AGID00362	2119	ab137078	Set163	Melanoma-gp100	0.1148404
+AGID00337	1951	12711	Set163	MERIT40	0.2155349
+AGID00338	1952	12110	Set163	MERIT40_pS29	-0.0807995
+AGID02212	2574	ab195352	Set163	METTL3	0.1149605
+AGID00225	1323	sc-20121	Set163	MIF	0.5153305
+AGID00137	1062	WH0054206M1	Old	MIG6	0.086928
+AGID00403	2117	ab20663	Set163	MITF	0.2173851
+AGID00503	1067	ab3298	Old	MITOCHONDRIA	NA
+AGID00321	1809	14739	Set163	Mitofusin-1	-0.4537883
+AGID00322	1810	11925	Set163	Mitofusin-2	0.2401304
+AGID00389	2324	3515	Set163	MLH1	0.2092904
+AGID00312	1780	14993	Set163	MLKL	-0.7738797
+AGID00402	2359	MAB3328	Set163	MMP14	0.5844604
+AGID00045	435	4022	Set163	MMP2	-0.2584624
+AGID00122	1005	2195	Set163	Mnk1	-0.04378072
+AGID00331	1899	sc-377312	Set163	MR1	-0.1030647
+AGID00273	1589	ab103319	Set163	MRAP	-0.0406295
+AGID00530	440	4847	Old	MRE11	0.071596
+AGID00390	905	2850	Old	MSH2	0.27224
+AGID00138	1063	22030002	Old	MSH6	-0.38994
+AGID00299	1675	ab76148	Set163	MSI2	0.4005155
+AGID00232	1344	ab14705	Set163	MTCO1	-0.5406512
+AGID00046	444	2983	Old	MTOR	-0.078565
+AGID00047	446	2971	Old	MTOR_pS2448	0.041801
+AGID00204	1247	H00009788-M01A	Set163	MTSS1	-0.3168447
+AGID00401	1139	21370002	Old	MYH11	1.3186
+AGID00291	1647	3403	Old	MYOSINIIA	0.19812
+AGID00173	1160	5026	Old	MYOSINIIA_pS1943	0.26894
+AGID00318	1803	4282	Set163	Myt1	-0.1966198
+AGID00216	1274	5795-1/ab129189	Old	NAPSINA	NA
+AGID00418	452	4061	Old	NCADHERIN	-0.0067494
+AGID00156	1126	3217	Old	NDRG1_pT346	-0.33067
+AGID02133	2436	PA5-45913	Set163	NDUFB4	0.0907305
+AGID00134	1046	22710002	Old	NF2	-0.062575
+AGID00048	457	3033	Old	NFKBP65_pS536	-0.18515
+AGID02155	2461	3608	Old	NOTCH1	-0.21876
+AGID00340	1969	4147	Set163	Notch1-cleaved	-0.09981475
+AGID00087	767	sc-5593	Set163	Notch3	-0.1537495
+AGID00258	1420	3187	Set163	NQO1	0.008635313
+AGID00162	1136	sc-31	Old	NRAS	0.016167
+AGID00257	1419	12721	Old	NRF2	NA
+AGID00297	1669	2750	Set163	Oct-4	-0.1898745
+AGID00420	466	1712-1/ab40803	Old	P16INK4A	-0.61346
+AGID00384	470	sc-6246	Old	P21	-0.21937
+AGID00105	897	1591-1/ab32034	Old	P27	0.19878
+AGID00096	842	AF1555	Old	P27_pT157	-0.072404
+AGID00099	878	ab64949	Old	P27_pT198	0.018685
+AGID00181	1175	9228	Set163	p38-a	-0.09825061
+AGID00098	479	9211	Old	P38_pT180Y182	0.5258
+AGID00049	478	9212	Old	P38MAPK	0.15171
+AGID00151	1119	4695	Set163	p44-42-MAPK	0.2126255
+AGID00050	481	9282	Old	P53	-0.24405
+AGID00490	1187	610833	Old	P62LCKLIGAND	-0.11954
+AGID00545	1415	ab53039	Old	P63	NA
+AGID00052	494	9205	Old	P70S6K_pT389	-0.17274
+AGID00051	493	1494-1/ab32529	Old	P70S6K1	-0.0032283
+AGID00085	759	9347	Old	P90RSK	0.20493
+AGID00531	770	9344	Old	P90RSK_pT359S363	0.32285
+AGID00182	1178	9346	Set163	p90RSK_pT573	-0.2191096
+AGID00053	499	612024	Old	PAI1	0.76896
+AGID00224	1322	HPA035895	Set163	PAICS	0.2707405
+AGID00323	1811	2602	Set163	PAK1	0.5322501
+AGID02199	2517	PA5-69540	Set163	PAK4	-0.1574046
+AGID00245	1370	4336-BPC-100	Set163	PAR	0.73053
+AGID00374	2209	66564	Set163	PARG	-0.1416798
+AGID00370	1372	sc-7150	Old	PARP1	0.066977
+AGID00468	501	9546	Old	PARPCLEAVED	-0.077805
+AGID00274	1591	ab53715	Set163	Patched	-0.09827954
+AGID00513	2486	60433	Set163	PAX6	-0.0587696
+AGID00441	1621	9857	Set163	PAX8	0.3261541
+AGID00054	504	2542	Old	PAXILLIN	-0.29338
+AGID00055	509	2130	Old	PCADHERIN	-0.12808
+AGID00248	511	ab29	Old	PCNA	-0.13413
+AGID00413	2095	43248	Old	PDCD1	NA
+AGID00094	816	600-401-965	Old	PDCD4	0.061269
+AGID00385	1225	3169	Set163	PDGFRB	0.3774655
+AGID00210	1258	ab110332	Set163	PDH	-0.03002566
+AGID00324	1817	3205	Set163	PDHA1	0.1853948
+AGID00280	1622	3820	Set163	PDHK1	0.001160493
+AGID00056	515	3062	Old	PDK1	0.13137
+AGID00057	516	3061	Old	PDK1_pS241	0.078143
+AGID00300	1234	sc-19090	Old	PDL1	-0.2966
+AGID00124	1017	2780	Old	PEA15	-0.19457
+AGID00125	1018	44-836G	Old	PEA15_pS116	-0.38108
+AGID00440	2429	3192	Set163	PERK	0.2211799
+AGID02207	2569	ab192876	Set163	PGM1	0.03977985
+AGID00281	1623	13428	Set163	PHGDH	0.06218988
+AGID00425	2399	22789-1-AP	Set163	PHLPP	-0.1537095
+AGID00226	1330	sc-376412	Set163	PI3K-p110-b	-0.06464951
+AGID00093	808	4255	Old	PI3KP110ALPHA	0.065903
+AGID00058	523	06-195	Old	PI3KP85	0.16271
+AGID00296	1667	5675	Set163	PKA-a	-0.4287646
+AGID00259	1426	9375	Set163	PKC-a-b-II_pT638_T641	-0.4405395
+AGID00172	529	05-154	Old	PKCALPHA	-0.85878
+AGID00460	530	06-822	Old	PKCALPHA_pS657	-0.79061
+AGID00114	932	07-875	Old	PKCDELTA_pS664	-0.073359
+AGID00163	1137	9371	Old	PKCPANBETAII_pS660	-0.48026
+AGID00126	1025	4053	Old	PKM2	NA
+AGID00512	2489	5690	Set163	PLC-gamma1	-0.4361603
+AGID02138	2441	GTX133463	Set163	PLC-gamma2_pY759	-0.1577147
+AGID00084	754	4513	Set163	PLK1	0.5069404
+AGID00203	1246	22510002	Set163	PMS2	0.6394805
+AGID00207	1254	ab14734	Set163	Porin	-0.3598595
+AGID00381	549	1483-1/ab32085	Old	PR	0.3127
+AGID00081	738	AHO1031	Set163	PRAS40	-0.0654695
+AGID00082	739	44-1100G	Old	PRAS40_pT246	-0.46456
+AGID00424	2398	OAAF05458	Set163	PRC1_pT481	0.1209105
+AGID00492	1205	HPA007730	Old	PRDX1	-0.093802
+AGID00190	1204	ab102739	Old	PREX1	0.99484
+AGID00061	566	9552	Old	PTEN	0.40716
+AGID00364	2154	ab76942	Set163	PTPN12	0.2513003
+AGID00218	1290	4976	Set163	Puma	0.4710455
+AGID00200	1242	SAB2900066	Old	PYGB	NA
+AGID00535	1494	ab61013	Old	PYGL	NA
+AGID00202	1245	H00005837-M10	Old	PYGM	NA
+AGID00275	1607	3291	Set163	Pyk2_pY402	-0.3402351
+AGID00145	1083	3539	Old	RAB11	0.22701
+AGID00169	1150	4314	Old	RAB25	0.80346
+AGID00342	1979	24555	Set163	Rad23A	0.1785454
+AGID00261	987	05-525	Old	RAD50	0.12633
+AGID00360	579	NA71	Old	RAD51	-0.072737
+AGID00158	1128	2280	Old	RAPTOR	-0.25062
+AGID00059	552	9309	Old	RB	-0.12365
+AGID00060	557	9308	Old	RB_pS807S811	0.24368
+AGID00164	1138	21390002	Old	RBM15	-0.71679
+AGID00547	735	3221	Old	RET_pY905	NA
+AGID00097	847	MAB3426	Set163	Rheb	-0.03574959
+AGID00159	1129	2114	Old	RICTOR	0.24403
+AGID00160	1130	3806	Old	RICTOR_pT1135	0.11728
+AGID00282	1624	4926	Set163	RIP	0.1587655
+AGID00283	1625	13526	Set163	RIP3	0.01039975
+AGID00416	1368	2208	Set163	RPA32	0.4094055
+AGID00246	1375	A300-245A	Set163	RPA32_pS4_S8	-0.2392706
+AGID00341	1978	3388	Set163	RRM1	0.03194528
+AGID00344	1981	PA5-27856	Set163	RRM2	0.1958538
+AGID00554	2425	8408	Set163	RSK1	0.3859526
+AGID00353	2031	13018	Set163	S100A4	-0.2331845
+AGID00330	1874	2317	Old	S6	0.092216
+AGID00062	600	2211	Old	S6_pS235S236	-0.54621
+AGID00063	601	2215	Old	S6_pS240S244	-0.41558
+AGID00157	1127	sc-58420	Old	SCD1	0.043135
+AGID00230	1339	11998	Set163	SDHA	-0.3238095
+AGID00294	1039	ab69836	Old	SETD2	-0.11415
+AGID00161	1131	32-4500	Old	SF2	-0.11075
+AGID02179	2495	3534	Set163	SFRP1	-0.1342455
+AGID00431	2411	12103	Set163	SGK1	0.1528298
+AGID00430	2409	8156	Set163	SGK3	-0.2728245
+AGID02168	2476	bs-3413R	Old	SHC_pY317	0.2543
+AGID00376	2241	3397	Set163	SHP2	0.1706202
+AGID00183	1180	3751	Old	SHP2_pY542	0.1301
+AGID02208	2570	ab8120	Set163	SIRP-alpha	-0.3003252
+AGID00222	1133	sc-99002	Old	SLC1A5	0.29119
+AGID00255	1411	sc-136891	Set163	Slfn11	0.09564041
+AGID00064	610	2954	Old	SMAC	-0.40647
+AGID00113	922	1649-1/ab33902	Old	SMAD1	0.24448
+AGID00091	796	1735-1/ab40854	Old	SMAD3	-0.15243
+AGID02160	2467	46535	Old	SMAD4	-0.016517
+AGID00065	616	3895	Old	SNAIL	-0.152
+AGID00325	1818	4266	Set163	SOD1	-0.256281
+AGID00380	1328	13141	Set163	SOD2	-0.01297473
+AGID00298	1670	2748	Set163	Sox2	-0.09190971
+AGID00066	621	05-184	Old	SRC	0.21176
+AGID02157	2463	6943	Old	SRC_pY416	-0.57161
+AGID00068	626	2105	Old	SRC_pY527	-0.051777
+AGID00185	1197	4904	Set163	Stat3	0.4972873
+AGID00388	637	9131	Old	STAT3_pY705	0.12811
+AGID00069	638	1289-1/ab32043	Old	STAT5ALPHA	-0.23484
+AGID00077	718	1972-1/ab52630	Old	STATHMIN	0.076821
+AGID00357	2099	13647	Set163	STING	-0.1921245
+AGID00128	1033	sc-1240	Old	SYK	-0.50322
+AGID00070	646	05-348	Set163	Tau	-0.2243545
+AGID00327	777	2149	Old	TAZ	-0.095463
+AGID00228	1333	7495	Set163	TFAM	0.1021142
+AGID00165	1140	22500002	Old	TFRC	-0.97898
+AGID00149	1107	S1711/ab137573	Old	TIGAR	-0.15228
+AGID00109	908	MS-224-P1	Old	TRANSGLUTAMINASE	-0.70379
+AGID00406	2370	612344	Set163	TRAP1	-0.1490495
+AGID00559	2537	PA5-34561	Set163	TRIM24	-0.2550368
+AGID00306	1756	ab167154	Set163	TRIM25	0.01396478
+AGID00426	2400	PA5-52193	Set163	TRIP13	0.4369955
+AGID00155	1125	4906	Old	TSC1	-0.3567
+AGID00144	1081	2044-1/ab76013	Old	TTF1	NA
+AGID00071	670	1613-1/ab32554	Old	TUBERIN	0.0067272
+AGID02194	2511	ab109403	Old	TUBERIN_pT1462	-0.27867
+AGID00417	1842	ab173300	Set163	TUFM	-0.03330953
+AGID00238	1353	sc-81417	Set163	Twist	-0.1514495
+AGID00436	1080	5585	Set163	Tyro3	0.12675
+AGID00295	1662	5546	Set163	U-Histone-H2B	0.8199053
+AGID00214	1270	HPA005651	Set163	UBAC1	0.1614054
+AGID00351	2020	sc-136145	Set163	UBQLN4	0.3103005
+AGID00213	1267	sc-271268	Set163	UGT1A	-0.4121345
+AGID00284	1626	6888	Set163	ULK1_pS757	-0.3087774
+AGID00208	1256	MS304/ab14745	Set163	UQCRC2	-0.4022495
+AGID00313	1781	13115	Set163	UVRAG	0.01603049
+AGID00073	678	3112	Set163	VASP	0.6103301
+AGID00184	1181	2502	Set163	VAV1	-0.1656754
+AGID00074	688	2479	Old	VEGFR2	0.37828
+AGID00421	2394	68547	Set163	VHL	0.5729105
+AGID00231	1343	SAB4200080	Set163	Vinculin	0.5121901
+AGID00317	1802	4936	Set163	Wee1	0.8207743
+AGID00354	2058	4910	Set163	Wee1_pS642	0.4817802
+AGID00285	1627	12124	Set163	WIPI1	-0.5289995
+AGID00286	1628	8567	Set163	WIPI2	-0.0784045
+AGID02214	2576	ab195380	Set163	WTAP	0.4679098
+AGID00133	1044	sc-32136	Old	XBP1	0.041181
+AGID00076	699	2042	Set163	XIAP	0.15264
+AGID00241	1359	sc-56813	Set163	XPA	0.1297055
+AGID00349	1354	ab3299	Set163	XPF	0.08399787
+AGID02137	2440	PA5-29359	Old	XRCC1	0.38999
+AGID00088	780	sc-15407	Old	YAP	-0.01852
+AGID00089	782	4911	Old	YAP_pS127	-0.2584
+AGID00504	700	17250002	Old	YB1	-0.053858
+AGID00095	835	2900	Old	YB1_pS102	-0.48918
+AGID02217	2579	ab220163	Set163	YTHDF2	0.6653355
+AGID02210	2572	ab220161	Set163	YTHDF3	0.01937045
+AGID00326	1828	2705	Set163	ZAP-70	-0.003986663
+AGID00432	2244	sc-25388	Set163	ZEB1	0.2938088

data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/TCGA-E2-A15L-01Z-00-DX1.626032DC-D396-48E7-B888-DFEBCF7102FF.svs

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data/gdc_data_organized/37242f5a-25ae-4b1f-9ce6-09ce1dc92539/nationwidechildrens.org_clinical.TCGA-E2-A15L.xml

@@ -0,0 +1,244 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<brca:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/brca/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/brca/2.7/TCGA_BCR.BRCA_Clinical.xsd" schemaVersion="2.7" xmlns:brca="http://tcga.nci/bcr/xml/clinical/brca/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:brca_shared="http://tcga.nci/bcr/xml/clinical/brca/shared/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:brca_nte="http://tcga.nci/bcr/xml/clinical/brca/shared/new_tumor_event/2.7/1.0" xmlns:nte="http://tcga.nci/bcr/xml/clinical/shared/new_tumor_event/2.7" xmlns:follow_up_v2.1="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/2.1" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">26625FDC-01EF-4230-AEC5-CA069754E828</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">93.87.0</admin:batch_number>
+        <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+        <admin:patient_withdrawal>
+            <admin:withdrawn>false</admin:withdrawn>
+        </admin:patient_withdrawal>
+        <admin:program xsi:nil="true" xsd_ver="2.7"/>
+        <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
+    </admin:admin>
+    <brca:patient>
+        <admin:additional_studies/>
+        <clin_shared:tumor_tissue_site preferred_name="submitted_tumor_site" display_order="9999" cde="3427536" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834630">Breast</clin_shared:tumor_tissue_site>
+        <clin_shared:tumor_tissue_site_other preferred_name="site_of_primary_tumor_other" display_order="999" cde="2584114" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
+        <shared:other_dx preferred_name="history_other_malignancy" display_order="14" cde="3382736" cde_ver="2.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834620">No</shared:other_dx>
+        <shared:gender preferred_name="gender" display_order="10" cde="2200604" cde_ver="3.000" xsd_ver="1.8" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834616">FEMALE</shared:gender>
+        <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834622">Alive</clin_shared:vital_status>
+        <clin_shared:days_to_birth precision="day" xsd_ver="1.12" tier="1" cde="3008233" owner="TSS" procurement_status="Completed" preferred_name="birth_days_to" display_order="9" cde_ver="1.000">-23845</clin_shared:days_to_birth>
+        <clin_shared:days_to_last_known_alive precision="day" xsd_ver="2.1" tier="2" cde="" owner="TSS" procurement_status="Not Available" preferred_name="" display_order="9999" cde_ver=""/>
+        <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+        <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">331</clin_shared:days_to_last_followup>
+        <clin_shared:race_list>
+            <clin_shared:race preferred_name="race" display_order="12" cde="2192199" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834618">BLACK OR AFRICAN AMERICAN</clin_shared:race>
+        </clin_shared:race_list>
+        <shared:bcr_patient_barcode preferred_name="" display_order="9999" cde="2003301" cde_ver="" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false">TCGA-E2-A15L</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">E2</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A15L</shared:patient_id>
+        <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">37242f5a-25ae-4b1f-9ce6-09ce1dc92539</shared:bcr_patient_uuid>
+        <shared:history_of_neoadjuvant_treatment preferred_name="history_neoadjuvant_treatment" display_order="15" cde="3382737" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834621">No</shared:history_of_neoadjuvant_treatment>
+        <clin_shared:informed_consent_verified preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.4" tier="1" owner="TSS" procurement_status="Completed" restricted="false">YES</clin_shared:informed_consent_verified>
+        <clin_shared:icd_o_3_site preferred_name="" display_order="9999" cde="3226281" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_o_3_site>
+        <clin_shared:icd_o_3_histology preferred_name="" display_order="9999" cde="3226275" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">8520/3</clin_shared:icd_o_3_histology>
+        <clin_shared:icd_10 preferred_name="" display_order="9999" cde="3226287" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">C50.9</clin_shared:icd_10>
+        <clin_shared:days_to_initial_pathologic_diagnosis precision="day" xsd_ver="1.12" tier="1" cde="3131740" owner="TSS" procurement_status="Completed" preferred_name="initial_pathologic_dx_days_to" display_order="9999" cde_ver="1.000">0</clin_shared:days_to_initial_pathologic_diagnosis>
+        <clin_shared:age_at_initial_pathologic_diagnosis precision="day" xsd_ver="1.12" tier="1" cde="2006657" owner="TSS" procurement_status="Completed">65</clin_shared:age_at_initial_pathologic_diagnosis>
+        <clin_shared:year_of_initial_pathologic_diagnosis preferred_name="initial_pathologic_dx_year" display_order="34" cde="2896960" cde_ver="1.000" xsd_ver="1.12" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834636">2010</clin_shared:year_of_initial_pathologic_diagnosis>
+        <clin_shared:ethnicity preferred_name="ethnicity" display_order="13" cde="2192217" cde_ver="2.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834619">NOT HISPANIC OR LATINO</clin_shared:ethnicity>
+        <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834629">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+        <clin_shared:primary_lymph_node_presentation_assessment preferred_name="lymph_nodes_examined" display_order="47" cde="2200396" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834648">YES</clin_shared:primary_lymph_node_presentation_assessment>
+        <clin_shared:lymph_node_examined_count preferred_name="lymph_nodes_examined_count" display_order="48" cde="3" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834649">3</clin_shared:lymph_node_examined_count>
+        <brca_shared:er_detection_method_text preferred_name="er_positivity_method" display_order="63" cde="69" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834664">Allred score 5+3 = 8</brca_shared:er_detection_method_text>
+        <brca_shared:pgr_detection_method_text preferred_name="pr_positivity_define_method" display_order="69" cde="785" cde_ver="2.310" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834670">Allred score 5+3 = 8</brca_shared:pgr_detection_method_text>
+        <brca:anatomic_neoplasm_subdivisions>
+            <clin_shared:anatomic_neoplasm_subdivision preferred_name="anatomic_organ_subdivision" display_order="9999" cde="3108203" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834631">Right</clin_shared:anatomic_neoplasm_subdivision>
+        </brca:anatomic_neoplasm_subdivisions>
+        <brca_shared:her2_neu_chromosone_17_signal_ratio_value preferred_name="her2_cent17_ratio" display_order="79" cde="2497552" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834680">0.9</brca_shared:her2_neu_chromosone_17_signal_ratio_value>
+        <brca:axillary_lymph_node_stage_method_type preferred_name="axillary_staging_method" display_order="44" cde="2516112" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834645">Sentinel node biopsy alone</brca:axillary_lymph_node_stage_method_type>
+        <brca:axillary_lymph_node_stage_other_method_descriptive_text preferred_name="axillary_staging_method_other" display_order="45" cde="3124496" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834646"/>
+        <brca:breast_carcinoma_surgical_procedure_name preferred_name="surgical_procedure_first" display_order="38" cde="2739580" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834639">Simple Mastectomy</brca:breast_carcinoma_surgical_procedure_name>
+        <brca:breast_neoplasm_other_surgical_procedure_descriptive_text preferred_name="surgery_for_positive_margins_other" display_order="42" cde="3124493" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="834643" xsi:nil="true"/>
+        <brca:breast_carcinoma_primary_surgical_procedure_name preferred_name="surgery_for_positive_margins" display_order="41" cde="1218" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834642"/>
+        <brca:surgical_procedure_purpose_other_text preferred_name="first_surgical_procedure_other" display_order="39" cde="3020338" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834640"/>
+        <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834632">Infiltrating Lobular Carcinoma</shared:histological_type>
+        <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="834633" xsi:nil="true"/>
+        <clin_shared:menopause_status preferred_name="menopause_status" display_order="11" cde="2957270" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834617">Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)</clin_shared:menopause_status>
+        <brca_shared:breast_carcinoma_progesterone_receptor_status preferred_name="pr_status_by_ihc" display_order="64" cde="2957357" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834665">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
+        <brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator preferred_name="micromet_detection_by_ihc" display_order="46" cde="3086152" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834647">NO</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
+        <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834661"/>
+        <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834662"/>
+        <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834673">2+</brca_shared:her2_immunohistochemistry_level_result>
+        <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834644"/>
+        <clin_shared:margin_status preferred_name="margin_status" display_order="40" cde="3114007" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834641">Negative</clin_shared:margin_status>
+        <clin_shared:initial_pathologic_diagnosis_method preferred_name="method_initial_path_dx" display_order="36" cde="2757941" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834637">Tumor resection</clin_shared:initial_pathologic_diagnosis_method>
+        <clin_shared:init_pathology_dx_method_other preferred_name="method_initial_path_dx_other" display_order="37" cde="2757948" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="834638" xsi:nil="true"/>
+        <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834676">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
+        <brca_shared:breast_carcinoma_estrogen_receptor_status preferred_name="er_status_by_ihc" display_order="58" cde="2957359" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834659">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
+        <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834671">Equivocal</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
+        <clin_shared:number_of_lymphnodes_positive_by_ihc preferred_name="lymph_nodes_examined_ihc_count" display_order="50" cde="3086383" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834651"/>
+        <clin_shared:number_of_lymphnodes_positive_by_he preferred_name="lymph_nodes_examined_he_count" display_order="49" cde="3086388" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834650">0</clin_shared:number_of_lymphnodes_positive_by_he>
+        <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834669">Allred score = 8</brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text>
+        <brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text preferred_name="er_positivity_scale_other" display_order="62" cde="3086851" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834663">Allred score = 8</brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text>
+        <brca_shared:her2_erbb_pos_finding_cell_percent_category preferred_name="her2_ihc_percent_positive" display_order="71" cde="3086980" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834672">30-39%</brca_shared:her2_erbb_pos_finding_cell_percent_category>
+        <brca_shared:pos_finding_her2_erbb2_other_measurement_scale_text preferred_name="her2_positivity_scale_other" display_order="73" cde="3087479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834674"/>
+        <brca_shared:her2_erbb_method_calculation_method_text preferred_name="her2_positivity_method_text" display_order="74" cde="3087487" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834675"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count preferred_name="her2_and_cent17_cells_count" display_order="78" cde="3087902" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834679"/>
+        <brca_shared:her2_and_centromere_17_positive_finding_other_measurement_scale_text preferred_name="her2_and_cent17_scale_other" display_order="80" cde="3087923" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834681"/>
+        <brca_shared:her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="her2_fish_method" display_order="81" cde="3087929" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834682"/>
+        <clin_shared:tissue_prospective_collection_indicator preferred_name="prospective_collection" display_order="4" cde="3088492" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834611">NO</clin_shared:tissue_prospective_collection_indicator>
+        <clin_shared:tissue_retrospective_collection_indicator preferred_name="retrospective_collection" display_order="5" cde="3088528" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834612">YES</clin_shared:tissue_retrospective_collection_indicator>
+        <brca_shared:fluorescence_in_situ_hybridization_diagnostic_procedure_chromosome_17_signal_result_range preferred_name="cent17_copy_number" display_order="77" cde="3104295" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834678"/>
+        <brca:first_nonlymph_node_metastasis_anatomic_sites>
+            <clin_shared:metastatic_site_at_diagnosis preferred_name="metastasis_site" display_order="56" cde="3124499" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834657"/>
+            <clin_shared:metastatic_site_at_diagnosis_other preferred_name="metastasis_site_other" display_order="57" cde="3124503" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834658"/>
+        </brca:first_nonlymph_node_metastasis_anatomic_sites>
+        <brca_shared:er_level_cell_percentage_category preferred_name="er_status_ihc_Percent_Positive" display_order="59" cde="3128341" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834660"/>
+        <brca_shared:progesterone_receptor_level_cell_percent_category preferred_name="pr_status_ihc_percent_positive" display_order="65" cde="3128342" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834666"/>
+        <brca:distant_metastasis_present_ind2 preferred_name="metastatic_tumor_indicator" display_order="999" cde="2194698" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834683">NO</brca:distant_metastasis_present_ind2>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834684"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834685"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834687"/>
+        <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834688"/>
+        <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834689"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834690"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834696"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834691"/>
+        <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834693"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834694"/>
+        <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834695"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834697"/>
+        <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834698"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834699"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834700"/>
+        <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834701"/>
+        <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834703"/>
+        <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834704"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834705"/>
+        <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834706"/>
+        <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834707"/>
+        <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834702"/>
+        <brca_shared:her2_neu_breast_carcinoma_copy_analysis_input_total_number preferred_name="her2_copy_number" display_order="76" cde="3133738" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834677"/>
+        <brca:breast_carcinoma_immunohistochemistry_progesterone_receptor_pos_finding_scale preferred_name="pr_positivity_scale_used" display_order="66" cde="3203083" cde_ver="1.000" xsd_ver="2.4.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834667"/>
+        <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="834668"/>
+        <shared_stage:stage_event system="AJCC">
+            <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834652">7th</shared_stage:system_version>
+            <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834656">Stage IIA</shared_stage:pathologic_stage>
+            <shared_stage:tnm_categories>
+                <shared_stage:clinical_categories>
+                    <shared_stage:clinical_T preferred_name="ajcc_tumor_clinical_ct" display_order="9999" cde="3440328" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <shared_stage:clinical_N preferred_name="ajcc_nodes_clinical_cn" display_order="9999" cde="3440330" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                    <shared_stage:clinical_M preferred_name="ajcc_metastasis_clinical_cm" display_order="9999" cde="3440331" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                </shared_stage:clinical_categories>
+                <shared_stage:pathologic_categories>
+                    <shared_stage:pathologic_T preferred_name="ajcc_tumor_pathologic_pt" display_order="52" cde="3045435" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834653">T2</shared_stage:pathologic_T>
+                    <shared_stage:pathologic_N preferred_name="ajcc_nodes_pathologic_pn" display_order="53" cde="3203106" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834654">N0</shared_stage:pathologic_N>
+                    <shared_stage:pathologic_M preferred_name="ajcc_metastasis_pathologic_pm" display_order="54" cde="3045439" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834655">M0</shared_stage:pathologic_M>
+                </shared_stage:pathologic_categories>
+            </shared_stage:tnm_categories>
+            <shared_stage:psa>
+                <shared_stage:psa_value preferred_name="psa_most_recent_results" display_order="9999" cde="3351903" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:days_to_psa precision="day" xsd_ver="2.6" tier="2" cde="3414608" owner="TSS" procurement_status="Not Applicable" preferred_name="days_to_psa_most_recent" display_order="9999" cde_ver="1.000"/>
+            </shared_stage:psa>
+            <shared_stage:gleason_grading>
+                <shared_stage:gleason_score preferred_name="gleason_score" display_order="9999" cde="2534619" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:primary_pattern preferred_name="gleason_pattern_primary" display_order="9999" cde="2534617" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:secondary_pattern preferred_name="gleason_pattern_secondary" display_order="9999" cde="2534618" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:tertiary_pattern preferred_name="gleason_pattern_tertiary" display_order="9999" cde="2783875" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:gleason_grading>
+            <shared_stage:ann_arbor>
+                <shared_stage:b_symptoms preferred_name="b_symptoms_present_indicator" display_order="9999" cde="2902402" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                <shared_stage:extranodal_involvement preferred_name="extranodal_lymphomatous_involvement" display_order="9999" cde="3364582" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            </shared_stage:ann_arbor>
+            <shared_stage:serum_markers preferred_name="" display_order="9999" cde="3901772" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:igcccg_stage preferred_name="" display_order="9999" cde="3901822" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:masaoka_stage preferred_name="" display_order="9999" cde="3952848" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+        </shared_stage:stage_event>
+        <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        <brca_nte:new_tumor_events>
+            <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+        </brca_nte:new_tumor_events>
+        <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834609">13</clin_shared:day_of_form_completion>
+        <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834608">4</clin_shared:month_of_form_completion>
+        <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="834610">2011</clin_shared:year_of_form_completion>
+        <brca:follow_ups>
+            <follow_up_v2.1:follow_up version="2.1" sequence="1">
+                <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-E2-A15L-F18885</clin_shared:bcr_followup_barcode>
+                <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">CA37A855-FA95-4FBE-A554-B8424DF1544F</clin_shared:bcr_followup_uuid>
+                <clin_shared:followup_case_report_form_submission_reason preferred_name="followup_reason" display_order="999" cde="3233305" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427873">Scheduled Follow-up Submission</clin_shared:followup_case_report_form_submission_reason>
+                <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427879">NO</clin_shared:radiation_therapy>
+                <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427880">YES</clin_shared:postoperative_rx_tx>
+                <clin_shared:vital_status preferred_name="vital_status" display_order="17" cde="5" cde_ver="5.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427881">Alive</clin_shared:vital_status>
+                <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">626</clin_shared:days_to_last_followup>
+                <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
+                <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427888">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
+                <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427889">NO</nte:new_tumor_event_after_initial_treatment>
+                <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Applicable" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
+                <nte:new_neoplasm_event_type preferred_name="new_tumor_event_type" display_order="83" cde="3119721" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427893"/>
+                <nte:new_neoplasm_event_occurrence_anatomic_site preferred_name="new_tumor_event_site" display_order="84" cde="3108271" cde_ver="2.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427894"/>
+                <nte:new_neoplasm_occurrence_anatomic_site_text preferred_name="new_tumor_event_site_other" display_order="85" cde="3128033" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427895"/>
+                <nte:additional_surgery_locoregional_procedure preferred_name="new_tumor_event_surgery" display_order="999" cde="3008755" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427896"/>
+                <nte:days_to_additional_surgery_metastatic_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408682" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_met" display_order="9999" cde_ver="1.000"/>
+                <nte:additional_radiation_therapy preferred_name="new_tumor_event_radiation_tx" display_order="95" cde="3427615" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427900"/>
+                <nte:additional_pharmaceutical_therapy preferred_name="new_tumor_event_pharmaceutical_tx" display_order="96" cde="3427616" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427901"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427902"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427903"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_positive_finding_scale_type preferred_name="nte_er_positivity_scale_used" display_order="99" cde="3203082" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427904"/>
+                <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427905"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427906"/>
+                <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427907"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427908"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427909"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_progesterone_receptor_positive_finding_scale_type preferred_name="nte_pr_positivity_scale_used" display_order="105" cde="3203085" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427910"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427911"/>
+                <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427912"/>
+                <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427913"/>
+                <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427914"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427915"/>
+                <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427916"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427917"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427918"/>
+                <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427919"/>
+                <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427920"/>
+                <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427921"/>
+                <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427922"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427923"/>
+                <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427924"/>
+                <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427925"/>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427871">15</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427870">11</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427872">2011</clin_shared:year_of_form_completion>
+            </follow_up_v2.1:follow_up>
+        </brca:follow_ups>
+        <rx:drugs>
+            <rx:drug>
+                <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427931">1</rx:regimen_number>
+                <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-E2-A15L-D18887</rx:bcr_drug_barcode>
+                <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">50C9B52E-A733-4A39-89C6-A845EDDC1CC5</rx:bcr_drug_uuid>
+                <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427940">1</rx:total_dose>
+                <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427941">mg/day</rx:total_dose_units>
+                <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427938">1</rx:prescribed_dose>
+                <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427939">mg/day</rx:prescribed_dose_units>
+                <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427937"/>
+                <rx:days_to_drug_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">45</rx:days_to_drug_therapy_start>
+                <rx:days_to_drug_therapy_end precision="day" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Not Available" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000"/>
+                <rx:therapy_types>
+                    <rx:therapy_type preferred_name="pharmaceutical_therapy_type" display_order="7" cde="2793530" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427934">Hormone Therapy</rx:therapy_type>
+                    <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1427935"/>
+                </rx:therapy_types>
+                <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427936">Arimidex</rx:drug_name>
+                <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427932">ADJUVANT</clin_shared:regimen_indication>
+                <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="1427933"/>
+                <rx:route_of_administrations>
+                    <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427942">PO</rx:route_of_administration>
+                </rx:route_of_administrations>
+                <rx:therapy_ongoing preferred_name="pharmaceutical_tx_ongoing_indicator" display_order="12" cde="3103479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427946">YES</rx:therapy_ongoing>
+                <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427929">15</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427928">11</clin_shared:month_of_form_completion>
+                <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1427930">2011</clin_shared:year_of_form_completion>
+            </rx:drug>
+        </rx:drugs>
+        <rad:radiations/>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/57ffb618-af4e-40fc-96aa-f88b7759fb62.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	39580	19787.358388	N
+hsa-let-7a-2	39759	19876.846441	N
+hsa-let-7a-3	39739	19866.847776	N
+hsa-let-7b	75764	37876.943428	N
+hsa-let-7c	23505	11750.931251	N
+hsa-let-7d	927	463.438131	N
+hsa-let-7e	2672	1335.821668	N
+hsa-let-7f-1	8954	4476.402400	N
+hsa-let-7f-2	9353	4675.875771	N
+hsa-let-7g	1134	566.924316	N
+hsa-let-7i	1465	732.402224	N
+hsa-mir-1-1	7	3.499533	N
+hsa-mir-1-2	7	3.499533	N
+hsa-mir-100	35246	17620.647644	Y
+hsa-mir-101-1	6975	3487.034481	N
+hsa-mir-101-2	7045	3522.029809	N
+hsa-mir-103a-1	14280	7139.046937	Y
+hsa-mir-103a-2	14267	7132.547805	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	1	0.499933	N
+hsa-mir-105-2	0	0.000000	N
+hsa-mir-106a	12	5.999199	Y
+hsa-mir-106b	600	299.959955	N
+hsa-mir-107	59	29.496062	Y
+hsa-mir-10a	83747	41867.910634	N
+hsa-mir-10b	603687	301803.209272	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	10	4.999333	N
+hsa-mir-1181	0	0.000000	N
+hsa-mir-1182	0	0.000000	N
+hsa-mir-1183	0	0.000000	N
+hsa-mir-1184-1	0	0.000000	N
+hsa-mir-1184-2	0	0.000000	N
+hsa-mir-1184-3	0	0.000000	N
+hsa-mir-1185-1	0	0.000000	N
+hsa-mir-1185-2	0	0.000000	N
+hsa-mir-1193	0	0.000000	N
+hsa-mir-1197	0	0.000000	N
+hsa-mir-1199	0	0.000000	N
+hsa-mir-1200	0	0.000000	N
+hsa-mir-1202	0	0.000000	N
+hsa-mir-1203	0	0.000000	N
+hsa-mir-1204	0	0.000000	N
+hsa-mir-1205	0	0.000000	N
+hsa-mir-1206	0	0.000000	N
+hsa-mir-1207	0	0.000000	N
+hsa-mir-1208	0	0.000000	N
+hsa-mir-122	0	0.000000	N
+hsa-mir-1224	0	0.000000	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	1	0.499933	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	0	0.000000	N
+hsa-mir-1229	0	0.000000	N
+hsa-mir-1231	0	0.000000	N
+hsa-mir-1233-1	0	0.000000	N
+hsa-mir-1233-2	0	0.000000	N
+hsa-mir-1234	0	0.000000	N
+hsa-mir-1236	0	0.000000	N
+hsa-mir-1237	0	0.000000	N
+hsa-mir-1238	0	0.000000	N
+hsa-mir-124-1	0	0.000000	N
+hsa-mir-124-2	0	0.000000	N
+hsa-mir-124-3	0	0.000000	N
+hsa-mir-1243	0	0.000000	N
+hsa-mir-1244-1	0	0.000000	N
+hsa-mir-1244-2	0	0.000000	N
+hsa-mir-1244-3	0	0.000000	N
+hsa-mir-1244-4	0	0.000000	N
+hsa-mir-1245a	6	2.999600	N
+hsa-mir-1245b	0	0.000000	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	207	103.486185	N
+hsa-mir-1248	1	0.499933	N
+hsa-mir-1249	15	7.498999	N
+hsa-mir-1250	0	0.000000	N
+hsa-mir-1251	0	0.000000	N
+hsa-mir-1252	0	0.000000	N
+hsa-mir-1253	0	0.000000	N
+hsa-mir-1254-1	0	0.000000	N
+hsa-mir-1254-2	2	0.999867	N
+hsa-mir-1255a	0	0.000000	N
+hsa-mir-1255b-1	0	0.000000	N
+hsa-mir-1255b-2	0	0.000000	N
+hsa-mir-1256	0	0.000000	N
+hsa-mir-1257	0	0.000000	N
+hsa-mir-1258	8	3.999466	N
+hsa-mir-125a	4672	2335.688186	N
+hsa-mir-125b-1	4079	2039.227763	N
+hsa-mir-125b-2	4171	2085.221623	N
+hsa-mir-126	11891	5944.706382	N
+hsa-mir-1260a	0	0.000000	N
+hsa-mir-1260b	0	0.000000	N
+hsa-mir-1261	0	0.000000	N
+hsa-mir-1262	3	1.499800	N
+hsa-mir-1263	0	0.000000	N
+hsa-mir-1264	0	0.000000	N
+hsa-mir-1265	0	0.000000	N
+hsa-mir-1266	21	10.498598	N
+hsa-mir-1267	0	0.000000	N
+hsa-mir-1268a	0	0.000000	N
+hsa-mir-1268b	0	0.000000	N
+hsa-mir-1269a	0	0.000000	N
+hsa-mir-1269b	0	0.000000	N
+hsa-mir-127	1950	974.869855	N
+hsa-mir-1270	2	0.999867	N
+hsa-mir-1271	7	3.499533	N
+hsa-mir-1272	0	0.000000	N
+hsa-mir-1273a	0	0.000000	N
+hsa-mir-1273c	0	0.000000	N
+hsa-mir-1273d	0	0.000000	N
+hsa-mir-1273e	0	0.000000	N
+hsa-mir-1273f	0	0.000000	N
+hsa-mir-1273g	0	0.000000	N
+hsa-mir-1273h	0	0.000000	N
+hsa-mir-1275	3	1.499800	N
+hsa-mir-1276	0	0.000000	N
+hsa-mir-1277	1	0.499933	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	113	56.492458	N
+hsa-mir-128-2	57	28.496196	N
+hsa-mir-1281	0	0.000000	N
+hsa-mir-1282	0	0.000000	N
+hsa-mir-1283-1	0	0.000000	N
+hsa-mir-1283-2	0	0.000000	N
+hsa-mir-1284	0	0.000000	N
+hsa-mir-1285-1	0	0.000000	N
+hsa-mir-1285-2	0	0.000000	N
+hsa-mir-1286	0	0.000000	N
+hsa-mir-1287	65	32.495662	N
+hsa-mir-1288	0	0.000000	N
+hsa-mir-1289-1	0	0.000000	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	5	2.499666	N
+hsa-mir-129-2	10	4.999333	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	3	1.499800	N
+hsa-mir-1292	0	0.000000	N
+hsa-mir-1293	0	0.000000	N
+hsa-mir-1294	0	0.000000	N
+hsa-mir-1295a	15	7.498999	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	35	17.497664	N
+hsa-mir-1297	0	0.000000	N
+hsa-mir-1298	0	0.000000	N
+hsa-mir-1299	0	0.000000	N
+hsa-mir-1301	9	4.499399	N
+hsa-mir-1302-1	0	0.000000	N
+hsa-mir-1302-10	0	0.000000	N
+hsa-mir-1302-11	0	0.000000	N
+hsa-mir-1302-2	0	0.000000	N
+hsa-mir-1302-3	0	0.000000	N
+hsa-mir-1302-4	0	0.000000	N
+hsa-mir-1302-5	0	0.000000	N
+hsa-mir-1302-6	0	0.000000	N
+hsa-mir-1302-7	0	0.000000	N
+hsa-mir-1302-8	0	0.000000	N
+hsa-mir-1302-9	0	0.000000	N
+hsa-mir-1303	0	0.000000	N
+hsa-mir-1304	3	1.499800	N
+hsa-mir-1305	1	0.499933	N
+hsa-mir-1306	14	6.999066	N
+hsa-mir-1307	919	459.438665	N
+hsa-mir-130a	435	217.470968	N
+hsa-mir-130b	15	7.498999	N
+hsa-mir-132	137	68.490856	N
+hsa-mir-1321	0	0.000000	N
+hsa-mir-1322	0	0.000000	N
+hsa-mir-1323	1	0.499933	N
+hsa-mir-1324	0	0.000000	N
+hsa-mir-133a-1	5	2.499666	N
+hsa-mir-133a-2	4	1.999733	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	873	436.441735	N
+hsa-mir-1343	3	1.499800	N
+hsa-mir-135a-1	0	0.000000	N
+hsa-mir-135a-2	3	1.499800	N
+hsa-mir-135b	5	2.499666	N
+hsa-mir-136	39	19.497397	N
+hsa-mir-137	0	0.000000	N
+hsa-mir-138-1	0	0.000000	N
+hsa-mir-138-2	0	0.000000	N
+hsa-mir-139	948	473.936729	N
+hsa-mir-140	3454	1726.769476	N
+hsa-mir-141	793	396.447074	N
+hsa-mir-142	774	386.948342	N
+hsa-mir-143	173999	86987.887117	N
+hsa-mir-144	199	99.486719	N
+hsa-mir-145	19322	9659.710429	N
+hsa-mir-1468	27	13.498198	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	133	66.491123	N
+hsa-mir-146b	697	348.453481	N
+hsa-mir-1470	0	0.000000	N
+hsa-mir-1471	0	0.000000	N
+hsa-mir-147a	0	0.000000	N
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+hsa-mir-148a	54931	27461.833845	N
+hsa-mir-148b	163	81.489121	N
+hsa-mir-149	317	158.478843	N
+hsa-mir-150	2044	1021.863581	N
+hsa-mir-151a	3057	1528.295972	N
+hsa-mir-151b	5	2.499666	N
+hsa-mir-152	455	227.469633	N
+hsa-mir-153-1	1	0.499933	N
+hsa-mir-153-2	17	8.498865	N
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+hsa-mir-154	18	8.998799	N
+hsa-mir-155	189	94.487386	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	91	45.493927	N
+hsa-mir-15b	150	74.989989	N
+hsa-mir-16-1	216	107.985584	N
+hsa-mir-16-2	196	97.986919	N
+hsa-mir-17	771	385.448543	Y
+hsa-mir-181a-1	1000	499.933259	N
+hsa-mir-181a-2	2021	1010.365116	N
+hsa-mir-181b-1	121	60.491924	N
+hsa-mir-181b-2	135	67.490990	N
+hsa-mir-181c	125	62.491657	N
+hsa-mir-181d	29	14.498065	N
+hsa-mir-182	12636	6317.156660	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	3353	1676.276217	N
+hsa-mir-184	4	1.999733	N
+hsa-mir-185	50	24.996663	N
+hsa-mir-186	789	394.447341	N
+hsa-mir-187	7	3.499533	N
+hsa-mir-188	0	0.000000	N
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+hsa-mir-190a	6	2.999600	N
+hsa-mir-190b	4	1.999733	N
+hsa-mir-191	977	488.434794	N
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+hsa-mir-1911	0	0.000000	N
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+hsa-mir-1915	0	0.000000	N
+hsa-mir-192	336	167.977575	Y
+hsa-mir-193a	1444	721.903626	N
+hsa-mir-193b	170	84.988654	N
+hsa-mir-194-1	90	44.993993	N
+hsa-mir-194-2	105	52.492992	N
+hsa-mir-195	236	117.984249	N
+hsa-mir-196a-1	84	41.994394	N
+hsa-mir-196a-2	110	54.992658	N
+hsa-mir-196b	635	317.457619	N
+hsa-mir-197	837	418.444138	N
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+hsa-mir-199a-1	4795	2397.179976	Y
+hsa-mir-199a-2	7333	3666.010588	Y
+hsa-mir-199b	8885	4441.907005	Y
+hsa-mir-19a	10	4.999333	N
+hsa-mir-19b-1	100	49.993326	N
+hsa-mir-19b-2	97	48.493526	N
+hsa-mir-200a	490	244.967297	N
+hsa-mir-200b	530	264.964627	N
+hsa-mir-200c	13384	6691.106737	N
+hsa-mir-202	4	1.999733	N
+hsa-mir-203a	4274	2136.714749	N
+hsa-mir-203b	24	11.998398	N
+hsa-mir-204	103	51.493126	N
+hsa-mir-205	27881	13938.639192	N
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+hsa-mir-20a	324	161.978376	N
+hsa-mir-20b	19	9.498732	N
+hsa-mir-21	69829	34909.839536	N
+hsa-mir-210	189	94.487386	N
+hsa-mir-211	0	0.000000	N
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+hsa-mir-2113	0	0.000000	N
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+hsa-mir-2116	1	0.499933	N
+hsa-mir-2117	0	0.000000	N
+hsa-mir-212	6	2.999600	N
+hsa-mir-214	63	31.495795	N
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+hsa-mir-216a	0	0.000000	N
+hsa-mir-216b	0	0.000000	N
+hsa-mir-217	24	11.998398	N
+hsa-mir-218-1	80	39.994661	N
+hsa-mir-218-2	68	33.995462	N
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+hsa-mir-219a-2	0	0.000000	N
+hsa-mir-219b	0	0.000000	N
+hsa-mir-22	128716	64349.409354	N
+hsa-mir-221	270	134.981980	N
+hsa-mir-222	121	60.491924	N
+hsa-mir-223	429	214.471368	N
+hsa-mir-224	111	55.492592	N
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+hsa-mir-2277	0	0.000000	N
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+hsa-mir-2355	69	34.495395	N
+hsa-mir-2392	0	0.000000	N
+hsa-mir-23a	6551	3275.062779	Y
+hsa-mir-23b	1525	762.398220	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	1144	571.923648	N
+hsa-mir-24-2	1216	607.918843	N
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+hsa-mir-25	13754	6876.082043	N
+hsa-mir-2681	0	0.000000	N
+hsa-mir-2682	0	0.000000	N
+hsa-mir-26a-1	2048	1023.863314	N
+hsa-mir-26a-2	2167	1083.355372	N
+hsa-mir-26b	1362	680.909099	N
+hsa-mir-27a	1246	622.916841	Y
+hsa-mir-27b	963	481.435728	Y
+hsa-mir-28	12756	6377.148651	N
+hsa-mir-2861	0	0.000000	N
+hsa-mir-2909	0	0.000000	N
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+hsa-mir-297	0	0.000000	N
+hsa-mir-298	0	0.000000	N
+hsa-mir-299	5	2.499666	N
+hsa-mir-29a	14749	7373.515636	N
+hsa-mir-29b-1	313	156.479110	N
+hsa-mir-29b-2	418	208.972102	N
+hsa-mir-29c	2848	1423.809921	N
+hsa-mir-300	0	0.000000	N
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+hsa-mir-3064	0	0.000000	N
+hsa-mir-3065	22	10.998532	N
+hsa-mir-3074	8	3.999466	N
+hsa-mir-30a	155350	77664.631772	Y
+hsa-mir-30b	1100	549.926585	Y
+hsa-mir-30c-1	1223	611.418376	Y
+hsa-mir-30c-2	1525	762.398220	Y
+hsa-mir-30d	16482	8239.899973	N
+hsa-mir-30e	25941	12968.768669	Y
+hsa-mir-31	15	7.498999	N
+hsa-mir-3115	0	0.000000	N
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+hsa-mir-3130-2	8	3.999466	N
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+hsa-mir-3667	1	0.499933	N
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+hsa-mir-3690-2	0	0.000000	N
+hsa-mir-3691	1	0.499933	N
+hsa-mir-3692	0	0.000000	N
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+hsa-mir-3714	0	0.000000	N
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+hsa-mir-373	0	0.000000	N
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+hsa-mir-375	7475	3737.001110	N
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+hsa-mir-376a-2	0	0.000000	N
+hsa-mir-376b	0	0.000000	N
+hsa-mir-376c	10	4.999333	N
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+hsa-mir-378b	0	0.000000	N
+hsa-mir-378c	10	4.999333	N
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+hsa-mir-378d-2	1	0.499933	N
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+hsa-mir-378f	0	0.000000	N
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+hsa-mir-378j	0	0.000000	N
+hsa-mir-379	1739	869.383937	N
+hsa-mir-380	0	0.000000	N
+hsa-mir-381	106	52.992925	N
+hsa-mir-382	38	18.997464	N
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+hsa-mir-3907	0	0.000000	N
+hsa-mir-3908	0	0.000000	N
+hsa-mir-3909	0	0.000000	N
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+hsa-mir-484	126	62.991591	N
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+hsa-mir-486-1	349	174.476707	N
+hsa-mir-486-2	339	169.477375	N
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+hsa-mir-490	0	0.000000	N
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+hsa-mir-492	0	0.000000	N
+hsa-mir-493	8	3.999466	N
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+hsa-mir-495	20	9.998665	N
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+hsa-mir-497	120	59.991991	N
+hsa-mir-498	0	0.000000	N
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+hsa-mir-500b	8	3.999466	Y
+hsa-mir-501	74	36.995061	N
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+hsa-mir-514a-2	1	0.499933	N
+hsa-mir-514a-3	2	0.999867	N
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+hsa-mir-519e	0	0.000000	N
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+hsa-mir-527	0	0.000000	N
+hsa-mir-532	1344	671.910300	N
+hsa-mir-539	22	10.998532	N
+hsa-mir-541	1	0.499933	N
+hsa-mir-542	242	120.983849	N
+hsa-mir-543	6	2.999600	N
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+hsa-mir-549a	0	0.000000	N
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+hsa-mir-550a-2	3	1.499800	N
+hsa-mir-550a-3	1	0.499933	N
+hsa-mir-550b-1	0	0.000000	N
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+hsa-mir-5587	0	0.000000	N
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+hsa-mir-5688	0	0.000000	N
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+hsa-mir-6087	1	0.499933	N
+hsa-mir-6088	0	0.000000	N
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+hsa-mir-6133	0	0.000000	N
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+hsa-mir-615	16	7.998932	N
+hsa-mir-616	1	0.499933	N
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+hsa-mir-618	1	0.499933	N
+hsa-mir-619	0	0.000000	N
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+hsa-mir-624	0	0.000000	N
+hsa-mir-625	331	165.477909	N
+hsa-mir-626	0	0.000000	N
+hsa-mir-627	1	0.499933	N
+hsa-mir-628	8	3.999466	N
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+hsa-mir-631	0	0.000000	N
+hsa-mir-632	0	0.000000	N
+hsa-mir-633	0	0.000000	N
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+hsa-mir-635	0	0.000000	N
+hsa-mir-636	0	0.000000	N
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+hsa-mir-639	0	0.000000	N
+hsa-mir-640	0	0.000000	N
+hsa-mir-641	1	0.499933	N
+hsa-mir-642a	5	2.499666	N
+hsa-mir-642b	0	0.000000	N
+hsa-mir-643	1	0.499933	N
+hsa-mir-644a	0	0.000000	N
+hsa-mir-645	0	0.000000	N
+hsa-mir-646	0	0.000000	N
+hsa-mir-647	0	0.000000	N
+hsa-mir-648	0	0.000000	N
+hsa-mir-649	0	0.000000	N
+hsa-mir-6499	0	0.000000	N
+hsa-mir-650	0	0.000000	N
+hsa-mir-6500	0	0.000000	N
+hsa-mir-6501	0	0.000000	N
+hsa-mir-6502	0	0.000000	N
+hsa-mir-6503	0	0.000000	N
+hsa-mir-6504	0	0.000000	N
+hsa-mir-6505	0	0.000000	N
+hsa-mir-6506	0	0.000000	N
+hsa-mir-6507	1	0.499933	N
+hsa-mir-6508	0	0.000000	N
+hsa-mir-6509	0	0.000000	N
+hsa-mir-651	5	2.499666	N
+hsa-mir-6510	87	43.494194	N
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+hsa-mir-6511a-2	0	0.000000	N
+hsa-mir-6511a-3	0	0.000000	N
+hsa-mir-6511a-4	0	0.000000	N
+hsa-mir-6511b-1	10	4.999333	N
+hsa-mir-6511b-2	12	5.999199	N
+hsa-mir-6512	0	0.000000	N
+hsa-mir-6513	0	0.000000	N
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data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/847cc85a-7133-4693-b222-5b2f0aea3c7c.wxs.aliquot_ensemble_masked.maf.gz

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data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_C06_748044.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,74 @@
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data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/TCGA-BH-A0BZ-01A-03-TSC.18e04e86-9ccb-4773-bcf3-d7f0c54c6e2a.svs

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d99320ad660cde98e14639d550bb0af4ee89b7a373c33bcffebb14b4a1e0ebfe
+size 630701859

data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/TCGA-BH-A0BZ-01A-21-A13B-20_RPPA_data.tsv

@@ -0,0 +1,488 @@
+AGID	lab_id	catalog_number	set_id	peptide_target	protein_expression
+AGID00100	882	sc-628	Old	1433BETA	0.040166
+AGID00111	913	sc-23957	Old	1433EPSILON	0.1144
+AGID00101	883	sc-1019	Old	1433ZETA	0.33188
+AGID00001	2	9452	Old	4EBP1	-0.079629
+AGID00002	3	9456	Old	4EBP1_pS65	-0.35774
+AGID00003	6	9459	Old	4EBP1_pT37T46	-0.64666
+AGID00443	8	9455	Old	4EBP1_pT70	-0.13855
+AGID00120	985	4937	Old	53BP1	-0.54653
+AGID00004	13	3661	Old	ACC_pS79	0.16845
+AGID00005	14	1768-1/ab45174	Old	ACC1	0.095871
+AGID00408	2372	3658	Set163	AceCS1	0.1867945
+AGID00473	1182	5335	Old	ACETYLATUBULINLYS40	0.33539
+AGID00404	2367	9189	Set163	ACSL1	0.101475
+AGID02144	2450	PA5-27081	Old	ACVRL1	0.024062
+AGID00186	1198	ab88574	Old	ADAR1	0.70282
+AGID00146	1084	4691	Old	AKT	0.044764
+AGID00028	230	9271	Old	AKT_pS473	-0.87648
+AGID00170	1154	2965	Old	AKT_pT308	-0.93749
+AGID00316	1800	3063	Set163	Akt2	-0.08804995
+AGID00347	2009	8599	Set163	Akt2_pS474	-0.5892155
+AGID02215	2577	ab195377	Set163	ALKBH5	0.2188998
+AGID00498	924	CA1030	Old	ALPHACATENIN	NA
+AGID00287	1630	ABC80	Set163	Ambra1_pS52	0.00268921
+AGID00236	1351	ab129081	Set163	AMPK-a2_pS345	-0.03704004
+AGID00006	39	2532	Old	AMPKALPHA	-0.046639
+AGID00007	40	2535	Old	AMPKALPHA_pT172	0.35913
+AGID00193	1208	610066	Old	ANNEXIN1	0.4327
+AGID00166	1142	610668	Old	ANNEXINVII	0.092531
+AGID00371	756	1852-1/ab52615	Old	AR	-0.013399
+AGID00194	1217	4432	Old	ARAF	0.21018
+AGID02191	2507	PA5-39728	Old	ARAF_pS299	0.22119
+AGID00260	1053	sc-32761	Old	ARID1A	0.091682
+AGID00264	1560	HPA029318	Old	ASNS	-0.28166
+AGID00276	1612	3415	Set163	Atg3	0.01188499
+AGID00309	1775	13507	Set163	Atg4B	-0.1707255
+AGID00310	1776	12994	Set163	Atg5	-0.496525
+AGID00277	1613	8558	Set163	Atg7	0.2574451
+AGID00242	1363	2873	Old	ATM	0.022768
+AGID02142	2447	13050	Set163	ATM_pS1981	-0.3759201
+AGID00217	1289	ab14748	Set163	ATP5A	-0.2669456
+AGID02145	2451	PA5-43776	Set163	ATP5H	-0.04290997
+AGID02150	2456	13934	Set163	ATR	0.111412
+AGID00315	1795	ab178407	Set163	ATR_pS428	-0.0139512
+AGID00268	1569	ab97508	Set163	ATRX	-0.1932676
+AGID00391	2332	14475	Set163	Aurora-A	0.4384351
+AGID00392	2333	2914	Set163	Aurora-ABC_pT288_pT232_pT198	0.1112751
+AGID02195	2512	MA5-27890	Set163	Aurora-B	-0.07430125
+AGID00215	1271	8661	Old	AXL	0.38235
+AGID02143	2449	8457	Set163	b-Actin	0.2305248
+AGID00179	1170	9565	Set163	b-Catenin_pT41_S45	0.09978006
+AGID00301	1725	14058	Set163	B7-H3	-0.6020259
+AGID00302	1726	14572	Set163	B7-H4	-0.2472303
+AGID00008	63	9291	Old	BAD_pS112	0.38991
+AGID00009	71	1542-1/ab32371	Old	BAK	-0.50633
+AGID00192	1207	sc-28383	Old	BAP1C4	-0.0040153
+AGID00010	73	2772	Old	BAX	-0.26074
+AGID00433	80	M0887	Old	BCL2	0.21615
+AGID00219	1299	PAB8528	Old	BCL2A1	-0.033191
+AGID00012	84	1018-1	Old	BCLXL	-0.16181
+AGID00377	87	sc-10086	Old	BECLIN	0.11813
+AGID00011	75	9562	Old	BETACATENIN	-0.45286
+AGID00013	88	1008-1/ab32060	Old	BID	-0.059978
+AGID00180	90	1036-1/ab32158	Old	BIM	-0.026657
+AGID00221	1311	610978	Set163	BiP-GRP78	-0.0776105
+AGID00373	2194	07-507	Set163	BMK1-Erk5_pT218_Y220	-0.05533491
+AGID00355	92	1647/ab33899	Old	BRAF	-0.175
+AGID00014	94	2696	Old	BRAF_pS445	-0.0030732
+AGID00445	761	9012	Old	BRCA2	-0.2266
+AGID00266	1567	13440	Old	BRD4	-0.011386
+AGID00168	1146	2865	Set163	c-Abl_pY412	0.04014432
+AGID00278	1615	3130	Set163	c-IAP2	0.04475994
+AGID00345	1990	5649	Old	CA9	NA
+AGID00265	1565	2862	Old	CABL	-0.053087
+AGID00429	2407	2679	Set163	Calnexin	-0.0983352
+AGID00176	1165	9496	Set163	Caspase-8-cleaved	-0.20973
+AGID00623	111	9665	Old	CASPASE3	-0.094873
+AGID00015	109	9491	Old	CASPASE7CLEAVEDD198	-0.30041
+AGID00118	951	9746	Old	CASPASE8	-0.0011509
+AGID00537	935	551246	Old	CASPASE9	NA
+AGID00016	114	3238	Old	CAVEOLIN1	-0.80581
+AGID00358	2100	ab76000	Set163	CD134	-0.1085064
+AGID00303	1737	826701	Set163	CD171	-0.128495
+AGID00410	125	1632-1/ab78237	Old	CD20	-0.17028
+AGID00220	1308	ab28340	Old	CD26	-0.055136
+AGID00191	1206	610467	Set163	CD29	-0.0863453
+AGID00017	127	M0823	Old	CD31	0.21465
+AGID00369	2174	ab108403	Set163	CD38	-0.06437494
+AGID00359	2104	ab133616	Set163	CD4	0.6298538
+AGID00411	1398	3570	Set163	CD44	-0.08758007
+AGID00237	1352	M070101-2	Set163	CD45	0.3102349
+AGID00115	937	611016	Old	CD49B	0.27724
+AGID02171	2482	91882	Set163	CD86	0.04869504
+AGID00329	1873	4688	Set163	cdc25C	0.1314601
+AGID00227	1332	4651	Set163	Cdc42	0.07894483
+AGID00422	2396	3387	Set163	Cdc6	0.05008494
+AGID00501	1007	9112	Old	CDK1	-0.084731
+AGID00293	1658	ab32384	Set163	CDK1_pT14	0.5639351
+AGID00314	1783	4539	Old	CDK1_pY15	-0.095817
+AGID00423	2397	8064	Set163	CDT1	-0.4434404
+AGID02101	2348	15102	Set163	cGAS	0.1395851
+AGID00447	2410	13460	Set163	CHD1L	-0.1185968
+AGID00189	1203	2360	Old	CHK1	0.0037835
+AGID00234	1348	ab79758	Old	CHK1_pS296	0.061088
+AGID00107	903	2348	Old	CHK1_pS345	-0.067467
+AGID00018	146	3440	Old	CHK2	-0.3745
+AGID00019	147	2197	Old	CHK2_pT68	0.16588
+AGID00527	2078	4952	Old	CIAP	0.25481
+AGID00350	2018	3793	Set163	CIITA	0.1557651
+AGID00434	155	9164	Old	CJUN_pS73	-0.16892
+AGID00020	157	1522-1/ab32363	Old	CKIT	-0.12036
+AGID00400	852	NB100-91714	Old	CLAUDIN7	0.18715
+AGID00466	726	3127	Old	CMET	-0.068492
+AGID00079	727	3129	Old	CMET_pY1235	-0.028593
+AGID00167	161	9402	Old	CMYC	0.14212
+AGID00292	1656	11130-1-AP	Old	COG3	0.17133
+AGID00021	171	sc-20649	Old	COLLAGENVI	-0.23105
+AGID00141	1069	459230	Old	COMPLEXIISUBUNIT30	NA
+AGID00267	1568	3512	Set163	Connexin-43	0.06231479
+AGID00269	1571	6434	Set163	Coup-TFII	0.1238851
+AGID00150	1116	4850	Set163	Cox-IV	0.0117344
+AGID00195	1218	4842	Set163	Cox2	-0.1507749
+AGID00188	803	05-739	Old	CRAF	0.064718
+AGID00022	179	9427	Old	CRAF_pS338	-0.056924
+AGID00023	181	9197	Set163	Creb	-0.4956261
+AGID00393	2334	9198	Set163	CREB_pS133	0.03099719
+AGID00365	2155	4980	Set163	CSK	0.211295
+AGID00367	2160	9201	Set163	CtIP	-0.3631603
+AGID00536	2096	ab107198	Old	CTLA4	NA
+AGID00025	198	2936	Set163	Cyclin-D3	0.5474449
+AGID00024	192	1495-1/ab32053	Old	CYCLINB1	-0.094826
+AGID00382	194	sc-718	Old	CYCLIND1	0.15092
+AGID00437	199	sc-25303	Old	CYCLINE1	-0.82577
+AGID00449	202	1142-1	Old	CYCLINE2	-0.16914
+AGID00209	1257	ab110324	Set163	Cyclophilin-F	-0.6261352
+AGID00247	1379	ab48389	Set163	D-a-Tubulin	-0.19128
+AGID00308	1770	GTX10524	Set163	DAPK1_pS308	0.035235
+AGID00304	1744	ab51601	Set163	DAPK2	-0.05966017
+AGID00343	1980	6998	Set163	DDB-1	0.141265
+AGID00427	2402	5583	Set163	DDR1	0.3847593
+AGID00428	2403	SAB4504671	Set163	DDR1_pY513	0.235355
+AGID00532	1273	Bast Lab	Old	DIRAS3	0.07819
+AGID00104	891	ab76008	Old	DJ1	-0.17483
+AGID02146	2452	4658	Set163	DM-Histone-H3	-0.1038003
+AGID00386	1397	ab32521	Set163	DM-K9-Histone-H3	-0.07170998
+AGID00352	2030	14649	Set163	DNA-Ligase-IV	-0.1340202
+AGID00407	2371	13609	Set163	DNA_POLG	-0.04901503
+AGID00399	2344	5032	Set163	DNMT1	0.5929249
+AGID00409	2373	5391	Set163	DRP1	-0.08011652
+AGID00253	1406	5149	Old	DUSP4	0.1064
+AGID00334	1936	ab76310	Set163	DUSP6	-0.04038528
+AGID00116	940	3218	Old	DVL3	0.16204
+AGID00211	1261	sc-251	Old	E2F1	NA
+AGID00148	1099	3195	Old	ECADHERIN	0.56787
+AGID00135	1060	2332	Old	EEF2	-0.24706
+AGID00136	1061	3692	Old	EEF2K	-0.0088933
+AGID00152	1120	2232	Old	EGFR	-0.60295
+AGID00450	217	2234	Old	EGFR_pY1068	-0.14654
+AGID00026	221	1124-1/ab32578	Old	EGFR_pY1173	-0.026539
+AGID00078	722	9742	Old	EIF4E	-0.26737
+AGID00328	1871	ab76256	Set163	eIF4E_pS209	4.73462e-06
+AGID00154	1124	2498	Old	EIF4G	-0.11447
+AGID00027	228	9181	Set163	Elk1_pS383	-0.1245799
+AGID00235	1350	M061329-2	Set163	EMA	0.9996246
+AGID00394	2337	3810	Set163	Enolase-1	-0.2233802
+AGID00395	2338	8171	Set163	Enolase-2	-0.09809994
+AGID00196	1219	GTX629542	Old	ENY2	0.15478
+AGID00438	1849	A302-024A	Set163	EphA2	0.2203251
+AGID00552	2422	6347	Set163	EphA2_pS897	0.2491051
+AGID00553	2423	12677	Set163	EphA2_pY588	-0.05307344
+AGID00075	693	556347	Old	EPPK1	0.81999
+AGID00335	238	RM-9101	Old	ERALPHA	3.0199
+AGID00029	241	1091-1/ab32396	Old	ERALPHA_pS118	0.91691
+AGID00240	247	MS-671	Old	ERCC1	-0.05566
+AGID00239	1355	11331-1-AP	Old	ERCC5	-0.1571
+AGID00484	249	sc-154	Old	ERK2	-0.051168
+AGID00372	2193	3552	Set163	Erk5	0.03763506
+AGID00405	2369	13826	Set163	ERRalpha	0.4901099
+AGID00187	1200	A303-501A	Old	ETS1	-0.53621
+AGID00511	2492	2593	Set163	EVI1	0.2895795
+AGID00485	1284	4905	Old	EZH2	NA
+AGID00030	252	1700-1/ab40794	Set163	FAK	-0.3302849
+AGID02151	2457	8556	Set163	FAK_pY397	0.1130784
+AGID00171	1156	3180	Old	FASN	2.797
+AGID00356	2085	500-P18/10775-082	Set163	FGF-basic	-0.1659099
+AGID00031	262	1574-1/ab45688	Old	FIBRONECTIN	1.1904
+AGID00339	1959	4403	Set163	FN14	0.05624006
+AGID02152	2458	20459	Old	FOXM1	-0.0068266
+AGID00378	269	9467	Old	FOXO3A	-0.20822
+AGID02197	2515	orb6051	Old	FOXO3A_pS318S321	0.14899
+AGID02167	2475	PA5-64616	Set163	FRS2-alpha_pY196	-0.02202494
+AGID02213	2575	ab124892	Set163	FTO	-0.1328149
+AGID02141	2446	12263	Old	G6PD	0.21766
+AGID00117	943	3239	Old	GAB2	-0.21788
+AGID00412	274	AM4300	Old	GAPDH	-1.9398
+AGID00086	764	558686	Old	GATA3	1.6504
+AGID00383	1578	4253	Old	GATA6	0.33172
+AGID00289	1634	12601-1-AP	Set163	GCLC	-0.11431
+AGID00305	1745	ab124827	Set163	GCLM	-0.04919495
+AGID00212	1263	3305	Old	GCN5L2	0.15262
+AGID00270	1579	3538	Set163	Gli1	-0.1407353
+AGID00263	1520	ab69838	Set163	Gli3	-0.2610661
+AGID00548	2530	3660	Set163	Glucocorticoid-Receptor	0.4685501
+AGID00387	1617	12793	Set163	Glutamate-D1-2	-0.02160608
+AGID00262	1491	ab156876	Set163	Glutaminase	-0.090185
+AGID00319	1807	4275	Set163	Granzyme-B	-0.65626
+AGID00368	2169	ab183737	Set163	GRB7	-0.08963572
+AGID00396	2339	3593	Set163	Grp75	0.23124
+AGID00174	1163	9315	Set163	GSK-3B	-0.08168582
+AGID00502	1082	9336	Old	GSK3_pS9	0.012041
+AGID00033	284	sc-7291	Old	GSK3ALPHABETA	0.068887
+AGID00034	285	9331	Old	GSK3ALPHABETA_pS21S9	0.43504
+AGID00129	1035	3886	Old	GYS	NA
+AGID00130	1036	3891	Old	GYS_pS641	NA
+AGID01354	1342	9718	Set163	H2AX_pS139	-0.08270498
+AGID00363	1409	MA1-2022	Set163	H2AX_pS140	0.02812999
+AGID00131	1038	MS-325-P1	Old	HER2	-0.11064
+AGID00142	299	06-229	Old	HER2_pY1248	0.016478
+AGID00110	911	sc-285	Old	HER3	0.23373
+AGID00080	728	4791	Old	HER3_pY1289	-0.22228
+AGID00103	890	2573	Old	HEREGULIN	-0.12727
+AGID00271	1582	11988	Set163	HES1	-0.6113252
+AGID00397	2340	2024	Set163	Hexokinase-I	0.1641048
+AGID00442	1023	2867	Set163	Hexokinase-II	0.0465035
+AGID00419	1402	610958	Old	HIF1ALPHA	NA
+AGID00205	1250	ab1791	Set163	Histone-H3	-0.08184512
+AGID00398	2341	3377	Set163	Histone-H3_pS10	0.4276299
+AGID00332	1901	ab128959	Set163	HLA-DQA1	-0.01261632
+AGID00333	1902	14832-1-AP	Set163	HMHA1	1.235645
+AGID00035	321	2402	Set163	HSP27	0.0553
+AGID00036	323	2401	Set163	HSP27_pS82	0.911865
+AGID00320	1808	12165	Set163	HSP60	-0.09738016
+AGID00037	325	4872	Old	HSP70	-0.1509
+AGID00366	2158	86630	Set163	IDO	1.32974
+AGID00197	1221	3024	Old	IGF1R_pY1135Y1136	0.13053
+AGID00038	335	3922	Old	IGFBP2	-0.32921
+AGID00090	793	611504	Set163	IGFBP3	0.1000947
+AGID00039	336	3027	Set163	IGFRb	0.2382351
+AGID00336	1949	12153	Set163	IL-6	-0.5129203
+AGID02221	2583	57145	Set163	IMP3	-0.1105651
+AGID02153	2459	14543	Old	INPP4B	1.1758
+AGID00272	1586	3025	Set163	IR-b	-0.371865
+AGID00519	2519	4302	Set163	IRF-3	0.1833003
+AGID00520	2520	4947	Set163	IRF-3_pS396	-0.006875482
+AGID00223	1316	sc-497	Old	IRF1	0.058548
+AGID00092	802	06-248	Old	IRS1	-0.16463
+AGID00040	371	4502	Set163	IRS2	-0.2043154
+AGID00250	1394	sc-13157	Old	JAB1	0.10713
+AGID00256	1413	ab109536	Set163	Jagged1	-0.008819415
+AGID00177	1166	3230	Old	JAK2	-0.034661
+AGID00758	377	4671	Old	JNK_pT183Y185	0.024714
+AGID02136	2439	PA5-28262	Old	JNK2	-0.088864
+AGID00307	1757	ab10484	Set163	KAP1	-0.1461805
+AGID00528	904	2180	Old	KU80	-0.042491
+AGID00375	2237	HPA028732	Set163	LAD1	0.2347801
+AGID00290	1643	IHC-00439	Set163	Lasu1	0.08953003
+AGID00279	1618	4108	Set163	LC3A-B	-0.04812021
+AGID00042	397	2752	Old	LCK	0.35567
+AGID00119	976	3582	Old	LDHA	NA
+AGID00533	977	ab85319	Old	LDHB	NA
+AGID00529	1477	3050	Old	LKB1	-0.019121
+AGID00244	1367	2568	Set163	LRP6_pS1490	-0.18394
+AGID00439	2424	2796	Set163	Lyn	0.20688
+AGID02154	2460	4370	Old	MAPK_pT202Y204	0.68885
+AGID00198	1222	5453	Set163	Mcl-1	0.04413401
+AGID00288	1633	AB3314P	Set163	MCT4	0.3585449
+AGID00175	1164	3521	Set163	MDM2_pS166	0.1699501
+AGID00044	417	1235-1/ab32576	Old	MEK1	-0.1334
+AGID00143	1076	9154	Old	MEK1_pS217S221	0.24647
+AGID00201	1243	9125	Set163	MEK2	-0.05776541
+AGID00361	2118	ab51061	Set163	MelanA	0.06006004
+AGID00362	2119	ab137078	Set163	Melanoma-gp100	0.07248496
+AGID00337	1951	12711	Set163	MERIT40	-0.05347058
+AGID00338	1952	12110	Set163	MERIT40_pS29	-0.2174149
+AGID02212	2574	ab195352	Set163	METTL3	0.1977851
+AGID00225	1323	sc-20121	Set163	MIF	-0.3726149
+AGID00137	1062	WH0054206M1	Old	MIG6	-0.25505
+AGID00403	2117	ab20663	Set163	MITF	0.09060967
+AGID00503	1067	ab3298	Old	MITOCHONDRIA	NA
+AGID00321	1809	14739	Set163	Mitofusin-1	-0.3879037
+AGID00322	1810	11925	Set163	Mitofusin-2	0.08181493
+AGID00389	2324	3515	Set163	MLH1	-0.03926508
+AGID00312	1780	14993	Set163	MLKL	0.4258049
+AGID00402	2359	MAB3328	Set163	MMP14	-0.108095
+AGID00045	435	4022	Set163	MMP2	-0.2823678
+AGID00122	1005	2195	Set163	Mnk1	0.1701838
+AGID00331	1899	sc-377312	Set163	MR1	-0.2538901
+AGID00273	1589	ab103319	Set163	MRAP	-0.03046494
+AGID00530	440	4847	Old	MRE11	0.18883
+AGID00390	905	2850	Old	MSH2	0.13201
+AGID00138	1063	22030002	Old	MSH6	0.12279
+AGID00299	1675	ab76148	Set163	MSI2	-0.3206799
+AGID00232	1344	ab14705	Set163	MTCO1	0.4283834
+AGID00046	444	2983	Old	MTOR	0.35425
+AGID00047	446	2971	Old	MTOR_pS2448	0.28907
+AGID00204	1247	H00009788-M01A	Set163	MTSS1	0.05205988
+AGID00401	1139	21370002	Old	MYH11	0.44564
+AGID00291	1647	3403	Old	MYOSINIIA	0.18315
+AGID00173	1160	5026	Old	MYOSINIIA_pS1943	0.3236
+AGID00318	1803	4282	Set163	Myt1	-0.0620552
+AGID00216	1274	5795-1/ab129189	Old	NAPSINA	NA
+AGID00418	452	4061	Old	NCADHERIN	-0.13046
+AGID00156	1126	3217	Old	NDRG1_pT346	-0.35761
+AGID02133	2436	PA5-45913	Set163	NDUFB4	0.1662451
+AGID00134	1046	22710002	Old	NF2	-0.56729
+AGID00048	457	3033	Old	NFKBP65_pS536	0.42884
+AGID02155	2461	3608	Old	NOTCH1	-0.28863
+AGID00340	1969	4147	Set163	Notch1-cleaved	-0.2389602
+AGID00087	767	sc-5593	Set163	Notch3	-0.01525496
+AGID00258	1420	3187	Set163	NQO1	-0.2371401
+AGID00162	1136	sc-31	Old	NRAS	-0.073802
+AGID00257	1419	12721	Old	NRF2	NA
+AGID00297	1669	2750	Set163	Oct-4	-0.3714499
+AGID00420	466	1712-1/ab40803	Old	P16INK4A	0.50785
+AGID00384	470	sc-6246	Old	P21	0.18044
+AGID00105	897	1591-1/ab32034	Old	P27	0.1609
+AGID00096	842	AF1555	Old	P27_pT157	0.13689
+AGID00099	878	ab64949	Old	P27_pT198	-0.034142
+AGID00181	1175	9228	Set163	p38-a	0.1039039
+AGID00098	479	9211	Old	P38_pT180Y182	0.3718
+AGID00049	478	9212	Old	P38MAPK	0.23157
+AGID00151	1119	4695	Set163	p44-42-MAPK	0.3193
+AGID00050	481	9282	Old	P53	-0.12332
+AGID00490	1187	610833	Old	P62LCKLIGAND	0.65056
+AGID00545	1415	ab53039	Old	P63	NA
+AGID00052	494	9205	Old	P70S6K_pT389	-0.038975
+AGID00051	493	1494-1/ab32529	Old	P70S6K1	-0.025853
+AGID00085	759	9347	Old	P90RSK	-0.20903
+AGID00531	770	9344	Old	P90RSK_pT359S363	0.18975
+AGID00182	1178	9346	Set163	p90RSK_pT573	-0.01640506
+AGID00053	499	612024	Old	PAI1	0.13573
+AGID00224	1322	HPA035895	Set163	PAICS	-0.4871549
+AGID00323	1811	2602	Set163	PAK1	-0.3227754
+AGID02199	2517	PA5-69540	Set163	PAK4	0.05064995
+AGID00245	1370	4336-BPC-100	Set163	PAR	0.4145746
+AGID00374	2209	66564	Set163	PARG	-0.06627521
+AGID00370	1372	sc-7150	Old	PARP1	0.13261
+AGID00468	501	9546	Old	PARPCLEAVED	0.018678
+AGID00274	1591	ab53715	Set163	Patched	-0.04008497
+AGID00513	2486	60433	Set163	PAX6	-0.285655
+AGID00441	1621	9857	Set163	PAX8	-0.03015132
+AGID00054	504	2542	Old	PAXILLIN	-0.073816
+AGID00055	509	2130	Old	PCADHERIN	0.01081
+AGID00248	511	ab29	Old	PCNA	-0.22643
+AGID00413	2095	43248	Old	PDCD1	NA
+AGID00094	816	600-401-965	Old	PDCD4	0.13981
+AGID00385	1225	3169	Set163	PDGFRB	0.2829701
+AGID00210	1258	ab110332	Set163	PDH	-0.008031097
+AGID00324	1817	3205	Set163	PDHA1	-0.1260506
+AGID00280	1622	3820	Set163	PDHK1	-0.1689649
+AGID00056	515	3062	Old	PDK1	0.10709
+AGID00057	516	3061	Old	PDK1_pS241	0.11637
+AGID00300	1234	sc-19090	Old	PDL1	0.2491
+AGID00124	1017	2780	Old	PEA15	0.10695
+AGID00125	1018	44-836G	Old	PEA15_pS116	-0.11781
+AGID00440	2429	3192	Set163	PERK	0.2454744
+AGID02207	2569	ab192876	Set163	PGM1	-0.04939559
+AGID00281	1623	13428	Set163	PHGDH	-0.4491156
+AGID00425	2399	22789-1-AP	Set163	PHLPP	-0.1270849
+AGID00226	1330	sc-376412	Set163	PI3K-p110-b	-0.08752495
+AGID00093	808	4255	Old	PI3KP110ALPHA	0.18582
+AGID00058	523	06-195	Old	PI3KP85	-0.18013
+AGID00296	1667	5675	Set163	PKA-a	1.64467
+AGID00259	1426	9375	Set163	PKC-a-b-II_pT638_T641	-0.05818494
+AGID00172	529	05-154	Old	PKCALPHA	-0.46961
+AGID00460	530	06-822	Old	PKCALPHA_pS657	-0.017748
+AGID00114	932	07-875	Old	PKCDELTA_pS664	0.23343
+AGID00163	1137	9371	Old	PKCPANBETAII_pS660	0.3663
+AGID00126	1025	4053	Old	PKM2	NA
+AGID00512	2489	5690	Set163	PLC-gamma1	0.7116842
+AGID02138	2441	GTX133463	Set163	PLC-gamma2_pY759	0.02755989
+AGID00084	754	4513	Set163	PLK1	0.524665
+AGID00203	1246	22510002	Set163	PMS2	0.1405251
+AGID00207	1254	ab14734	Set163	Porin	0.06471506
+AGID00381	549	1483-1/ab32085	Old	PR	-0.13711
+AGID00081	738	AHO1031	Set163	PRAS40	-0.1098249
+AGID00082	739	44-1100G	Old	PRAS40_pT246	-0.11655
+AGID00424	2398	OAAF05458	Set163	PRC1_pT481	0.06195504
+AGID00492	1205	HPA007730	Old	PRDX1	0.25338
+AGID00190	1204	ab102739	Old	PREX1	1.1848
+AGID00061	566	9552	Old	PTEN	0.43845
+AGID00364	2154	ab76942	Set163	PTPN12	0.1260249
+AGID00218	1290	4976	Set163	Puma	0.03686006
+AGID00200	1242	SAB2900066	Old	PYGB	NA
+AGID00535	1494	ab61013	Old	PYGL	NA
+AGID00202	1245	H00005837-M10	Old	PYGM	NA
+AGID00275	1607	3291	Set163	Pyk2_pY402	0.01216948
+AGID00145	1083	3539	Old	RAB11	-0.060415
+AGID00169	1150	4314	Old	RAB25	-0.099715
+AGID00342	1979	24555	Set163	Rad23A	0.10922
+AGID00261	987	05-525	Old	RAD50	-0.61876
+AGID00360	579	NA71	Old	RAD51	-0.22602
+AGID00158	1128	2280	Old	RAPTOR	0.35921
+AGID00059	552	9309	Old	RB	-0.12499
+AGID00060	557	9308	Old	RB_pS807S811	-0.24971
+AGID00164	1138	21390002	Old	RBM15	0.33811
+AGID00547	735	3221	Old	RET_pY905	NA
+AGID00097	847	MAB3426	Set163	Rheb	0.111315
+AGID00159	1129	2114	Old	RICTOR	-0.21348
+AGID00160	1130	3806	Old	RICTOR_pT1135	0.16405
+AGID00282	1624	4926	Set163	RIP	0.14363
+AGID00283	1625	13526	Set163	RIP3	-0.02682569
+AGID00416	1368	2208	Set163	RPA32	0.04314003
+AGID00246	1375	A300-245A	Set163	RPA32_pS4_S8	-0.02026604
+AGID00341	1978	3388	Set163	RRM1	0.1028898
+AGID00344	1981	PA5-27856	Set163	RRM2	0.3189384
+AGID00554	2425	8408	Set163	RSK1	-0.1364128
+AGID00353	2031	13018	Set163	S100A4	0.1854501
+AGID00330	1874	2317	Old	S6	-0.26539
+AGID00062	600	2211	Old	S6_pS235S236	-0.16871
+AGID00063	601	2215	Old	S6_pS240S244	0.18814
+AGID00157	1127	sc-58420	Old	SCD1	0.17978
+AGID00230	1339	11998	Set163	SDHA	0.04181506
+AGID00294	1039	ab69836	Old	SETD2	0.16645
+AGID00161	1131	32-4500	Old	SF2	0.1011
+AGID02179	2495	3534	Set163	SFRP1	-0.203861
+AGID00431	2411	12103	Set163	SGK1	0.01817432
+AGID00430	2409	8156	Set163	SGK3	0.37471
+AGID02168	2476	bs-3413R	Old	SHC_pY317	0.10063
+AGID00376	2241	3397	Set163	SHP2	0.3693048
+AGID00183	1180	3751	Old	SHP2_pY542	0.0072364
+AGID02208	2570	ab8120	Set163	SIRP-alpha	0.1846394
+AGID00222	1133	sc-99002	Old	SLC1A5	0.77379
+AGID00255	1411	sc-136891	Set163	Slfn11	-0.288225
+AGID00064	610	2954	Old	SMAC	-0.46312
+AGID00113	922	1649-1/ab33902	Old	SMAD1	-0.054524
+AGID00091	796	1735-1/ab40854	Old	SMAD3	-0.26095
+AGID02160	2467	46535	Old	SMAD4	-0.17507
+AGID00065	616	3895	Old	SNAIL	0.031726
+AGID00325	1818	4266	Set163	SOD1	0.04531357
+AGID00380	1328	13141	Set163	SOD2	0.2785198
+AGID00298	1670	2748	Set163	Sox2	-0.1292751
+AGID00066	621	05-184	Old	SRC	-0.35746
+AGID02157	2463	6943	Old	SRC_pY416	0.077928
+AGID00068	626	2105	Old	SRC_pY527	-0.028742
+AGID00185	1197	4904	Set163	Stat3	0.09885189
+AGID00388	637	9131	Old	STAT3_pY705	-0.12811
+AGID00069	638	1289-1/ab32043	Old	STAT5ALPHA	0.55816
+AGID00077	718	1972-1/ab52630	Old	STATHMIN	0.021601
+AGID00357	2099	13647	Set163	STING	0.7359601
+AGID00128	1033	sc-1240	Old	SYK	0.30748
+AGID00070	646	05-348	Set163	Tau	0.21813
+AGID00327	777	2149	Old	TAZ	-0.027129
+AGID00228	1333	7495	Set163	TFAM	-0.3020613
+AGID00165	1140	22500002	Old	TFRC	0.1724
+AGID00149	1107	S1711/ab137573	Old	TIGAR	-0.04424
+AGID00109	908	MS-224-P1	Old	TRANSGLUTAMINASE	0.0051209
+AGID00406	2370	612344	Set163	TRAP1	0.02598506
+AGID00559	2537	PA5-34561	Set163	TRIM24	0.00444781
+AGID00306	1756	ab167154	Set163	TRIM25	0.2205593
+AGID00426	2400	PA5-52193	Set163	TRIP13	0.3239901
+AGID00155	1125	4906	Old	TSC1	-0.26472
+AGID00144	1081	2044-1/ab76013	Old	TTF1	NA
+AGID00071	670	1613-1/ab32554	Old	TUBERIN	0.39764
+AGID02194	2511	ab109403	Old	TUBERIN_pT1462	0.10431
+AGID00417	1842	ab173300	Set163	TUFM	0.05043503
+AGID00238	1353	sc-81417	Set163	Twist	-0.003394942
+AGID00436	1080	5585	Set163	Tyro3	-0.4422155
+AGID00295	1662	5546	Set163	U-Histone-H2B	-0.4296101
+AGID00214	1270	HPA005651	Set163	UBAC1	-0.08400008
+AGID00351	2020	sc-136145	Set163	UBQLN4	-0.203745
+AGID00213	1267	sc-271268	Set163	UGT1A	0.01652006
+AGID00284	1626	6888	Set163	ULK1_pS757	-0.1728829
+AGID00208	1256	MS304/ab14745	Set163	UQCRC2	-0.108965
+AGID00313	1781	13115	Set163	UVRAG	-0.03251495
+AGID00073	678	3112	Set163	VASP	-0.1932953
+AGID00184	1181	2502	Set163	VAV1	0.9227592
+AGID00074	688	2479	Old	VEGFR2	0.35284
+AGID00421	2394	68547	Set163	VHL	-0.04840494
+AGID00231	1343	SAB4200080	Set163	Vinculin	0.1281446
+AGID00317	1802	4936	Set163	Wee1	0.2393289
+AGID00354	2058	4910	Set163	Wee1_pS642	-0.1355052
+AGID00285	1627	12124	Set163	WIPI1	-0.197765
+AGID00286	1628	8567	Set163	WIPI2	-0.1709499
+AGID02214	2576	ab195380	Set163	WTAP	0.1044244
+AGID00133	1044	sc-32136	Old	XBP1	0.020372
+AGID00076	699	2042	Set163	XIAP	0.09965453
+AGID00241	1359	sc-56813	Set163	XPA	-0.4094699
+AGID00349	1354	ab3299	Set163	XPF	0.1003024
+AGID02137	2440	PA5-29359	Old	XRCC1	0.31769
+AGID00088	780	sc-15407	Old	YAP	-0.2032
+AGID00089	782	4911	Old	YAP_pS127	-0.2971
+AGID00504	700	17250002	Old	YB1	0.039045
+AGID00095	835	2900	Old	YB1_pS102	-0.09174
+AGID02217	2579	ab220163	Set163	YTHDF2	0.24318
+AGID02210	2572	ab220161	Set163	YTHDF3	0.166745
+AGID00326	1828	2705	Set163	ZAP-70	1.268198
+AGID00432	2244	sc-25388	Set163	ZEB1	0.03736333

data/gdc_data_organized/4a032bad-e726-48f2-8f39-e3acc109cc91/TCGA-BH-A0BZ-11A-06-TSF.8926f914-ba66-41ff-b779-574f25cb99b4.svs

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