Auto-upload batch data to clear storage

.gitattributes

@@ -1111,3 +1111,55 @@ data/gdc_data_organized/e3c336f5-c32f-4c5d-81fb-e2408ae145b2/a7fd4ada-7db5-4418-
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data/__notebook__.ipynb

@@ -34503,6 +34503,1657 @@
      },
      "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",
+      "[4192/10000] (15.01GB) Downloading: e97bfeb5-0152-424a-9e1d-3b59499663be_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4193/10000] (0.01GB) Downloading: TCGA-OL-A6VQ-01Z-00-DX1.E3B81163-0239-47C3-B53F-064405B58685.svs (1663.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4194/10000] (1.63GB) Downloading: nationwidechildrens.org_clinical.TCGA-OL-A6VQ.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4195/10000] (1.63GB) Downloading: TCGA-OL-A6VQ-01A-01-TSA.0CD11145-841A-4FE3-BACB-C014D4782C9E.svs (188.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4196/10000] (1.82GB) Downloading: 5cafbd32-22e8-4627-8cc5-af88a7a4de2d.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4197/10000] (1.82GB) Downloading: nationwidechildrens.org_ssf.TCGA-OL-A6VQ.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4198/10000] (1.82GB) Downloading: TCGA-OL-A6VQ-01A-11D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4199/10000] (1.82GB) Downloading: e97bfeb5-0152-424a-9e1d-3b59499663be.methylation_array.sesame.level3betas.txt (12.20 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4200/10000] (1.83GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A1R2.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4201/10000] (1.83GB) Downloading: TCGA-BRCA.82aeac9e-e169-41dc-8580-4165d4ea0ac9.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4202/10000] (1.83GB) Downloading: TCGA-BRCA.2e6cebd3-ce33-4553-a190-ac2dd9bcf91a.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4203/10000] (1.84GB) Downloading: TCGA-D8-A1XB-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4204/10000] (1.84GB) Downloading: d261492c-49be-4689-b196-43a1c65d7245.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4205/10000] (1.84GB) Downloading: b98ee315-9370-4071-ba67-7bf4c91b4777_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4206/10000] (1.84GB) Downloading: 690429bd-2f88-45bd-b81d-e1f79748cb3d_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4207/10000] (1.85GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A4RW.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4208/10000] (1.85GB) Downloading: b98ee315-9370-4071-ba67-7bf4c91b4777.methylation_array.sesame.level3betas.txt (12.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4209/10000] (1.86GB) Downloading: d261492c-49be-4689-b196-43a1c65d7245.mirbase21.isoforms.quantification.txt (0.26 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4210/10000] (1.86GB) Downloading: TCGA-BRCA.2e6cebd3-ce33-4553-a190-ac2dd9bcf91a.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4211/10000] (1.87GB) Downloading: fdfefe69-47d8-4d05-9bbc-7a066c02a802.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4212/10000] (1.87GB) Downloading: TCGA-BRCA.0eae4d42-893c-48ff-b1a3-52ae7d1220ce.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4213/10000] (1.87GB) Downloading: TCGA-BRCA.b4ebf80f-787e-4a3f-b0a1-63ad56d36aa2.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4214/10000] (1.87GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A1XB.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4215/10000] (1.87GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A1XB.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4216/10000] (1.87GB) Downloading: bca245d6-09df-48d0-9845-b31a7b4ebf11.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4217/10000] (1.87GB) Downloading: 3937670b-62c1-4b7c-b32f-69f9d5c673e1_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4218/10000] (1.88GB) Downloading: TCGA-BRCA.b4ebf80f-787e-4a3f-b0a1-63ad56d36aa2.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4219/10000] (1.88GB) Downloading: 3937670b-62c1-4b7c-b32f-69f9d5c673e1_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4220/10000] (1.89GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_C09_777692.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4221/10000] (1.89GB) Downloading: TCGA-BRCA.b4ebf80f-787e-4a3f-b0a1-63ad56d36aa2.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4222/10000] (1.89GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_A12_777694.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4223/10000] (1.89GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_A12_777694.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4224/10000] (1.89GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H10_844874.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4225/10000] (1.89GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H07_844748.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4226/10000] (1.89GB) Downloading: 648d4780-8dab-4abf-b2e1-22c26413b8e2.methylation_array.sesame.level3betas.txt (12.58 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4227/10000] (1.90GB) Downloading: 8b1e6d14-7421-481c-92a0-f926e6b26bbd.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4228/10000] (1.90GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A2LM.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4229/10000] (1.90GB) Downloading: TCGA-BRCA.56fb1d49-78c7-4965-9a17-a90a2c1a9b95.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4230/10000] (1.90GB) Downloading: TCGA-AR-A2LM-01Z-00-DX1.CB64A062-2E35-41F9-97C7-07BB60754799.svs (1468.87 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4231/10000] (3.33GB) Downloading: TCGA-BH-A0BS-11A-01-TSA.2830eb43-a695-49c0-a69d-0b17545f8bde.svs (304.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4232/10000] (3.63GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A07S.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4233/10000] (3.63GB) Downloading: TCGA-A8-A07S-01A-01-BS1.84cf353c-1994-430c-9ad3-f8dfe6f72b4b.svs (216.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4234/10000] (3.84GB) Downloading: nationwidechildrens.org_ssf.TCGA-E2-A1IG.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4235/10000] (3.84GB) Downloading: 1b8fc655-8f38-4d99-9945-131af673f31e.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4236/10000] (3.84GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_A06_747912.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4237/10000] (3.84GB) Downloading: 7f81c4e4-c26a-414d-9a51-8d3a0e9aa335.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4238/10000] (3.84GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_B11_747940.grch38.seg.v2.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4239/10000] (3.84GB) Downloading: b58811d7-8ee0-4b65-a892-17319cc9ecaf.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4240/10000] (3.85GB) Downloading: 6b2ed09e-dbe3-4174-aff0-a04cdf94560d.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4241/10000] (3.85GB) Downloading: TCGA-BRCA.e3df00a4-ca76-4515-b652-ba5903b82f99.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4242/10000] (3.85GB) Downloading: TCGA-BH-A0BS-01A-11D-A890-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4243/10000] (3.85GB) Downloading: e2210b82-0dd9-4b1d-92ba-414fd60c0ca9.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4244/10000] (3.85GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_F02_667030.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4245/10000] (3.85GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_A02_778042.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4246/10000] (3.85GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_C02_778018.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4247/10000] (3.85GB) Downloading: 90a1bbd2-6b26-4d1c-b255-df5499d1da6c.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4248/10000] (3.85GB) Downloading: TCGA-C8-A134-01Z-00-DX1.78D10BCC-98B3-4587-897D-3E27DA28D2EB.svs (700.46 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4249/10000] (4.53GB) Downloading: TCGA-BH-A0BS-11A-01-BSA.2ed5f08c-08ac-4da1-b02a-58b66bd41eff.svs (317.74 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4250/10000] (4.84GB) Downloading: e022cf37-0cb5-4efb-af76-696e877eb862_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4251/10000] (4.85GB) Downloading: TCGA-BRCA.59d70e3c-da53-46e9-9f46-177223c25d95.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4252/10000] (4.85GB) Downloading: TCGA-E2-A1IG-11A-01-TSA.740f9016-5033-43e1-ad49-9c4675b068ec.svs (45.89 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4253/10000] (4.90GB) Downloading: 1253b76a-ef4a-4782-9de1-e6e76f33a8ee.mirbase21.isoforms.quantification.txt (0.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4254/10000] (4.90GB) Downloading: TCGA-BRCA.8689ec70-41c0-43fb-9d1d-723c0ef60a16.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4255/10000] (4.90GB) Downloading: 394d3409-2498-4498-a45b-b36ca401eb17.mirbase21.isoforms.quantification.txt (0.30 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4256/10000] (4.90GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A2LE.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4257/10000] (4.90GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A134.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4258/10000] (4.90GB) Downloading: TCGA-BRCA.aad64468-8c93-47ce-bc77-829f4fb8b2d6.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4259/10000] (4.90GB) Downloading: TCGA-A8-A06P-01Z-00-DX1.37660D0F-1595-43C5-9D30-58D6CB93B52C.svs (547.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4260/10000] (5.44GB) Downloading: 49e0a55e-cd18-438c-890a-f14c6d149743.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4261/10000] (5.44GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_A08_735326.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4262/10000] (5.44GB) Downloading: TCGA-BRCA.8689ec70-41c0-43fb-9d1d-723c0ef60a16.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4263/10000] (5.45GB) Downloading: TCGA-BRCA.90ef86f0-9b29-4f97-b8c8-128a5771ed75.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4264/10000] (5.45GB) Downloading: TCGA-C8-A134-01A-01-BSA.f8e29c16-ea94-4398-8e3b-c50294afc3e8.svs (120.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4265/10000] (5.56GB) Downloading: b51e7467-de97-4c89-926a-f71e775764d6.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4266/10000] (5.56GB) Downloading: TCGA-C8-A134-01A-11D-A894-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.18 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4267/10000] (5.56GB) Downloading: TCGA-AR-A2LE.95DC80AB-C070-4613-8C11-A124AEDF9754.PDF (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4268/10000] (5.56GB) Downloading: TCGA-BRCA.aad64468-8c93-47ce-bc77-829f4fb8b2d6.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4269/10000] (5.57GB) Downloading: ac54b5ff-8e6d-4035-97da-2c21bd113b1e_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4270/10000] (5.57GB) Downloading: 90454a2d-7a76-43ec-9865-c6e847c249bc_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4271/10000] (5.57GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H02_844824.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4272/10000] (5.57GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_G12_628256.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4273/10000] (5.57GB) Downloading: b51e7467-de97-4c89-926a-f71e775764d6.mirbase21.isoforms.quantification.txt (0.23 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4274/10000] (5.57GB) Downloading: 6a6360e4-6f47-49f6-b902-af2c5e661df2_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4275/10000] (5.57GB) Downloading: TCGA-BRCA.51577886-4016-4714-8b35-c7a61a85baa2.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4276/10000] (5.57GB) Downloading: 20506607-d21c-46a9-9675-c089a8e523fb.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4277/10000] (5.57GB) Downloading: TCGA-A8-A06P-01A-01-BS1.841bd06a-953c-4c04-af50-23d530579908.svs (547.71 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4278/10000] (6.11GB) Downloading: c69c4dcd-349a-4c8a-9c71-67dd9df9d820_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4279/10000] (6.11GB) Downloading: TCGA-BRCA.51577886-4016-4714-8b35-c7a61a85baa2.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4280/10000] (6.11GB) Downloading: TCGA-A8-A06P-01A-01-TS1.bfe56de2-bb0d-4164-ac99-cd126521b63d.svs (287.94 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4281/10000] (6.40GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_E08_748054.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4282/10000] (6.40GB) Downloading: c69c4dcd-349a-4c8a-9c71-67dd9df9d820_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4283/10000] (6.40GB) Downloading: TCGA-AR-A0TS-01A-01-BSA.9076c507-2ebb-463c-a0c0-12ad08f5d5c5.svs (340.89 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4284/10000] (6.74GB) Downloading: 47c23d13-25d3-4d3c-b817-6fbd2a329b99_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4285/10000] (6.74GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A28Q.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4286/10000] (6.74GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_C01_799988.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4287/10000] (6.74GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A0TS.xml (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4288/10000] (6.74GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_C01_747962.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4289/10000] (6.74GB) Downloading: 4db0f24e-8a4a-4249-8df8-97ca2b41770b.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4290/10000] (6.74GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AR-A0TS.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4291/10000] (6.74GB) Downloading: TCGA-BRCA.51577886-4016-4714-8b35-c7a61a85baa2.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4292/10000] (6.75GB) Downloading: TCGA-BH-A28Q-01Z-00-DX1.C6D1CA93-6B2A-4722-9270-5D56592D833D.svs (2079.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4293/10000] (8.78GB) Downloading: 774aebfe-dbba-49c4-9343-0bf4f4933e73.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4294/10000] (8.78GB) Downloading: 442631ff-566b-4ae2-8e07-7bb4d8c3e7cc_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4295/10000] (8.78GB) Downloading: TCGA-BRCA.9c593bef-cf0b-42a4-9cb1-02d9d13b16dd.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4296/10000] (8.79GB) Downloading: ea030b7d-26eb-4f0e-b7b9-c6b165061118.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4297/10000] (8.79GB) Downloading: TCGA-BH-A28Q-01A-11D-A89A-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4298/10000] (8.79GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0HA.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4299/10000] (8.79GB) Downloading: TCGA-BRCA.101abe3f-d317-4f8b-9b20-042da3d22457.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4300/10000] (8.80GB) Downloading: 4db0f24e-8a4a-4249-8df8-97ca2b41770b.mirbase21.isoforms.quantification.txt (0.39 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4301/10000] (8.80GB) Downloading: 940cb016-0dd8-4ff5-9d82-dc169a2a4092.mirbase21.isoforms.quantification.txt (0.34 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4302/10000] (8.80GB) Downloading: 940cb016-0dd8-4ff5-9d82-dc169a2a4092.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4303/10000] (8.80GB) Downloading: TCGA-AR-A24T-01A-21-A17I-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4304/10000] (8.80GB) Downloading: nationwidechildrens.org_ssf.TCGA-A2-A0CO.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4305/10000] (8.80GB) Downloading: TCGA-BRCA.f40a7b59-1b58-45d6-940b-3b33b6ca261a.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4306/10000] (8.80GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0B2.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4307/10000] (8.80GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A24T.xml (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4308/10000] (8.80GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_F01_802418.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4309/10000] (8.80GB) Downloading: 1ea21002-a85f-4b9c-9978-85485d45b78f.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4310/10000] (8.80GB) Downloading: 93ffddaf-81af-4a27-91a8-1939513da8b0.methylation_array.sesame.level3betas.txt (12.56 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4311/10000] (8.81GB) Downloading: TCGA-A2-A0CO-01Z-00-DX1.B191DADE-7DEA-4575-AED7-1C52BE15B8D5.svs (693.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4312/10000] (9.49GB) Downloading: COMIC_p_TCGA_b142_SNP_S_GenomeWideSNP_6_H05_804520.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4313/10000] (9.49GB) Downloading: TCGA-AR-A24T-01Z-00-DX1.3B325D54-38EC-4E16-BDE1-628894CC15AA.svs (1690.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4314/10000] (11.14GB) Downloading: KEBAB_p_TCGASNP_226_227_N_GenomeWideSNP_6_G01_1151594.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4315/10000] (11.14GB) Downloading: TCGA-AR-A252-01A-21-A17I-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4316/10000] (11.14GB) Downloading: TCGA-BRCA.101abe3f-d317-4f8b-9b20-042da3d22457.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4317/10000] (11.14GB) Downloading: 54b0dfa1-2cf6-4d98-9bf4-59099a11a20c.mirbase21.isoforms.quantification.txt (0.38 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4318/10000] (11.14GB) Downloading: ee2501e6-36a2-4414-a9af-bf618f36bcb7.mirbase21.isoforms.quantification.txt (0.39 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4319/10000] (11.14GB) Downloading: b67697af-c85c-432a-b8dd-175bba5cd607_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4320/10000] (11.14GB) Downloading: TCGA-BRCA.04dc714b-e905-4d74-a53a-f41ecfbbbe7c.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4321/10000] (11.14GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_G07_1365108.grch38.seg.v2.txt (0.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4322/10000] (11.15GB) Downloading: TCGA-BH-A0DI.5B7CE4A4-E1D5-4D0B-B9B4-71B94E32D782.PDF (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4323/10000] (11.15GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_G06_1365066.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4324/10000] (11.15GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_D09_748024.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4325/10000] (11.15GB) Downloading: TCGA-BRCA.bdeb88bb-5ce8-4221-988e-1386605e693f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4326/10000] (11.15GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_D04_799870.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4327/10000] (11.15GB) Downloading: TCGA-BRCA.dd174335-cc95-4d3d-a25b-9abaaaa432a2.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4328/10000] (11.15GB) Downloading: TCGA-BH-A0DI-11A-03-TSC.4debf838-7aef-4d9c-996a-0d0549222fb0.svs (43.96 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4329/10000] (11.19GB) Downloading: 860733cb-1290-47c9-9fe8-4ea9d9ecc4a0_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4330/10000] (11.20GB) Downloading: TCGA-A2-A259-01Z-00-DX1.7289CD72-CB74-41D4-B4AC-4EA5FDFEC666.svs (1686.16 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4331/10000] (12.85GB) Downloading: TCGA-BRCA.dd174335-cc95-4d3d-a25b-9abaaaa432a2.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4332/10000] (12.85GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_D04_799870.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4333/10000] (12.85GB) Downloading: TCGA-BRCA.bdeb88bb-5ce8-4221-988e-1386605e693f.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4334/10000] (12.85GB) Downloading: TCGA-BRCA.dd174335-cc95-4d3d-a25b-9abaaaa432a2.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4335/10000] (12.85GB) Downloading: TCGA-BH-A0DI-01A-11-A13B-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4336/10000] (12.85GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A0DI.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4337/10000] (12.85GB) Downloading: TCGA-BRCA.ec4242c5-4c16-43d6-9fe3-0fc2766928a1.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4338/10000] (12.85GB) Downloading: 228e17a9-9761-4dd2-9e99-775da7045ff1_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4339/10000] (12.86GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0DI.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4340/10000] (12.86GB) Downloading: TCGA-E2-A572-01A-11D-A89D-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4341/10000] (12.86GB) Downloading: 860733cb-1290-47c9-9fe8-4ea9d9ecc4a0_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4342/10000] (12.87GB) Downloading: TCGA-BRCA.ec4242c5-4c16-43d6-9fe3-0fc2766928a1.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4343/10000] (12.87GB) Downloading: TCGA-BRCA.c5b1d103-453a-4fe5-aef2-63683a56d262.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4344/10000] (12.87GB) Downloading: TCGA-BRCA.ec4242c5-4c16-43d6-9fe3-0fc2766928a1.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4345/10000] (12.87GB) Downloading: 441b536e-3c1d-4262-9763-5c31fb8dead5_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4346/10000] (12.88GB) Downloading: 441b536e-3c1d-4262-9763-5c31fb8dead5.methylation_array.sesame.level3betas.txt (12.55 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4347/10000] (12.89GB) Downloading: TCGA-BH-A0DI-11A-02-TSB.07e1b819-2663-42a7-a85d-ea27aa3669d0.svs (43.96 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4348/10000] (12.93GB) Downloading: DOUSE_p_TCGA_287_288_289_N_GenomeWideSNP_6_C09_1361050.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4349/10000] (12.93GB) Downloading: nationwidechildrens.org_clinical.TCGA-PE-A5DC.xml (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4350/10000] (12.93GB) Downloading: TCGA-BRCA.c5b1d103-453a-4fe5-aef2-63683a56d262.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4351/10000] (12.94GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_E03_735222.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4352/10000] (12.94GB) Downloading: DOUSE_p_TCGA_287_288_289_N_GenomeWideSNP_6_C09_1361050.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4353/10000] (12.94GB) Downloading: c0b8139b-5df2-4db8-bb8b-c0205a67a392.wxs.aliquot_ensemble_masked.maf.gz (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4354/10000] (12.94GB) Downloading: TCGA-BRCA.c5b1d103-453a-4fe5-aef2-63683a56d262.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4355/10000] (12.94GB) Downloading: 653efe38-b379-4233-aea6-ce3428f50c78.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4356/10000] (12.94GB) Downloading: TCGA-BRCA.63eeed5c-ee46-43e0-8886-3ad9b50634e3.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4357/10000] (12.94GB) Downloading: TCGA-BRCA.37d17072-0bcc-41ed-a80e-87a27ea956d4.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4358/10000] (12.94GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_A05_628560.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4359/10000] (12.94GB) Downloading: TCGA-BRCA.63eeed5c-ee46-43e0-8886-3ad9b50634e3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4360/10000] (12.94GB) Downloading: 520bc510-f1fb-4b7f-b6d6-c71e6ed25e42.methylation_array.sesame.level3betas.txt (0.74 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4361/10000] (12.94GB) Downloading: TCGA-A8-A09T-01Z-00-DX1.4183BBA4-AF11-4602-9EC2-35083C34A393.svs (352.51 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4362/10000] (13.29GB) Downloading: TCGA-E2-A15R-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4363/10000] (13.29GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H12_628496.grch38.seg.v2.txt (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4364/10000] (13.29GB) Downloading: TCGA-BRCA.37d17072-0bcc-41ed-a80e-87a27ea956d4.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4365/10000] (13.29GB) Downloading: 565188cc-c642-4794-887b-a8aa2720da56_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4366/10000] (13.29GB) Downloading: TCGA-BRCA.63eeed5c-ee46-43e0-8886-3ad9b50634e3.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4367/10000] (13.29GB) Downloading: TCGA-A8-A09T-01A-11D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4368/10000] (13.29GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E2-A15R.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4369/10000] (13.29GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H12_628496.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4370/10000] (13.29GB) Downloading: 6525a77a-cdff-456a-857d-ebf5ea6a880d.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4371/10000] (13.29GB) Downloading: 8b257703-a94c-4d47-848e-8107f11ce712.mirbase21.isoforms.quantification.txt (0.33 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4372/10000] (13.29GB) Downloading: TCGA-A8-A09T-01A-01-BS1.ea346b92-4ab8-40b7-a058-681a2a269463.svs (236.19 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4373/10000] (13.52GB) Downloading: TCGA-E2-A15R-01A-01-TSA.710a5229-c19b-42ea-87fb-1e8293fbcfd9.svs (151.67 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4374/10000] (13.67GB) Downloading: 9f78d690-db76-49ad-b90b-a1a8d45542e1.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4375/10000] (13.67GB) Downloading: TCGA-BRCA.37d17072-0bcc-41ed-a80e-87a27ea956d4.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4376/10000] (13.67GB) Downloading: TCGA-BRCA.37d17072-0bcc-41ed-a80e-87a27ea956d4.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4377/10000] (13.67GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A09T.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4378/10000] (13.67GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_A10_735374.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "LỖI: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response'))\n",
+      "[4379/10000] (13.67GB) Downloading: TCGA-E2-A15R-01Z-00-DX1.B58D2D9D-05EE-4D66-8DC0-9E5C6AD2E3D3.svs (1156.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4380/10000] (14.80GB) Downloading: 41f18e0d-b33e-4438-8bdf-c39bc2d7d463_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4381/10000] (14.81GB) Downloading: TCGA-E2-A15R.0F708C6E-0262-46EE-8ED2-67E791D5C379.PDF (0.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4382/10000] (14.81GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A1NA.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4383/10000] (14.81GB) Downloading: TCGA-E2-A1IO.A9D36308-DAEF-48B9-A4EC-6B9B24EE3DC2.PDF (0.19 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4384/10000] (14.81GB) Downloading: TCGA-BRCA.1123e3e5-8125-432d-9246-195e8114be97.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4385/10000] (14.81GB) Downloading: TCGA-E9-A1NA-01A-01-TSA.54bbd049-8dd8-432e-b015-9325819ba587.svs (450.85 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.26 GB).\n",
+      "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "\n"
+     ]
+    },
+    {
+     "data": {
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+      },
+      "text/plain": [
+       "Processing Files (0 / 0): |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
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+      },
+      "text/plain": [
+       "New Data Upload: |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Lỗi khi Upload: 503 Server Error: Service Unavailable for url: https://huggingface.co/api/datasets/enzosama154/BRCancer/commit/main\n",
+      "[4386/10000] (15.26GB) Downloading: TCGA-BRCA.06885aa5-33ae-4eab-ae31-f5f9c9b16480.ascat2.allelic_specific.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.26 GB).\n",
+      "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "\n"
+     ]
+    },
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+     "data": {
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+       "Processing Files (0 / 0): |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
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+    {
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+6768d75c-08fa-4de4-8d68-2508de2d6686	8	75201954	144182542	40453	-0.0018
+6768d75c-08fa-4de4-8d68-2508de2d6686	9	789794	138044505	68457	-0.0012
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	366509	1880921	709	-0.0071
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	1881008	1881021	2	-1.4957
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	1881202	123550999	74907	0.0027
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	123551144	123551956	2	-1.4596
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	123553390	123563319	11	-0.233
+6768d75c-08fa-4de4-8d68-2508de2d6686	10	123563813	133411599	5650	-0.0061
+6768d75c-08fa-4de4-8d68-2508de2d6686	11	456012	23968501	15293	0.0011
+6768d75c-08fa-4de4-8d68-2508de2d6686	11	23969458	23970694	2	-1.589
+6768d75c-08fa-4de4-8d68-2508de2d6686	11	23971111	134272740	62236	0.0021
+6768d75c-08fa-4de4-8d68-2508de2d6686	12	780472	10962425	5572	0.0072
+6768d75c-08fa-4de4-8d68-2508de2d6686	12	10966407	10967854	6	-1.0406
+6768d75c-08fa-4de4-8d68-2508de2d6686	12	10972872	132605822	68751	0.0032
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	18874255	30999503	7364	0.001
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	31000104	31000114	2	-1.3758
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	31000952	88768399	33091	0.0025
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	88768642	88769489	2	-1.3029
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	88772056	89112208	160	0.0326
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	89112482	89114094	6	-0.5004
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	89118320	89298088	72	0.0492
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	89298442	89298832	2	-1.2925
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	89300554	92961429	2298	0.0091
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	92962461	92970987	2	-1.3182
+6768d75c-08fa-4de4-8d68-2508de2d6686	13	92971100	114226675	13970	-0.0021
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	20033191	71994443	29052	0.0023
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	71994564	71994581	2	-1.2705
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	71995485	72467083	456	-0.0163
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	72469977	72470246	2	-1.0657
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	72470412	79757711	4649	0.0016
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	79760880	79762709	2	-1.2956
+6768d75c-08fa-4de4-8d68-2508de2d6686	14	79765171	105533894	15605	0.0034
+6768d75c-08fa-4de4-8d68-2508de2d6686	15	23437561	59098504	19361	-0.0007
+6768d75c-08fa-4de4-8d68-2508de2d6686	15	59099645	59100812	2	-2.3216
+6768d75c-08fa-4de4-8d68-2508de2d6686	15	59109021	101344124	25413	-0.0029
+6768d75c-08fa-4de4-8d68-2508de2d6686	16	603333	89317317	41185	-0.0048
+6768d75c-08fa-4de4-8d68-2508de2d6686	17	1074619	82959812	37277	-0.0023
+6768d75c-08fa-4de4-8d68-2508de2d6686	18	326691	79349796	42948	0.0001
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	283868	16702881	6438	0.0117
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	16704096	16704882	3	-1.0221
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	16706196	33564863	6743	-0.0002
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	33568111	33568135	2	-1.2059
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	33570032	35577160	1314	-0.0069
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	35578730	35578887	2	-1.3231
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	35579114	50600126	6305	0.0075
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	50606536	50610660	2	-1.5725
+6768d75c-08fa-4de4-8d68-2508de2d6686	19	50621474	58370362	3342	0.0089
+6768d75c-08fa-4de4-8d68-2508de2d6686	20	472817	56298651	32677	0.0007
+6768d75c-08fa-4de4-8d68-2508de2d6686	20	56298681	56298703	2	-2.038
+6768d75c-08fa-4de4-8d68-2508de2d6686	20	56300476	63588502	4862	-0.0076
+6768d75c-08fa-4de4-8d68-2508de2d6686	21	13974127	16235733	1380	-0.0021
+6768d75c-08fa-4de4-8d68-2508de2d6686	21	16238872	16261525	13	-0.5504
+6768d75c-08fa-4de4-8d68-2508de2d6686	21	16261816	46262057	19188	-0.0024
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	16934932	17593757	390	0.0004
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	17596752	17597388	2	-1.0909
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	17598370	41849115	11841	0.0005
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	41849665	41849786	3	-1.025
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	41855723	45028479	1989	-0.0175
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	45029654	45029860	3	-1.165
+6768d75c-08fa-4de4-8d68-2508de2d6686	22	45029963	48940621	2853	-0.0141
+6768d75c-08fa-4de4-8d68-2508de2d6686	X	3236359	155677414	63940	0.0009

data/gdc_data_organized/06ef6e83-5583-45b9-a0bd-edea68943083/TCGA-BRCA.bdeb88bb-5ce8-4221-988e-1386605e693f.ascat3.allelic_specific.seg.txt

@@ -0,0 +1,42 @@
+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr1	61735	248930189	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr2	12784	242147305	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr3	18667	198169247	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr4	12281	190106768	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr5	15532	181363319	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr6	149661	58416362	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr6	58432750	79453425	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr6	79454602	79470403	0	0	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr6	79471226	170741917	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr7	43259	159334314	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr8	81254	145072769	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr9	46587	138200944	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr10	26823	133769379	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	198572	50560016	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	50561088	57774617	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	57775721	58257567	3	2	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	58257960	58266216	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	58272821	58650488	2	2	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	58653538	60728348	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	60731810	61902474	3	2	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	61902827	65903039	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	65906669	65935152	6	4	2
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	65936447	65936447	2	2	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	65941956	66318501	5	4	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	66320152	69075127	3	2	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	69079537	70195663	5	4	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr11	70198918	135074876	1	1	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr12	51460	133201603	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr13	18452809	114342922	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr14	18225647	40033056	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr14	40035087	40046851	0	0	0
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr14	40049637	106877229	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr15	19811075	101928837	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr16	10777	90221127	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr17	150733	83090856	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr18	48133	80257174	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr19	90910	58586487	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr20	80664	64324800	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr21	10336543	46677045	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chr22	15294545	50796027	2	1	1
+bdeb88bb-5ce8-4221-988e-1386605e693f	chrX	251810	156004181	2	1	1

data/gdc_data_organized/06ef6e83-5583-45b9-a0bd-edea68943083/TCGA-E2-A572-01A-11D-A89D-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt

@@ -0,0 +1,483 @@
+GDC_Aliquot_ID	Chromosome	Start	End	Num_Probes	Segment_Mean
+TCGA-E2-A572-01A-11D-A89D-36	chr1	17001	16534000	15133	-0.043259
+TCGA-E2-A572-01A-11D-A89D-36	chr1	16534001	16720000	114	-0.136203
+TCGA-E2-A572-01A-11D-A89D-36	chr1	16720001	16949000	129	-0.639686
+TCGA-E2-A572-01A-11D-A89D-36	chr1	16949001	59225000	41964	-0.025808
+TCGA-E2-A572-01A-11D-A89D-36	chr1	59225001	115684000	55643	0.014026
+TCGA-E2-A572-01A-11D-A89D-36	chr1	115684001	115690000	6	-29.690185
+TCGA-E2-A572-01A-11D-A89D-36	chr1	115690001	120672000	4380	0.009942
+TCGA-E2-A572-01A-11D-A89D-36	chr1	120805001	120860000	8	-1.337944
+TCGA-E2-A572-01A-11D-A89D-36	chr1	120878001	121743000	283	0.012157
+TCGA-E2-A572-01A-11D-A89D-36	chr1	121743001	122706000	24	-0.697317
+TCGA-E2-A572-01A-11D-A89D-36	chr1	122709001	122731000	2	-5.946607
+TCGA-E2-A572-01A-11D-A89D-36	chr1	122741001	122799000	7	0.652088
+TCGA-E2-A572-01A-11D-A89D-36	chr1	122806001	122901000	15	-1.029715
+TCGA-E2-A572-01A-11D-A89D-36	chr1	122904001	122905000	1	-5.900644
+TCGA-E2-A572-01A-11D-A89D-36	chr1	122912001	123467000	61	-0.324221
+TCGA-E2-A572-01A-11D-A89D-36	chr1	123507001	123532000	9	-3.872705
+TCGA-E2-A572-01A-11D-A89D-36	chr1	123535001	123551000	3	1.519684
+TCGA-E2-A572-01A-11D-A89D-36	chr1	123551001	123721000	22	-2.379507
+TCGA-E2-A572-01A-11D-A89D-36	chr1	123742001	124069000	36	-1.414193
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124069001	124070000	1	-9.908066
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124096001	124207000	17	0.261675
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124216001	124330000	19	-1.051397
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124343001	124352000	2	-3.962094
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124364001	124439000	16	-1.981807
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124446001	124539000	20	-0.510590
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124544001	124545000	1	-6.419867
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124552001	124556000	2	2.328794
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124562001	124584000	6	-1.734729
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124590001	124592000	2	2.649395
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124597001	124598000	1	-4.499077
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124599001	124613000	5	0.882813
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124613001	124706000	21	-1.652367
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124712001	124716000	4	-5.292481
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124722001	124909000	28	-0.242524
+TCGA-E2-A572-01A-11D-A89D-36	chr1	124925001	143505000	322	0.023714
+TCGA-E2-A572-01A-11D-A89D-36	chr1	143529001	144105000	245	-0.799033
+TCGA-E2-A572-01A-11D-A89D-36	chr1	144140001	248931000	99759	0.013916
+TCGA-E2-A572-01A-11D-A89D-36	chr2	11001	9784000	9665	-0.002993
+TCGA-E2-A572-01A-11D-A89D-36	chr2	9784001	9789000	5	-0.093848
+TCGA-E2-A572-01A-11D-A89D-36	chr2	9789001	41014000	31022	0.006986
+TCGA-E2-A572-01A-11D-A89D-36	chr2	41014001	41023000	9	-14.430242
+TCGA-E2-A572-01A-11D-A89D-36	chr2	41023001	242159000	192195	0.008992
+TCGA-E2-A572-01A-11D-A89D-36	chr3	12001	186000	171	0.030624
+TCGA-E2-A572-01A-11D-A89D-36	chr3	186001	193000	7	-0.054239
+TCGA-E2-A572-01A-11D-A89D-36	chr3	193001	46754000	46325	0.006947
+TCGA-E2-A572-01A-11D-A89D-36	chr3	46754001	46810000	48	-0.741440
+TCGA-E2-A572-01A-11D-A89D-36	chr3	46810001	51142000	4314	-0.001628
+TCGA-E2-A572-01A-11D-A89D-36	chr3	51142001	52831000	1685	-0.109195
+TCGA-E2-A572-01A-11D-A89D-36	chr3	52831001	75375000	22434	0.003089
+TCGA-E2-A572-01A-11D-A89D-36	chr3	75375001	75593000	192	-0.974555
+TCGA-E2-A572-01A-11D-A89D-36	chr3	75593001	90889000	15003	0.018196
+TCGA-E2-A572-01A-11D-A89D-36	chr3	90896001	90942000	6	-1.679987
+TCGA-E2-A572-01A-11D-A89D-36	chr3	91152001	195493000	101184	0.012091
+TCGA-E2-A572-01A-11D-A89D-36	chr3	195493001	195507000	3	-2.502051
+TCGA-E2-A572-01A-11D-A89D-36	chr3	195507001	195619000	112	0.000894
+TCGA-E2-A572-01A-11D-A89D-36	chr3	195619001	195727000	81	-0.396406
+TCGA-E2-A572-01A-11D-A89D-36	chr3	195727001	195751000	24	0.148961
+TCGA-E2-A572-01A-11D-A89D-36	chr3	195751001	197618000	1830	0.003037
+TCGA-E2-A572-01A-11D-A89D-36	chr3	197618001	197657000	27	-0.323811
+TCGA-E2-A572-01A-11D-A89D-36	chr3	197657001	198175000	483	0.010922
+TCGA-E2-A572-01A-11D-A89D-36	chr4	15001	8950000	8752	-0.011549
+TCGA-E2-A572-01A-11D-A89D-36	chr4	8950001	9485000	298	0.551400
+TCGA-E2-A572-01A-11D-A89D-36	chr4	9485001	9613000	127	0.022237
+TCGA-E2-A572-01A-11D-A89D-36	chr4	9618001	9622000	4	-8.304020
+TCGA-E2-A572-01A-11D-A89D-36	chr4	9622001	9627000	5	-7.085881
+TCGA-E2-A572-01A-11D-A89D-36	chr4	9627001	9631000	4	-7.267298
+TCGA-E2-A572-01A-11D-A89D-36	chr4	9631001	21104000	11344	0.009924
+TCGA-E2-A572-01A-11D-A89D-36	chr4	21104001	21112000	8	-1.425559
+TCGA-E2-A572-01A-11D-A89D-36	chr4	21112001	49098000	27851	0.013720
+TCGA-E2-A572-01A-11D-A89D-36	chr4	49098001	49166000	59	0.113541
+TCGA-E2-A572-01A-11D-A89D-36	chr4	49166001	49289000	86	0.257029
+TCGA-E2-A572-01A-11D-A89D-36	chr4	49296001	49640000	128	0.831401
+TCGA-E2-A572-01A-11D-A89D-36	chr4	49640001	50663000	22	-0.308601
+TCGA-E2-A572-01A-11D-A89D-36	chr4	50679001	50680000	1	-5.705013
+TCGA-E2-A572-01A-11D-A89D-36	chr4	51059001	69258000	17113	0.017429
+TCGA-E2-A572-01A-11D-A89D-36	chr4	69260001	69366000	103	-0.638249
+TCGA-E2-A572-01A-11D-A89D-36	chr4	69366001	119406000	49656	0.014894
+TCGA-E2-A572-01A-11D-A89D-36	chr4	119406001	119462000	33	-0.093422
+TCGA-E2-A572-01A-11D-A89D-36	chr4	119462001	190204000	69985	0.022287
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+TCGA-E2-A572-01A-11D-A89D-36	chr22	38992001	50796000	11703	-0.010867
+TCGA-E2-A572-01A-11D-A89D-36	chrX	251001	832000	538	0.013012
+TCGA-E2-A572-01A-11D-A89D-36	chrX	832001	850000	16	-0.992694
+TCGA-E2-A572-01A-11D-A89D-36	chrX	850001	9407000	1682	0.016782
+TCGA-E2-A572-01A-11D-A89D-36	chrX	9409001	141052000	58	0.560348
+TCGA-E2-A572-01A-11D-A89D-36	chrX	141514001	156026000	314	0.024807
+TCGA-E2-A572-01A-11D-A89D-36	chrY	6534001	10658000	12	-0.514043
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10660001	10679000	11	-3.613820
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10683001	10693000	3	-2.924431
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10755001	10809000	8	-1.037694
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10821001	10861000	2	-5.709853
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10863001	10867000	2	-0.946788
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10869001	10922000	4	-3.644042
+TCGA-E2-A572-01A-11D-A89D-36	chrY	10926001	11118000	24	-0.362291
+TCGA-E2-A572-01A-11D-A89D-36	chrY	11123001	11278000	5	-2.122876
+TCGA-E2-A572-01A-11D-A89D-36	chrY	11289001	11319000	20	0.099798
+TCGA-E2-A572-01A-11D-A89D-36	chrY	11319001	11410000	34	-0.556790
+TCGA-E2-A572-01A-11D-A89D-36	chrY	11414001	11556000	5	-5.537099
+TCGA-E2-A572-01A-11D-A89D-36	chrY	11643001	26442000	16	-0.489453
+TCGA-E2-A572-01A-11D-A89D-36	chrY	26638001	56708000	6	-8.258029
+TCGA-E2-A572-01A-11D-A89D-36	chrY	56821001	56887000	66	0.195943
+TCGA-E2-A572-01A-11D-A89D-36	chrM	1	16569	17	0.954676

data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/6525a77a-cdff-456a-857d-ebf5ea6a880d.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	17493	8034.963782	N
+hsa-let-7a-2	17380	7983.060112	N
+hsa-let-7a-3	17785	8169.086541	N
+hsa-let-7b	100533	46177.271704	N
+hsa-let-7c	6653	3055.886014	N
+hsa-let-7d	1429	656.374735	N
+hsa-let-7e	3865	1775.289260	N
+hsa-let-7f-1	3652	1677.453137	N
+hsa-let-7f-2	3632	1668.266647	N
+hsa-let-7g	1840	845.157112	N
+hsa-let-7i	1134	520.874003	N
+hsa-mir-1-1	2	0.918649	N
+hsa-mir-1-2	4	1.837298	N
+hsa-mir-100	4243	1948.913927	N
+hsa-mir-101-1	9511	4368.635485	N
+hsa-mir-101-2	9572	4396.654280	N
+hsa-mir-103a-1	27171	12480.306461	Y
+hsa-mir-103a-2	26971	12388.441558	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	1	0.459325	N
+hsa-mir-105-2	3	1.377974	N
+hsa-mir-106a	80	36.745961	Y
+hsa-mir-106b	650	298.560936	N
+hsa-mir-107	131	60.171512	Y
+hsa-mir-10a	14582	6697.870112	N
+hsa-mir-10b	45448	20875.380665	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	78	35.827312	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	17	7.808517	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	2	0.918649	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	1	0.459325	N
+hsa-mir-1229	1	0.459325	N
+hsa-mir-1231	1	0.459325	N
+hsa-mir-1233-1	0	0.000000	N
+hsa-mir-1233-2	0	0.000000	N
+hsa-mir-1234	1	0.459325	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	22	10.105139	N
+hsa-mir-1245b	0	0.000000	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	84	38.583259	N
+hsa-mir-1248	8	3.674596	N
+hsa-mir-1249	5	2.296623	N
+hsa-mir-1250	0	0.000000	N
+hsa-mir-1251	47	21.588252	N
+hsa-mir-1252	0	0.000000	N
+hsa-mir-1253	0	0.000000	N
+hsa-mir-1254-1	1	0.459325	N
+hsa-mir-1254-2	3	1.377974	N
+hsa-mir-1255a	3	1.377974	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	2	0.918649	N
+hsa-mir-125a	3060	1405.533023	N
+hsa-mir-125b-1	661	303.613506	N
+hsa-mir-125b-2	692	317.852566	N
+hsa-mir-126	5451	2503.777944	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	0.459325	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	23	10.564464	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	7	3.215272	N
+hsa-mir-1269b	4	1.837298	N
+hsa-mir-127	1701	781.311004	N
+hsa-mir-1270	9	4.133921	N
+hsa-mir-1271	6	2.755947	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	4	1.837298	N
+hsa-mir-1276	1	0.459325	N
+hsa-mir-1277	5	2.296623	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	407	186.945079	N
+hsa-mir-128-2	260	119.424375	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	4	1.837298	N
+hsa-mir-1285-1	0	0.000000	N
+hsa-mir-1285-2	0	0.000000	N
+hsa-mir-1286	1	0.459325	N
+hsa-mir-1287	109	50.066372	N
+hsa-mir-1288	3	1.377974	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	0.459325	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	2	0.918649	N
+hsa-mir-1292	2	0.918649	N
+hsa-mir-1293	0	0.000000	N
+hsa-mir-1294	1	0.459325	N
+hsa-mir-1295a	1	0.459325	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	10	4.593245	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	40	18.372981	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	0	0.000000	N
+hsa-mir-1305	0	0.000000	N
+hsa-mir-1306	23	10.564464	N
+hsa-mir-1307	1698	779.933030	N
+hsa-mir-130a	358	164.438177	N
+hsa-mir-130b	33	15.157709	N
+hsa-mir-132	134	61.549485	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	2	0.918649	N
+hsa-mir-133a-2	0	0.000000	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	1184	543.840229	N
+hsa-mir-1343	1	0.459325	N
+hsa-mir-135a-1	80	36.745961	N
+hsa-mir-135a-2	102	46.851101	N
+hsa-mir-135b	10	4.593245	N
+hsa-mir-136	58	26.640822	N
+hsa-mir-137	0	0.000000	N
+hsa-mir-138-1	1	0.459325	N
+hsa-mir-138-2	0	0.000000	N
+hsa-mir-139	56	25.722173	N
+hsa-mir-140	999	458.865193	N
+hsa-mir-141	5563	2555.222290	N
+hsa-mir-142	4394	2018.271929	N
+hsa-mir-143	35244	16188.433290	N
+hsa-mir-144	16	7.349192	N
+hsa-mir-145	2999	1377.514228	N
+hsa-mir-1468	2	0.918649	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	212	97.376798	N
+hsa-mir-146b	1725	792.334792	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	7	3.215272	N
+hsa-mir-148a	120581	55385.809628	N
+hsa-mir-148b	1488	683.474882	N
+hsa-mir-149	172	79.003817	N
+hsa-mir-150	56	25.722173	N
+hsa-mir-151a	5446	2501.481322	N
+hsa-mir-151b	4	1.837298	N
+hsa-mir-152	1100	505.256969	N
+hsa-mir-153-1	0	0.000000	N
+hsa-mir-153-2	32	14.698385	N
+hsa-mir-1537	0	0.000000	N
+hsa-mir-1538	0	0.000000	N
+hsa-mir-1539	0	0.000000	N
+hsa-mir-154	16	7.349192	N
+hsa-mir-155	576	264.570922	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	558	256.303081	N
+hsa-mir-15b	664	304.991480	N
+hsa-mir-16-1	1913	878.687802	N
+hsa-mir-16-2	2037	935.644042	N
+hsa-mir-17	1149	527.763870	Y
+hsa-mir-181a-1	1667	765.693970	N
+hsa-mir-181a-2	3985	1830.408202	N
+hsa-mir-181b-1	378	173.624668	N
+hsa-mir-181b-2	348	159.844932	N
+hsa-mir-181c	488	224.150364	N
+hsa-mir-181d	177	81.300440	N
+hsa-mir-182	92557	42513.699354	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	41649	19130.406824	N
+hsa-mir-184	114	52.362995	N
+hsa-mir-185	168	77.166519	N
+hsa-mir-186	1000	459.324517	N
+hsa-mir-187	23	10.564464	N
+hsa-mir-188	5	2.296623	N
+hsa-mir-18a	18	8.267841	N
+hsa-mir-18b	1	0.459325	N
+hsa-mir-1908	1	0.459325	N
+hsa-mir-1909	0	0.000000	N
+hsa-mir-190a	8	3.674596	N
+hsa-mir-190b	71	32.612041	N
+hsa-mir-191	5554	2551.088369	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	1704	782.688978	Y
+hsa-mir-193a	924	424.415854	N
+hsa-mir-193b	348	159.844932	N
+hsa-mir-194-1	224	102.888692	N
+hsa-mir-194-2	238	109.319235	N
+hsa-mir-195	241	110.697209	N
+hsa-mir-196a-1	2095	962.284864	N
+hsa-mir-196a-2	2754	1264.979721	N
+hsa-mir-196b	856	393.181787	N
+hsa-mir-197	808	371.134210	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	12	5.511894	N
+hsa-mir-198	0	0.000000	N
+hsa-mir-199a-1	6911	3174.391740	Y
+hsa-mir-199a-2	11750	5397.063079	Y
+hsa-mir-199b	15108	6939.474808	Y
+hsa-mir-19a	110	50.525697	N
+hsa-mir-19b-1	207	95.080175	N
+hsa-mir-19b-2	193	88.649632	N
+hsa-mir-200a	3328	1528.631994	N
+hsa-mir-200b	2272	1043.585303	N
+hsa-mir-200c	24665	11329.239221	N
+hsa-mir-202	0	0.000000	N
+hsa-mir-203a	9620	4418.701857	N
+hsa-mir-203b	162	74.410572	N
+hsa-mir-204	2	0.918649	N
+hsa-mir-205	2899	1331.581776	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	38	17.454332	N
+hsa-mir-208a	0	0.000000	N
+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	382	175.461966	N
+hsa-mir-20b	63	28.937445	N
+hsa-mir-21	517157	237542.889427	N
+hsa-mir-210	5200	2388.487490	N
+hsa-mir-211	0	0.000000	N
+hsa-mir-2110	17	7.808517	N
+hsa-mir-2113	0	0.000000	N
+hsa-mir-2114	0	0.000000	N
+hsa-mir-2115	0	0.000000	N
+hsa-mir-2116	0	0.000000	N
+hsa-mir-2117	0	0.000000	N
+hsa-mir-212	11	5.052570	N
+hsa-mir-214	154	70.735976	N
+hsa-mir-215	9	4.133921	Y
+hsa-mir-216a	1	0.459325	N
+hsa-mir-216b	0	0.000000	N
+hsa-mir-217	60	27.559471	N
+hsa-mir-218-1	28	12.861086	N
+hsa-mir-218-2	20	9.186490	N
+hsa-mir-219a-1	5	2.296623	N
+hsa-mir-219a-2	0	0.000000	N
+hsa-mir-219b	1	0.459325	N
+hsa-mir-22	146622	67347.079385	N
+hsa-mir-221	300	137.797355	N
+hsa-mir-222	225	103.348016	N
+hsa-mir-223	130	59.712187	N
+hsa-mir-224	12	5.511894	N
+hsa-mir-2276	1	0.459325	N
+hsa-mir-2277	0	0.000000	N
+hsa-mir-2278	0	0.000000	N
+hsa-mir-2355	87	39.961233	N
+hsa-mir-2392	0	0.000000	N
+hsa-mir-23a	14215	6529.298014	Y
+hsa-mir-23b	2663	1223.181190	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	2298	1055.527741	N
+hsa-mir-24-2	2522	1158.416433	N
+hsa-mir-2467	0	0.000000	N
+hsa-mir-25	15899	7302.800502	N
+hsa-mir-2681	0	0.000000	N
+hsa-mir-2682	0	0.000000	N
+hsa-mir-26a-1	3246	1490.967383	N
+hsa-mir-26a-2	3306	1518.526854	N
+hsa-mir-26b	2990	1373.380307	N
+hsa-mir-27a	5197	2387.109517	Y
+hsa-mir-27b	2245	1031.183541	Y
+hsa-mir-28	7318	3361.336818	N
+hsa-mir-2861	0	0.000000	N
+hsa-mir-2909	0	0.000000	N
+hsa-mir-296	6	2.755947	N
+hsa-mir-297	0	0.000000	N
+hsa-mir-298	0	0.000000	N
+hsa-mir-299	2	0.918649	N
+hsa-mir-29a	12516	5748.905659	N
+hsa-mir-29b-1	1247	572.777673	Y
+hsa-mir-29b-2	1569	720.680168	Y
+hsa-mir-29c	3788	1739.921272	Y
+hsa-mir-300	0	0.000000	N
+hsa-mir-301a	100	45.932452	N
+hsa-mir-301b	5	2.296623	N
+hsa-mir-302a	0	0.000000	N
+hsa-mir-302b	0	0.000000	N
+hsa-mir-302c	0	0.000000	N
+hsa-mir-302d	0	0.000000	N
+hsa-mir-302e	0	0.000000	N
+hsa-mir-302f	0	0.000000	N
+hsa-mir-3064	2	0.918649	N
+hsa-mir-3065	163	74.869896	N
+hsa-mir-3074	46	21.128928	N
+hsa-mir-30a	322115	147955.316911	Y
+hsa-mir-30b	2865	1315.964742	Y
+hsa-mir-30c-1	5330	2448.199678	Y
+hsa-mir-30c-2	5741	2636.982054	Y
+hsa-mir-30d	34048	15639.081167	N
+hsa-mir-30e	40604	18650.412703	Y
+hsa-mir-31	16	7.349192	N
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+hsa-mir-3130-2	2	0.918649	N
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+hsa-mir-323a	8	3.674596	N
+hsa-mir-323b	10	4.593245	N
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+hsa-mir-325	0	0.000000	N
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+hsa-mir-328	179	82.219089	N
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+hsa-mir-329-2	0	0.000000	N
+hsa-mir-330	42	19.291630	N
+hsa-mir-331	163	74.869896	N
+hsa-mir-335	243	111.615858	N
+hsa-mir-337	57	26.181497	N
+hsa-mir-338	598	274.676061	N
+hsa-mir-339	131	60.171512	N
+hsa-mir-33a	49	22.506901	N
+hsa-mir-33b	254	116.668427	N
+hsa-mir-340	63	28.937445	N
+hsa-mir-342	2003	920.027008	N
+hsa-mir-345	107	49.147723	N
+hsa-mir-346	1	0.459325	N
+hsa-mir-34a	791	363.325693	N
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+hsa-mir-34c	16	7.349192	N
+hsa-mir-3529	0	0.000000	N
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+hsa-mir-361	548	251.709836	N
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+hsa-mir-3612	0	0.000000	N
+hsa-mir-3613	41	18.832305	N
+hsa-mir-3614	2	0.918649	N
+hsa-mir-3615	3	1.377974	N
+hsa-mir-3616	0	0.000000	N
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+hsa-mir-3618	0	0.000000	N
+hsa-mir-3619	1	0.459325	N
+hsa-mir-362	16	7.349192	N
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+hsa-mir-3652	5	2.296623	N
+hsa-mir-3653	15	6.889868	N
+hsa-mir-3654	1	0.459325	N
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+hsa-mir-365b	229	105.185314	Y
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+hsa-mir-375	24572	11286.522041	N
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+hsa-mir-376a-2	3	1.377974	N
+hsa-mir-376b	1	0.459325	N
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+hsa-mir-3926-2	1	0.459325	N
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+hsa-mir-4441	0	0.000000	N
+hsa-mir-4442	3	1.377974	N
+hsa-mir-4443	1	0.459325	N
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+hsa-mir-450a-2	2	0.918649	N
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+hsa-mir-451a	64	29.396769	N
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+hsa-mir-4540	0	0.000000	N
+hsa-mir-455	919	422.119231	N
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+hsa-mir-4636	1	0.459325	N
+hsa-mir-4637	0	0.000000	N
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+hsa-mir-4639	1	0.459325	N
+hsa-mir-4640	2	0.918649	N
+hsa-mir-4641	0	0.000000	N
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+hsa-mir-4661	6	2.755947	N
+hsa-mir-4662a	41	18.832305	N
+hsa-mir-4662b	0	0.000000	N
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+hsa-mir-4664	5	2.296623	N
+hsa-mir-4665	1	0.459325	N
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+hsa-mir-4668	27	12.401762	N
+hsa-mir-4669	0	0.000000	N
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+hsa-mir-532	787	361.488395	N
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+hsa-mir-541	0	0.000000	N
+hsa-mir-542	218	100.132745	N
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+hsa-mir-545	4	1.837298	N
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+hsa-mir-548k	1	0.459325	N
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+hsa-mir-548m	0	0.000000	N
+hsa-mir-548n	0	0.000000	N
+hsa-mir-548o	1	0.459325	N
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+hsa-mir-548p	0	0.000000	N
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+hsa-mir-548s	0	0.000000	N
+hsa-mir-548t	1	0.459325	N
+hsa-mir-548u	0	0.000000	N
+hsa-mir-548v	1	0.459325	N
+hsa-mir-548w	0	0.000000	N
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+hsa-mir-548z	0	0.000000	N
+hsa-mir-549a	1	0.459325	N
+hsa-mir-550a-1	6	2.755947	N
+hsa-mir-550a-2	3	1.377974	N
+hsa-mir-550a-3	3	1.377974	N
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+hsa-mir-5681a	1	0.459325	Y
+hsa-mir-5681b	5	2.296623	Y
+hsa-mir-5682	0	0.000000	N
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+hsa-mir-5691	3	1.377974	N
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+hsa-mir-5694	1	0.459325	N
+hsa-mir-5695	4	1.837298	N
+hsa-mir-5696	0	0.000000	N
+hsa-mir-5697	0	0.000000	N
+hsa-mir-5698	2	0.918649	N
+hsa-mir-5699	3	1.377974	N
+hsa-mir-570	2	0.918649	N
+hsa-mir-5700	0	0.000000	N
+hsa-mir-5701-1	0	0.000000	N
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+hsa-mir-573	0	0.000000	N
+hsa-mir-5739	0	0.000000	N
+hsa-mir-574	235	107.941262	N
+hsa-mir-575	0	0.000000	N
+hsa-mir-576	14	6.430543	N
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+hsa-mir-578	0	0.000000	N
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+hsa-mir-582	555	254.925107	N
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+hsa-mir-585	0	0.000000	N
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+hsa-mir-588	0	0.000000	N
+hsa-mir-589	332	152.495740	N
+hsa-mir-590	32	14.698385	N
+hsa-mir-591	0	0.000000	N
+hsa-mir-592	12	5.511894	N
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+hsa-mir-598	15	6.889868	N
+hsa-mir-599	0	0.000000	N
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+hsa-mir-6074	0	0.000000	N
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+hsa-mir-615	92	42.257856	N
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+hsa-mir-619	0	0.000000	N
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+hsa-mir-625	450	206.696033	N
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+hsa-mir-628	214	98.295447	N
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+hsa-mir-640	0	0.000000	N
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+hsa-mir-642a	21	9.645815	N
+hsa-mir-642b	0	0.000000	N
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+hsa-mir-6509	3	1.377974	N
+hsa-mir-651	6	2.755947	N
+hsa-mir-6510	30	13.779736	N
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+hsa-mir-6511b-1	6	2.755947	N
+hsa-mir-6511b-2	2	0.918649	N
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+hsa-mir-6516	2	0.918649	N
+hsa-mir-652	79	36.286637	N
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+hsa-mir-655	1	0.459325	N
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+hsa-mir-657	0	0.000000	N
+hsa-mir-658	1	0.459325	N
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+hsa-mir-660	60	27.559471	N
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+hsa-mir-671	16	7.349192	N
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+hsa-mir-6765	0	0.000000	N
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+hsa-mir-6769b	0	0.000000	N
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+hsa-mir-6777	8	3.674596	N
+hsa-mir-6778	0	0.000000	N
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+hsa-mir-6781	1	0.459325	N
+hsa-mir-6782	0	0.000000	N
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+hsa-mir-6786	1	0.459325	N
+hsa-mir-6787	0	0.000000	N
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+hsa-mir-6789	0	0.000000	N
+hsa-mir-6790	0	0.000000	N
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+hsa-mir-6801	0	0.000000	N
+hsa-mir-6802	1	0.459325	N
+hsa-mir-6803	1	0.459325	N
+hsa-mir-6804	0	0.000000	N
+hsa-mir-6805	2	0.918649	N
+hsa-mir-6806	2	0.918649	N
+hsa-mir-6807	0	0.000000	N
+hsa-mir-6808	0	0.000000	N
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+hsa-mir-6811	1	0.459325	N
+hsa-mir-6812	0	0.000000	N
+hsa-mir-6813	0	0.000000	N
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+hsa-mir-6815	0	0.000000	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
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+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	2	0.918649	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	3	1.377974	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	0	0.000000	N
+hsa-mir-6843	1	0.459325	N
+hsa-mir-6844	1	0.459325	N
+hsa-mir-6845	0	0.000000	N
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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/653efe38-b379-4233-aea6-ce3428f50c78.wxs.aliquot_ensemble_masked.maf.gz

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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_A05_628560.nocnv_grch38.seg.v2.txt

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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H12_628496.grch38.seg.v2.txt

@@ -0,0 +1,1178 @@
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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H12_628496.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,212 @@
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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/TCGA-A8-A09T-01Z-00-DX1.4183BBA4-AF11-4602-9EC2-35083C34A393.svs

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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/TCGA-BRCA.63eeed5c-ee46-43e0-8886-3ad9b50634e3.ascat3.allelic_specific.seg.txt

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data/gdc_data_organized/0adf59c6-581a-475d-a2f4-40aa40060b5b/nationwidechildrens.org_clinical.TCGA-A8-A09T.xml

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+<?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">646390D9-E99B-412D-97C4-705FB43B7013</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="201949">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="201950" 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="201938">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="201929">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="201934">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">-25110</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">579</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="201936"/>
+        </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-A09T</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">A09T</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">0adf59c6-581a-475d-a2f4-40aa40060b5b</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="201939">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="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">68</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="201956">2009</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="201937"/>
+        <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="201935">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="201968"/>
+        <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="201981"/>
+        <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="201986"/>
+        <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="201951">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="201996"/>
+        <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="201965"/>
+        <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="201966"/>
+        <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="201959">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="201963" 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="201962"/>
+        <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="201960">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="201952">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="201953" 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="201933">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="201982">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="201967"/>
+        <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="201979"/>
+        <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="201989"/>
+        <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="201964"/>
+        <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="201961">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="201957"/>
+        <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="201958" 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="201992">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="201977">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="201987">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="201970"/>
+        <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="201969"/>
+        <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="201985"/>
+        <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="201980"/>
+        <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="201988"/>
+        <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="201990"/>
+        <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="201991"/>
+        <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="201995"/>
+        <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="201997"/>
+        <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="201998"/>
+        <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="201927">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="201928">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="201994"/>
+        <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="201975"/>
+            <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="201976"/>
+        </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="201978"/>
+        <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="201983"/>
+        <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="201999"/>
+        <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="202000"/>
+        <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="202001"/>
+        <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="202002"/>
+        <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="202003"/>
+        <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="202004"/>
+        <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="202009"/>
+        <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="202005"/>
+        <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="202006"/>
+        <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="202007"/>
+        <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="202008"/>
+        <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="202010"/>
+        <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="202011"/>
+        <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="202012"/>
+        <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="202013"/>
+        <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="202014"/>
+        <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="202016"/>
+        <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="202017"/>
+        <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="202018"/>
+        <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="202019"/>
+        <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="202020"/>
+        <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="202015"/>
+        <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="201993"/>
+        <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="201984"/>
+        <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="1079755">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="Discrepancy" restricted="false" source_system_identifier="201974"/>
+            <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="201971">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="201972">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="201973">MX</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="201925">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="201924">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="201926">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-A09T-F40329</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">C0DB6775-BC42-4631-9AAD-006977242B0E</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="2406804">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="2406805">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="2406806">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="2406807">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="2406808">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">579</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="2406817">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="2406818"/>
+                        <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="2406819"/>
+                        <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="2406820"/>
+                        <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="2406825"/>
+                        <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="2406830"/>
+                        <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="2406831"/>
+                        <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="2406832"/>
+                        <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="2406833"/>
+                        <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="2406834"/>
+                        <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="2406835"/>
+                        <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="2406836"/>
+                        <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="2406837"/>
+                        <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="2406838"/>
+                        <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="2406839"/>
+                        <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="2406840"/>
+                        <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="2406841"/>
+                        <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="2406842"/>
+                        <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="2406843"/>
+                        <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="2406844"/>
+                        <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="2406845"/>
+                        <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="2406846"/>
+                        <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="2406847"/>
+                        <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="2406848"/>
+                        <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="2406849"/>
+                        <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="2406850"/>
+                        <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="2406851"/>
+                        <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="2406852"/>
+                        <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="2406853"/>
+                        <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="2406854"/>
+                        <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="2406855"/>
+                    </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">17</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="2259131">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-A09T-D37898</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">BDD31916-FC21-4D48-B1B5-442465133D4B</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">122</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="2259134">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="2259132">Anastrozole</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" source_system_identifier="2259133"/>
+                <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="2259139">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="2259144" 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-A09T-R38191</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">3B9677B4-105D-478C-BB4A-25C46395FB94</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">61</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">92</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="2273831">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="2273833"/>
+                <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="Not Available" restricted="false" source_system_identifier="2273834"/>
+                <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="2273835"/>
+                <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="2273832">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="2273840">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="2273845">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>

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data/gdc_data_organized/0bf6e772-1aa1-4f54-9a50-c1414e2f22f3/PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H10_844874.grch38.seg.v2.txt

@@ -0,0 +1,553 @@
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data/gdc_data_organized/0bf6e772-1aa1-4f54-9a50-c1414e2f22f3/nationwidechildrens.org_clinical.TCGA-AR-A2LM.xml

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+<?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>
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+        <admin:batch_number xsd_ver="1.17">167.75.0</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>
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+        </admin:patient_withdrawal>
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+        <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
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+        <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="1480691">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="1480687">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="1480693">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">-18053</clin_shared:days_to_birth>
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+        <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">1218</clin_shared:days_to_last_followup>
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+        </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-AR-A2LM</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">AR</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A2LM</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">0BF6E772-1AA1-4F54-9A50-C1414E2F22F3</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="1480692">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">49</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="1501939">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="Completed" restricted="false" source_system_identifier="1480690">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="Not Available" restricted="false" source_system_identifier="1480700"/>
+        <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="1501951">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="1501952">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="Not Available" restricted="false" source_system_identifier="1501967"/>
+        <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="1501973"/>
+        <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="1501934">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="1501983"/>
+        <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="1501948">Sentinel lymph node biopsy plus axillary dissection</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="1501949"/>
+        <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="1501942">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="1501946" 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="1501945"/>
+        <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="1501943"/>
+        <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="1501935">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="1501936" 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="1480688">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="1501968">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="1501950">YES</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="1501964"/>
+        <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="1501965"/>
+        <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="1501976"/>
+        <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="1501947"/>
+        <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="1501944">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="1501940">Core needle biopsy</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="1501941" 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="1501979">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="1501962">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="1501974"/>
+        <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="1501954"/>
+        <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="1501953">1</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="1501972"/>
+        <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="1501966"/>
+        <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="1501975"/>
+        <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="1501977"/>
+        <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="1501978"/>
+        <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="1501982"/>
+        <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="1501984"/>
+        <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="1501985"/>
+        <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="1480662">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="1480663">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="1501981"/>
+        <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="1501960"/>
+            <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="1501961"/>
+        </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="Completed" restricted="false" source_system_identifier="1501963">70-79%</brca_shared:er_level_cell_percentage_category>
+        <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="Completed" restricted="false" source_system_identifier="1501969">70-79%</brca_shared:progesterone_receptor_level_cell_percent_category>
+        <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="1501986">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="1501987"/>
+        <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="1501988"/>
+        <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="1501990"/>
+        <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="1501991"/>
+        <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="1501992"/>
+        <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="1501993"/>
+        <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="1501999"/>
+        <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="1501994"/>
+        <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="1501996"/>
+        <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="1501997"/>
+        <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="1501998"/>
+        <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="1502000"/>
+        <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="1502001"/>
+        <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="1502002"/>
+        <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="1502003"/>
+        <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="1502004"/>
+        <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="1502006"/>
+        <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="1502007"/>
+        <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="1502008"/>
+        <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="1502009"/>
+        <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="1502010"/>
+        <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="1502005"/>
+        <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="1501980"/>
+        <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="1501970"/>
+        <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="1501971"/>
+        <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="1501955">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="1501959">Stage II</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="1501956">T1</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="1501957">N1</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="1501958">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="1480660">12</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="1480659">1</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="1480661">2012</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-AR-A2LM-F37336</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">D6D5F194-B9A7-44DB-B31C-AB8AF2E8F81B</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="2243987">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="2244009">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="2244010">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="2244011">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="2244012">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">1585</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="2244080">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="2244081"/>
+                        <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="2244082"/>
+                        <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="2244083"/>
+                        <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="2244088"/>
+                        <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="2244093"/>
+                        <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="2244094"/>
+                        <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="2244095"/>
+                        <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="2244096"/>
+                        <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="2244097"/>
+                        <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="2244098"/>
+                        <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="2244099"/>
+                        <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="2244100"/>
+                        <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="2244101"/>
+                        <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="2244102"/>
+                        <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="2244103"/>
+                        <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="2244104"/>
+                        <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="2244105"/>
+                        <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="2244106"/>
+                        <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="2244107"/>
+                        <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="2244108"/>
+                        <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="2244109"/>
+                        <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="2244110"/>
+                        <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="2244111"/>
+                        <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="2244112"/>
+                        <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="2244113"/>
+                        <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="2244114"/>
+                        <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="2244115"/>
+                        <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="2244116"/>
+                        <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="2244117"/>
+                        <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="2244118"/>
+                    </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">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>
+            </follow_up_v4.0: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-AR-A2LM-F71746</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">7E511158-49BC-41A4-B9B7-0A7639BED9D7</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="4135482">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="4135483">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="4135484">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="4135485">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="4135486">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">1935</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="4135495">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="4135496"/>
+                        <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="4135497"/>
+                        <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="4135498"/>
+                        <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="4135503"/>
+                        <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="4135508"/>
+                        <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="4135509"/>
+                        <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="4135510"/>
+                        <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="4135511"/>
+                        <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="4135512"/>
+                        <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="4135513"/>
+                        <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="4135514"/>
+                        <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="4135515"/>
+                        <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="4135516"/>
+                        <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="4135517"/>
+                        <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="4135518"/>
+                        <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="4135519"/>
+                        <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="4135520"/>
+                        <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="4135521"/>
+                        <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="4135522"/>
+                        <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="4135523"/>
+                        <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="4135524"/>
+                        <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="4135525"/>
+                        <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="4135526"/>
+                        <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="4135527"/>
+                        <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="4135528"/>
+                        <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="4135529"/>
+                        <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="4135530"/>
+                        <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="4135531"/>
+                        <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="4135532"/>
+                        <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="4135533"/>
+                    </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">30</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>
+            <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="2244161">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-AR-A2LM-D37338</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">AFF8E2B0-7981-4EDB-811C-11EBF3B60ED0</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="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">78</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">99</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="2244164">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="2244162">Docetaxel</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" source_system_identifier="2244163"/>
+                <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="2244169">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="Not Available" restricted="false" source_system_identifier="2244174"/>
+                <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="2244178">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-AR-A2LM-D37339</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">57372622-06C2-481D-8D49-98803E959075</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="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">78</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">141</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="2244181">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="2244179">Cytoxan</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" source_system_identifier="2244180"/>
+                <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="2244186">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="Not Available" restricted="false" source_system_identifier="2244191"/>
+                <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="2244408">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-AR-A2LM-D37345</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">955A2DF7-0D64-49CF-9A73-05F722680C2B</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="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">120</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">141</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="2244411">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="2244409">Abraxane</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" source_system_identifier="2244410"/>
+                <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="2244416">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="Not Available" restricted="false" source_system_identifier="2244421"/>
+                <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="2244425">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-AR-A2LM-D37346</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">F4D3BD0B-BC50-4E1A-A781-07B6C2A53B31</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="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">170</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">967</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="2244428">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="2244426">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="Not Available" restricted="false" source_system_identifier="2244427"/>
+                <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="2244433">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="Not Available" restricted="false" source_system_identifier="2244438"/>
+                <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/>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/0d146997-cfdc-4587-888c-e876fc455c80/fdfefe69-47d8-4d05-9bbc-7a066c02a802.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	21347	4863.225070	N
+hsa-let-7a-2	21375	4869.603966	N
+hsa-let-7a-3	21579	4916.078783	N
+hsa-let-7b	23331	5315.215445	N
+hsa-let-7c	5999	1366.678559	N
+hsa-let-7d	1037	236.246985	N
+hsa-let-7e	3903	889.172598	N
+hsa-let-7f-1	11268	2567.050175	N
+hsa-let-7f-2	11787	2685.287577	N
+hsa-let-7g	743	169.268573	N
+hsa-let-7i	1102	251.055138	N
+hsa-mir-1-1	8	1.822542	N
+hsa-mir-1-2	5	1.139089	N
+hsa-mir-100	5885	1340.707338	N
+hsa-mir-101-1	13626	3104.244381	N
+hsa-mir-101-2	13747	3131.810326	N
+hsa-mir-103a-1	89748	20446.185579	Y
+hsa-mir-103a-2	90055	20516.125622	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	259	59.004792	N
+hsa-mir-105-2	253	57.637886	N
+hsa-mir-106a	64	14.580335	Y
+hsa-mir-106b	1014	231.007178	N
+hsa-mir-107	136	30.983211	Y
+hsa-mir-10a	112522	25634.506549	N
+hsa-mir-10b	307069	69955.762353	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	16	3.645084	N
+hsa-mir-1181	1	0.227818	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	1	0.227818	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	1	0.227818	N
+hsa-mir-1224	1	0.227818	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	2	0.455635	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	2	0.455635	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	2	0.455635	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	17	3.872901	N
+hsa-mir-1245b	0	0.000000	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	43	9.796162	N
+hsa-mir-1248	2	0.455635	N
+hsa-mir-1249	2	0.455635	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	1	0.227818	N
+hsa-mir-1254-2	1	0.227818	N
+hsa-mir-1255a	1	0.227818	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	0.227818	N
+hsa-mir-125a	2798	637.434007	N
+hsa-mir-125b-1	785	178.836918	N
+hsa-mir-125b-2	866	197.290154	N
+hsa-mir-126	3593	818.549102	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	0.683453	N
+hsa-mir-1263	0	0.000000	N
+hsa-mir-1264	0	0.000000	N
+hsa-mir-1265	4	0.911271	N
+hsa-mir-1266	23	5.239808	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	1653	376.582707	N
+hsa-mir-1270	2	0.455635	N
+hsa-mir-1271	4	0.911271	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	2	0.455635	N
+hsa-mir-1277	1	0.227818	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	346	78.824934	N
+hsa-mir-128-2	158	35.995201	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	116	26.426857	N
+hsa-mir-1288	0	0.000000	N
+hsa-mir-1289-1	1	0.227818	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	2	0.455635	N
+hsa-mir-129-2	3	0.683453	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	1	0.227818	N
+hsa-mir-1292	2	0.455635	N
+hsa-mir-1293	0	0.000000	N
+hsa-mir-1294	0	0.000000	N
+hsa-mir-1295a	1	0.227818	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	9	2.050360	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	30	6.834532	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	2	0.455635	N
+hsa-mir-1305	0	0.000000	N
+hsa-mir-1306	7	1.594724	N
+hsa-mir-1307	4852	1105.371623	N
+hsa-mir-130a	115	26.199039	N
+hsa-mir-130b	18	4.100719	N
+hsa-mir-132	177	40.323738	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	5	1.139089	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	528	120.287761	N
+hsa-mir-1343	0	0.000000	N
+hsa-mir-135a-1	0	0.000000	N
+hsa-mir-135a-2	1	0.227818	N
+hsa-mir-135b	7	1.594724	N
+hsa-mir-136	83	18.908872	N
+hsa-mir-137	0	0.000000	N
+hsa-mir-138-1	2	0.455635	N
+hsa-mir-138-2	0	0.000000	N
+hsa-mir-139	138	31.438847	N
+hsa-mir-140	2201	501.426822	N
+hsa-mir-141	4159	947.493937	N
+hsa-mir-142	1867	425.335701	N
+hsa-mir-143	71673	16328.380120	N
+hsa-mir-144	53	12.074340	N
+hsa-mir-145	2465	561.570703	N
+hsa-mir-1468	19	4.328537	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	200	45.563546	N
+hsa-mir-146b	3594	818.776920	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	3	0.683453	N
+hsa-mir-148a	51295	11685.910430	N
+hsa-mir-148b	343	78.141481	N
+hsa-mir-149	795	181.115095	N
+hsa-mir-150	1265	288.189428	N
+hsa-mir-151a	5153	1173.944760	N
+hsa-mir-151b	3	0.683453	N
+hsa-mir-152	279	63.561147	N
+hsa-mir-153-1	1	0.227818	N
+hsa-mir-153-2	18	4.100719	N
+hsa-mir-1537	1	0.227818	N
+hsa-mir-1538	0	0.000000	N
+hsa-mir-1539	0	0.000000	N
+hsa-mir-154	16	3.645084	N
+hsa-mir-155	796	181.342913	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	609	138.740997	N
+hsa-mir-15b	592	134.868096	N
+hsa-mir-16-1	275	62.649876	N
+hsa-mir-16-2	274	62.422058	N
+hsa-mir-17	1356	308.920841	Y
+hsa-mir-181a-1	4844	1103.549081	N
+hsa-mir-181a-2	4473	1019.028704	N
+hsa-mir-181b-1	798	181.798548	N
+hsa-mir-181b-2	768	174.964016	N
+hsa-mir-181c	141	32.122300	N
+hsa-mir-181d	38	8.657074	N
+hsa-mir-182	725193	165211.822647	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	256796	58502.681642	N
+hsa-mir-184	47	10.707433	N
+hsa-mir-185	200	45.563546	N
+hsa-mir-186	770	175.419652	N
+hsa-mir-187	23	5.239808	N
+hsa-mir-188	3	0.683453	N
+hsa-mir-18a	29	6.606714	N
+hsa-mir-18b	0	0.000000	N
+hsa-mir-1908	0	0.000000	N
+hsa-mir-1909	0	0.000000	N
+hsa-mir-190a	11	2.505995	N
+hsa-mir-190b	56	12.757793	N
+hsa-mir-191	1770	403.237381	N
+hsa-mir-1910	2	0.455635	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	3	0.683453	N
+hsa-mir-1915	0	0.000000	N
+hsa-mir-192	1013	230.779360	Y
+hsa-mir-193a	1030	234.652261	N
+hsa-mir-193b	158	35.995201	N
+hsa-mir-194-1	385	87.709826	N
+hsa-mir-194-2	429	97.733806	N
+hsa-mir-195	54	12.302157	N
+hsa-mir-196a-1	988	225.083917	N
+hsa-mir-196a-2	1197	272.697822	N
+hsa-mir-196b	248	56.498797	N
+hsa-mir-197	1004	228.729000	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	11	2.505995	N
+hsa-mir-198	0	0.000000	N
+hsa-mir-199a-1	5729	1305.167772	Y
+hsa-mir-199a-2	8203	1868.788834	Y
+hsa-mir-199b	8535	1944.424321	Y
+hsa-mir-19a	75	17.086330	N
+hsa-mir-19b-1	177	40.323738	N
+hsa-mir-19b-2	144	32.805753	N
+hsa-mir-200a	1624	369.975993	N
+hsa-mir-200b	1371	312.338107	N
+hsa-mir-200c	52757	12018.979951	N
+hsa-mir-202	1	0.227818	N
+hsa-mir-203a	67119	15290.898181	N
+hsa-mir-203b	1443	328.740984	N
+hsa-mir-204	6	1.366906	N
+hsa-mir-205	1713	390.251770	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
+hsa-mir-208a	0	0.000000	N
+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	966	220.071927	N
+hsa-mir-20b	33	7.517985	N
+hsa-mir-21	1582589	360541.832575	N
+hsa-mir-210	76	17.314147	N
+hsa-mir-211	0	0.000000	N
+hsa-mir-2110	2	0.455635	N
+hsa-mir-2113	0	0.000000	N
+hsa-mir-2114	1	0.227818	N
+hsa-mir-2115	1	0.227818	N
+hsa-mir-2116	2	0.455635	N
+hsa-mir-2117	1	0.227818	N
+hsa-mir-212	2	0.455635	N
+hsa-mir-214	76	17.314147	N
+hsa-mir-215	4	0.911271	Y
+hsa-mir-216a	0	0.000000	N
+hsa-mir-216b	0	0.000000	N
+hsa-mir-217	26	5.923261	N
+hsa-mir-218-1	83	18.908872	N
+hsa-mir-218-2	56	12.757793	N
+hsa-mir-219a-1	11	2.505995	N
+hsa-mir-219a-2	0	0.000000	N
+hsa-mir-219b	4	0.911271	N
+hsa-mir-22	176928	40307.335230	N
+hsa-mir-221	327	74.496398	N
+hsa-mir-222	90	20.503596	N
+hsa-mir-223	335	76.318939	N
+hsa-mir-224	24	5.467626	N
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+hsa-mir-23b	816	185.899267	Y
+hsa-mir-23c	0	0.000000	N
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+hsa-mir-24-2	876	199.568331	N
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+hsa-mir-25	38160	8693.524554	N
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+hsa-mir-2682	0	0.000000	N
+hsa-mir-26a-1	1477	336.486786	N
+hsa-mir-26a-2	1513	344.688225	N
+hsa-mir-26b	1117	254.472404	N
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+hsa-mir-27b	827	188.405262	Y
+hsa-mir-28	12443	2834.736007	N
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+hsa-mir-299	13	2.961630	N
+hsa-mir-29a	7159	1630.947125	N
+hsa-mir-29b-1	502	114.364500	N
+hsa-mir-29b-2	658	149.904066	N
+hsa-mir-29c	3182	724.916015	N
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+hsa-mir-3064	2	0.455635	N
+hsa-mir-3065	69	15.719423	N
+hsa-mir-3074	59	13.441246	N
+hsa-mir-30a	218190	49707.550381	Y
+hsa-mir-30b	843	192.050346	N
+hsa-mir-30c-1	1518	345.827313	N
+hsa-mir-30c-2	1691	385.239780	N
+hsa-mir-30d	25137	5726.654264	N
+hsa-mir-30e	32920	7499.759652	Y
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+hsa-mir-3127	57	12.985611	N
+hsa-mir-3128	1	0.227818	N
+hsa-mir-3129	1	0.227818	N
+hsa-mir-3130-1	7	1.594724	N
+hsa-mir-3130-2	5	1.139089	N
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+hsa-mir-3171	0	0.000000	N
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+hsa-mir-3180-4	1	0.227818	N
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+hsa-mir-3199-2	2	0.455635	N
+hsa-mir-32	64	14.580335	N
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+hsa-mir-320a	1808	411.894455	Y
+hsa-mir-320b-1	0	0.000000	N
+hsa-mir-320b-2	3	0.683453	Y
+hsa-mir-320c-1	3	0.683453	N
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+hsa-mir-324	73	16.630694	N
+hsa-mir-325	0	0.000000	N
+hsa-mir-326	8	1.822542	N
+hsa-mir-328	37	8.429256	N
+hsa-mir-329-1	4	0.911271	N
+hsa-mir-329-2	3	0.683453	N
+hsa-mir-330	98	22.326137	N
+hsa-mir-331	61	13.896881	N
+hsa-mir-335	345	78.597117	N
+hsa-mir-337	88	20.047960	N
+hsa-mir-338	837	190.683440	N
+hsa-mir-339	128	29.160669	N
+hsa-mir-33a	7	1.594724	N
+hsa-mir-33b	1	0.227818	N
+hsa-mir-340	158	35.995201	N
+hsa-mir-342	1374	313.021560	N
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+hsa-mir-346	0	0.000000	N
+hsa-mir-34a	377	85.887284	N
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+hsa-mir-361	1289	293.657053	N
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+hsa-mir-3651	1	0.227818	N
+hsa-mir-3652	2	0.455635	N
+hsa-mir-3653	25	5.695443	N
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+hsa-mir-3912	2	0.455635	N
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+hsa-mir-3913-2	6	1.366906	N
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+hsa-mir-412	4	0.911271	N
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+hsa-mir-422a	0	0.000000	N
+hsa-mir-423	378	86.115102	N
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+hsa-mir-431	66	15.035970	N
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+hsa-mir-509-2	3	0.683453	N
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+hsa-mir-514a-2	5	1.139089	N
+hsa-mir-514a-3	10	2.278177	N
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+hsa-mir-7-1	96	21.870502	N
+hsa-mir-7-2	3	0.683453	N
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+hsa-mir-765	1	0.227818	N
+hsa-mir-766	18	4.100719	N
+hsa-mir-767	223	50.803354	N
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+hsa-mir-7705	10	2.278177	N
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+hsa-mir-9-1	863	196.606700	N
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+hsa-mir-92a-1	9782	2228.513029	N
+hsa-mir-92a-2	8076	1839.855983	N
+hsa-mir-92b	263	59.916063	N
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+hsa-mir-96	263	59.916063	N
+hsa-mir-98	238	54.220620	N
+hsa-mir-99a	1235	281.354896	N
+hsa-mir-99b	89248	20332.276715	N

data/gdc_data_organized/0d146997-cfdc-4587-888c-e876fc455c80/nationwidechildrens.org_biospecimen.TCGA-A2-A4RW.xml

@@ -0,0 +1,461 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">08A86855-EC41-406F-AB61-0D77B9FD79D8</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">271.57.0</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-A2-A4RW</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0D146997-CFDC-4587-888C-E876FC455C80</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A2</shared:tissue_source_site>
+        <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A4RW</shared:patient_id>
+        <shared:gender cde="2200604" xsd_ver="1.8" procurement_status="Completed" owner="">FEMALE</shared:gender>
+        <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="">1550</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>
+                <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="">567</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-A2-A4RW-01A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0201CF15-D073-447F-B96E-ECA0800B8CFF</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:shipment_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>
+                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A321</bio:plate_id>
+                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">20</bio:center_id>
+                        <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">16</bio:shipment_portion_day_of_shipment>
+                        <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">9</bio:shipment_portion_month_of_shipment>
+                        <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2013</bio:shipment_portion_year_of_shipment>
+                        <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-11-A321-20</bio:shipment_portion_bcr_aliquot_barcode>
+                        <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">CEE2C148-EFA3-45E2-8B28-F65E56A5D2B9</bio:bcr_shipment_portion_uuid>
+                        <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                    </bio:shipment_portion>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">21</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:portion_sequence>
+                        <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="">11</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2012</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-A2-A4RW-01A-21</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8DF82719-7C75-48B8-A07B-84F5DDA08246</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="Completed" owner="">1</bio:subportion_sequence>
+                                <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="">0.17</bio:concentration>
+                                <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-A2-A4RW-01A-21D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">474622A8-A45D-4102-93B8-6A290437D885</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="">A25N</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21D-A25N-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">82AEAC9E-E169-41DC-8580-4165D4EA0AC9</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="">1.14</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158976</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="">A25Q</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21D-A25Q-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0D0A7623-CC2D-443F-9798-DF420FC50D17</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132177769</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="">A268</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21D-A268-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">154B0BC0-18A1-4FCD-8F65-B2FE9529CD0A</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="">2.21</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="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132159127</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="">PicoGreen</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="">0.17</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.90</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-A2-A4RW-01A-21R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1D4A3EF8-B9DB-4D5D-A0BF-28697B556D6D</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="">A25Z</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21R-A25Z-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7336150D-D955-4DBE-8EE4-7B44928086A0</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="">3.40</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="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0128923780</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="">A266</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21R-A266-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F8BFD67A-1D78-44B0-9715-712DEE01B008</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="">2.21</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="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0128925215</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="">1.59</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.30</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-A2-A4RW-01A-21W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">715A29B0-A40E-4CAE-8092-6D1A0A30CCE4</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="">A292</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="">08</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-21W-A292-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9052CD07-1E5A-45A5-900B-AE5838F978BA</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="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132269472</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:analytes>
+                        <bio:slides>
+                            <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="">60</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="">10</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</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="">40</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</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="">10</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-A2-A4RW-01A-02-TSB</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">32243877-C7DF-4FA5-BCA9-031B6E8F085F</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A2-A4RW-01A-02-TSB.32243877-C7DF-4FA5-BCA9-031B6E8F085F.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="">C1D4D6BB-AF86-4208-A729-C61365941217</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A2-A4RW.C1D4D6BB-AF86-4208-A729-C61365941217.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="">4AF8656E-2478-4895-8C59-B0C969F3E474</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="">567</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-A2-A4RW-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A5484AD7-3E5F-47DC-9E68-A6A7EA6FA650</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="">01</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">11</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2012</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-A2-A4RW-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7A9310D3-02CA-4CE0-BC89-D6E015398416</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="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-A2-A4RW-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ADFD86FC-0BF4-4B09-8137-68DEB77FB38F</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="">A25N</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-10A-01D-A25N-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D5AE8B5E-CAA4-4863-97EE-BD58EA996397</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="">0.94</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158980</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="">A25Q</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="">30</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-10A-01D-A25Q-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ABD9CB0D-01DE-478E-8DD7-B8B93E099F58</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="">2.80</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158691</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="">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="">PicoGreen</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-A2-A4RW-10A-01W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">635C381A-5FED-4246-B30B-42E6E573801D</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="">A292</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="">08</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A4RW-10A-01W-A292-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">763DA8AF-A428-477E-99EE-73BD920A643E</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="">A</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132269192</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: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>

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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	8	38115306	38433805	152	1.8061
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	67224146	67235918	6	0.1909
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	67236827	67286673	19	1.0696
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	73646247	74342716	358	0.7414
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	74343378	78144176	2067	0.1739
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	87661482	87933866	193	0.4164
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	87934105	90246910	1121	0.5391
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	11	90247014	122112755	20649	-0.2319
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	12	780472	132605822	74224	0.0203
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	53738831	53738894	3	-1.2056
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	53741265	67508211	8440	0.0274
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	67512635	67512649	2	-1.2487
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	100027509	100444505	200	0.2076
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	100451035	103403998	1516	0.036
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	103407878	103626452	103	0.3289
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	14	103627184	105533894	563	0.0246
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	23437561	25241470	848	0.0357
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	25243076	25403517	77	0.2384
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	25403545	26945074	1101	0.0298
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	26945734	27709708	585	0.2352
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	27709725	36462802	3304	0.032
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	36468047	37262508	578	0.2332
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	37262767	37826452	362	0.0507
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	37830939	38448758	379	0.2559
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	38450424	70227738	19499	0.0213
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	70232168	70233040	3	-0.9594
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	70236858	93084410	13192	0.0239
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	93085911	93086315	2	-2.1848
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	15	93090725	101344124	4782	0.0278
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	16	603333	24355041	10657	0.0272
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	16	24360479	73332922	19499	0.026
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	17	3803211	9719227	3156	-0.2452
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	18	326691	79349796	42881	0.0267
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	19	283868	58370362	24115	0.0128
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	472817	15185350	9060	0.0229
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	15186129	15251550	47	-0.305
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	15254123	22819274	6007	0.0169
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	22823271	31376027	1874	0.0118
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	31381382	31401690	12	-0.9145
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	31403242	52230410	12652	0.0163
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	52235635	61953896	7219	0.0443
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	20	61957341	63588502	613	0.0126
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	21	13974127	46262057	20576	0.027
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	22	16934932	43317247	12914	0.0189
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	22	43318599	43354698	29	0.6367
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	X	3236359	31846719	13071	0.0238
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	X	31851487	31854777	4	-1.3189
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	X	31855776	153434224	50408	0.0214
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	X	153434261	155677414	391	-0.2713

data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/TCGA-BH-A0DI-01A-11-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	0.11874
+AGID00111	913	sc-23957	Old	1433EPSILON	0.14252
+AGID00101	883	sc-1019	Old	1433ZETA	-0.18688
+AGID00001	2	9452	Old	4EBP1	1.1895
+AGID00002	3	9456	Old	4EBP1_pS65	-0.34194
+AGID00003	6	9459	Old	4EBP1_pT37T46	-0.082833
+AGID00443	8	9455	Old	4EBP1_pT70	-0.099711
+AGID00120	985	4937	Old	53BP1	-0.54252
+AGID00004	13	3661	Old	ACC_pS79	0.1452
+AGID00005	14	1768-1/ab45174	Old	ACC1	0.33782
+AGID00408	2372	3658	Set163	AceCS1	-0.1231205
+AGID00473	1182	5335	Old	ACETYLATUBULINLYS40	-0.45693
+AGID00404	2367	9189	Set163	ACSL1	-0.47648
+AGID02144	2450	PA5-27081	Old	ACVRL1	0.10548
+AGID00186	1198	ab88574	Old	ADAR1	-0.2197
+AGID00146	1084	4691	Old	AKT	-0.13533
+AGID00028	230	9271	Old	AKT_pS473	-0.23453
+AGID00170	1154	2965	Old	AKT_pT308	-0.081751
+AGID00316	1800	3063	Set163	Akt2	0.175245
+AGID00347	2009	8599	Set163	Akt2_pS474	0.2332095
+AGID02215	2577	ab195377	Set163	ALKBH5	-0.00231519
+AGID00498	924	CA1030	Old	ALPHACATENIN	NA
+AGID00287	1630	ABC80	Set163	Ambra1_pS52	-0.03900582
+AGID00236	1351	ab129081	Set163	AMPK-a2_pS345	-0.1341151
+AGID00006	39	2532	Old	AMPKALPHA	-0.14075
+AGID00007	40	2535	Old	AMPKALPHA_pT172	0.23266
+AGID00193	1208	610066	Old	ANNEXIN1	0.69081
+AGID00166	1142	610668	Old	ANNEXINVII	0.1066
+AGID00371	756	1852-1/ab52615	Old	AR	1.017
+AGID00194	1217	4432	Old	ARAF	0.16797
+AGID02191	2507	PA5-39728	Old	ARAF_pS299	0.21536
+AGID00260	1053	sc-32761	Old	ARID1A	-0.004703
+AGID00264	1560	HPA029318	Old	ASNS	-0.81566
+AGID00276	1612	3415	Set163	Atg3	0.07711996
+AGID00309	1775	13507	Set163	Atg4B	0.5180895
+AGID00310	1776	12994	Set163	Atg5	0.09710993
+AGID00277	1613	8558	Set163	Atg7	0.09106002
+AGID00242	1363	2873	Old	ATM	-0.057128
+AGID02142	2447	13050	Set163	ATM_pS1981	0.1846149
+AGID00217	1289	ab14748	Set163	ATP5A	0.9556694
+AGID02145	2451	PA5-43776	Set163	ATP5H	0.246165
+AGID02150	2456	13934	Set163	ATR	-0.215213
+AGID00315	1795	ab178407	Set163	ATR_pS428	0.1754538
+AGID00268	1569	ab97508	Set163	ATRX	-0.6171426
+AGID00391	2332	14475	Set163	Aurora-A	-0.65613
+AGID00392	2333	2914	Set163	Aurora-ABC_pT288_pT232_pT198	-0.15127
+AGID02195	2512	MA5-27890	Set163	Aurora-B	0.06526371
+AGID00215	1271	8661	Old	AXL	0.36382
+AGID02143	2449	8457	Set163	b-Actin	0.1350498
+AGID00179	1170	9565	Set163	b-Catenin_pT41_S45	-0.04627497
+AGID00301	1725	14058	Set163	B7-H3	0.1129891
+AGID00302	1726	14572	Set163	B7-H4	0.3649647
+AGID00008	63	9291	Old	BAD_pS112	0.00034528
+AGID00009	71	1542-1/ab32371	Old	BAK	-0.42777
+AGID00192	1207	sc-28383	Old	BAP1C4	-0.42222
+AGID00010	73	2772	Old	BAX	-0.28354
+AGID00433	80	M0887	Old	BCL2	1.0989
+AGID00219	1299	PAB8528	Old	BCL2A1	0.065047
+AGID00012	84	1018-1	Old	BCLXL	-0.37721
+AGID00377	87	sc-10086	Old	BECLIN	0.22347
+AGID00011	75	9562	Old	BETACATENIN	0.25181
+AGID00013	88	1008-1/ab32060	Old	BID	0.017064
+AGID00180	90	1036-1/ab32158	Old	BIM	0.89439
+AGID00221	1311	610978	Set163	BiP-GRP78	-0.007695536
+AGID00373	2194	07-507	Set163	BMK1-Erk5_pT218_Y220	0.1142701
+AGID00355	92	1647/ab33899	Old	BRAF	-0.18899
+AGID00014	94	2696	Old	BRAF_pS445	-0.014294
+AGID00445	761	9012	Old	BRCA2	0.10677
+AGID00266	1567	13440	Old	BRD4	-0.084226
+AGID00168	1146	2865	Set163	c-Abl_pY412	-0.1056707
+AGID00278	1615	3130	Set163	c-IAP2	-0.03955509
+AGID00345	1990	5649	Old	CA9	NA
+AGID00265	1565	2862	Old	CABL	0.0089625
+AGID00429	2407	2679	Set163	Calnexin	-0.2590702
+AGID00176	1165	9496	Set163	Caspase-8-cleaved	-0.2064451
+AGID00623	111	9665	Old	CASPASE3	-0.10797
+AGID00015	109	9491	Old	CASPASE7CLEAVEDD198	-0.80464
+AGID00118	951	9746	Old	CASPASE8	-0.016693
+AGID00537	935	551246	Old	CASPASE9	NA
+AGID00016	114	3238	Old	CAVEOLIN1	0.99588
+AGID00358	2100	ab76000	Set163	CD134	-0.07588142
+AGID00303	1737	826701	Set163	CD171	0.09879
+AGID00410	125	1632-1/ab78237	Old	CD20	-0.077875
+AGID00220	1308	ab28340	Old	CD26	0.081024
+AGID00191	1206	610467	Set163	CD29	0.2304597
+AGID00017	127	M0823	Old	CD31	0.27663
+AGID00369	2174	ab108403	Set163	CD38	-0.21016
+AGID00359	2104	ab133616	Set163	CD4	-0.06229124
+AGID00411	1398	3570	Set163	CD44	-0.3198451
+AGID00237	1352	M070101-2	Set163	CD45	0.1904599
+AGID00115	937	611016	Old	CD49B	0.56293
+AGID02171	2482	91882	Set163	CD86	-0.01330999
+AGID00329	1873	4688	Set163	cdc25C	-0.169485
+AGID00227	1332	4651	Set163	Cdc42	0.3731798
+AGID00422	2396	3387	Set163	Cdc6	-0.3422201
+AGID00501	1007	9112	Old	CDK1	-0.32665
+AGID00293	1658	ab32384	Set163	CDK1_pT14	-0.61489
+AGID00314	1783	4539	Old	CDK1_pY15	-0.11858
+AGID00423	2397	8064	Set163	CDT1	0.003104574
+AGID02101	2348	15102	Set163	cGAS	0.07064002
+AGID00447	2410	13460	Set163	CHD1L	-0.0007218091
+AGID00189	1203	2360	Old	CHK1	0.063284
+AGID00234	1348	ab79758	Old	CHK1_pS296	0.071322
+AGID00107	903	2348	Old	CHK1_pS345	-0.118
+AGID00018	146	3440	Old	CHK2	-0.21517
+AGID00019	147	2197	Old	CHK2_pT68	0.2186
+AGID00527	2078	4952	Old	CIAP	0.037799
+AGID00350	2018	3793	Set163	CIITA	-0.15594
+AGID00434	155	9164	Old	CJUN_pS73	-0.16958
+AGID00020	157	1522-1/ab32363	Old	CKIT	1.1125
+AGID00400	852	NB100-91714	Old	CLAUDIN7	0.18887
+AGID00466	726	3127	Old	CMET	0.093951
+AGID00079	727	3129	Old	CMET_pY1235	0.0010144
+AGID00167	161	9402	Old	CMYC	0.37968
+AGID00292	1656	11130-1-AP	Old	COG3	0.10575
+AGID00021	171	sc-20649	Old	COLLAGENVI	2.4436
+AGID00141	1069	459230	Old	COMPLEXIISUBUNIT30	NA
+AGID00267	1568	3512	Set163	Connexin-43	1.03142
+AGID00269	1571	6434	Set163	Coup-TFII	0.11433
+AGID00150	1116	4850	Set163	Cox-IV	-0.1848706
+AGID00195	1218	4842	Set163	Cox2	-0.06849997
+AGID00188	803	05-739	Old	CRAF	-0.19657
+AGID00022	179	9427	Old	CRAF_pS338	-0.07292
+AGID00023	181	9197	Set163	Creb	0.0353389
+AGID00393	2334	9198	Set163	CREB_pS133	-0.02769784
+AGID00365	2155	4980	Set163	CSK	-0.2081
+AGID00367	2160	9201	Set163	CtIP	-0.09509531
+AGID00536	2096	ab107198	Old	CTLA4	NA
+AGID00025	198	2936	Set163	Cyclin-D3	-0.008420095
+AGID00024	192	1495-1/ab32053	Old	CYCLINB1	-1.8858
+AGID00382	194	sc-718	Old	CYCLIND1	0.067466
+AGID00437	199	sc-25303	Old	CYCLINE1	-0.81894
+AGID00449	202	1142-1	Old	CYCLINE2	-0.70642
+AGID00209	1257	ab110324	Set163	Cyclophilin-F	-0.3099203
+AGID00247	1379	ab48389	Set163	D-a-Tubulin	0.343265
+AGID00308	1770	GTX10524	Set163	DAPK1_pS308	0.05396997
+AGID00304	1744	ab51601	Set163	DAPK2	0.2778448
+AGID00343	1980	6998	Set163	DDB-1	0.19973
+AGID00427	2402	5583	Set163	DDR1	-0.1071057
+AGID00428	2403	SAB4504671	Set163	DDR1_pY513	0.03346
+AGID00532	1273	Bast Lab	Old	DIRAS3	0.19482
+AGID00104	891	ab76008	Old	DJ1	0.19736
+AGID02146	2452	4658	Set163	DM-Histone-H3	0.01912464
+AGID00386	1397	ab32521	Set163	DM-K9-Histone-H3	0.04284499
+AGID00352	2030	14649	Set163	DNA-Ligase-IV	-0.2735652
+AGID00407	2371	13609	Set163	DNA_POLG	-0.1250301
+AGID00399	2344	5032	Set163	DNMT1	-0.4449001
+AGID00409	2373	5391	Set163	DRP1	-0.2460915
+AGID00253	1406	5149	Old	DUSP4	-0.10266
+AGID00334	1936	ab76310	Set163	DUSP6	-0.04942031
+AGID00116	940	3218	Old	DVL3	-0.19826
+AGID00211	1261	sc-251	Old	E2F1	NA
+AGID00148	1099	3195	Old	ECADHERIN	0.7233
+AGID00135	1060	2332	Old	EEF2	-0.95765
+AGID00136	1061	3692	Old	EEF2K	-0.49365
+AGID00152	1120	2232	Old	EGFR	-0.16705
+AGID00450	217	2234	Old	EGFR_pY1068	0.46107
+AGID00026	221	1124-1/ab32578	Old	EGFR_pY1173	0.0093962
+AGID00078	722	9742	Old	EIF4E	-0.026361
+AGID00328	1871	ab76256	Set163	eIF4E_pS209	-0.2566503
+AGID00154	1124	2498	Old	EIF4G	-0.08163
+AGID00027	228	9181	Set163	Elk1_pS383	-0.171455
+AGID00235	1350	M061329-2	Set163	EMA	0.01398959
+AGID00394	2337	3810	Set163	Enolase-1	0.1014048
+AGID00395	2338	8171	Set163	Enolase-2	-0.180435
+AGID00196	1219	GTX629542	Old	ENY2	-0.15506
+AGID00438	1849	A302-024A	Set163	EphA2	-0.29726
+AGID00552	2422	6347	Set163	EphA2_pS897	0.0007300277
+AGID00553	2423	12677	Set163	EphA2_pY588	0.2912315
+AGID00075	693	556347	Old	EPPK1	2.7979
+AGID00335	238	RM-9101	Old	ERALPHA	1.4968
+AGID00029	241	1091-1/ab32396	Old	ERALPHA_pS118	-0.42945
+AGID00240	247	MS-671	Old	ERCC1	-0.019643
+AGID00239	1355	11331-1-AP	Old	ERCC5	-0.19925
+AGID00484	249	sc-154	Old	ERK2	0.018092
+AGID00372	2193	3552	Set163	Erk5	-0.14394
+AGID00405	2369	13826	Set163	ERRalpha	-0.3158051
+AGID00187	1200	A303-501A	Old	ETS1	-0.41836
+AGID00511	2492	2593	Set163	EVI1	-0.1918656
+AGID00485	1284	4905	Old	EZH2	NA
+AGID00030	252	1700-1/ab40794	Set163	FAK	-0.39482
+AGID02151	2457	8556	Set163	FAK_pY397	0.8308834
+AGID00171	1156	3180	Old	FASN	0.042113
+AGID00356	2085	500-P18/10775-082	Set163	FGF-basic	1.676865
+AGID00031	262	1574-1/ab45688	Old	FIBRONECTIN	1.693
+AGID00339	1959	4403	Set163	FN14	0.03617503
+AGID02152	2458	20459	Old	FOXM1	-0.76789
+AGID00378	269	9467	Old	FOXO3A	-0.0036134
+AGID02197	2515	orb6051	Old	FOXO3A_pS318S321	0.20825
+AGID02167	2475	PA5-64616	Set163	FRS2-alpha_pY196	-0.05532997
+AGID02213	2575	ab124892	Set163	FTO	0.38512
+AGID02141	2446	12263	Old	G6PD	-0.0065431
+AGID00117	943	3239	Old	GAB2	-0.57306
+AGID00412	274	AM4300	Old	GAPDH	-2.2103
+AGID00086	764	558686	Old	GATA3	1.8461
+AGID00383	1578	4253	Old	GATA6	0.32357
+AGID00289	1634	12601-1-AP	Set163	GCLC	-0.171755
+AGID00305	1745	ab124827	Set163	GCLM	0.34916
+AGID00212	1263	3305	Old	GCN5L2	-0.13793
+AGID00270	1579	3538	Set163	Gli1	0.2982696
+AGID00263	1520	ab69838	Set163	Gli3	0.2987089
+AGID00548	2530	3660	Set163	Glucocorticoid-Receptor	0.332005
+AGID00387	1617	12793	Set163	Glutamate-D1-2	0.06455889
+AGID00262	1491	ab156876	Set163	Glutaminase	0.16712
+AGID00319	1807	4275	Set163	Granzyme-B	-0.3709151
+AGID00368	2169	ab183737	Set163	GRB7	0.06663925
+AGID00396	2339	3593	Set163	Grp75	-0.170295
+AGID00174	1163	9315	Set163	GSK-3B	-0.4928209
+AGID00502	1082	9336	Old	GSK3_pS9	-0.18842
+AGID00033	284	sc-7291	Old	GSK3ALPHABETA	-0.03633
+AGID00034	285	9331	Old	GSK3ALPHABETA_pS21S9	-0.11871
+AGID00129	1035	3886	Old	GYS	NA
+AGID00130	1036	3891	Old	GYS_pS641	NA
+AGID01354	1342	9718	Set163	H2AX_pS139	0.30206
+AGID00363	1409	MA1-2022	Set163	H2AX_pS140	0.06422496
+AGID00131	1038	MS-325-P1	Old	HER2	0.094321
+AGID00142	299	06-229	Old	HER2_pY1248	0.2289
+AGID00110	911	sc-285	Old	HER3	0.4371
+AGID00080	728	4791	Old	HER3_pY1289	0.044759
+AGID00103	890	2573	Old	HEREGULIN	-0.082645
+AGID00271	1582	11988	Set163	HES1	0.6841698
+AGID00397	2340	2024	Set163	Hexokinase-I	-0.1061202
+AGID00442	1023	2867	Set163	Hexokinase-II	-1.411282
+AGID00419	1402	610958	Old	HIF1ALPHA	NA
+AGID00205	1250	ab1791	Set163	Histone-H3	0.1594399
+AGID00398	2341	3377	Set163	Histone-H3_pS10	-0.4167951
+AGID00332	1901	ab128959	Set163	HLA-DQA1	0.4368187
+AGID00333	1902	14832-1-AP	Set163	HMHA1	-0.5266505
+AGID00035	321	2402	Set163	HSP27	0.04028497
+AGID00036	323	2401	Set163	HSP27_pS82	-0.06881998
+AGID00320	1808	12165	Set163	HSP60	-0.2023652
+AGID00037	325	4872	Old	HSP70	0.325
+AGID00366	2158	86630	Set163	IDO	-0.3208855
+AGID00197	1221	3024	Old	IGF1R_pY1135Y1136	0.17943
+AGID00038	335	3922	Old	IGFBP2	-0.15278
+AGID00090	793	611504	Set163	IGFBP3	-0.0856903
+AGID00039	336	3027	Set163	IGFRb	-0.17151
+AGID00336	1949	12153	Set163	IL-6	0.4072447
+AGID02221	2583	57145	Set163	IMP3	0.05786988
+AGID02153	2459	14543	Old	INPP4B	2.1245
+AGID00272	1586	3025	Set163	IR-b	0.29014
+AGID00519	2519	4302	Set163	IRF-3	-0.08888473
+AGID00520	2520	4947	Set163	IRF-3_pS396	0.1351695
+AGID00223	1316	sc-497	Old	IRF1	-0.39
+AGID00092	802	06-248	Old	IRS1	0.05119
+AGID00040	371	4502	Set163	IRS2	-0.03813044
+AGID00250	1394	sc-13157	Old	JAB1	0.16797
+AGID00256	1413	ab109536	Set163	Jagged1	0.2835256
+AGID00177	1166	3230	Old	JAK2	-0.31734
+AGID00758	377	4671	Old	JNK_pT183Y185	0.26042
+AGID02136	2439	PA5-28262	Old	JNK2	-0.20067
+AGID00307	1757	ab10484	Set163	KAP1	0.2047845
+AGID00528	904	2180	Old	KU80	-0.41456
+AGID00375	2237	HPA028732	Set163	LAD1	1.069005
+AGID00290	1643	IHC-00439	Set163	Lasu1	-0.373575
+AGID00279	1618	4108	Set163	LC3A-B	0.3798348
+AGID00042	397	2752	Old	LCK	0.12018
+AGID00119	976	3582	Old	LDHA	NA
+AGID00533	977	ab85319	Old	LDHB	NA
+AGID00529	1477	3050	Old	LKB1	0.16737
+AGID00244	1367	2568	Set163	LRP6_pS1490	0.121995
+AGID00439	2424	2796	Set163	Lyn	-0.160225
+AGID02154	2460	4370	Old	MAPK_pT202Y204	0.7058
+AGID00198	1222	5453	Set163	Mcl-1	-0.396721
+AGID00288	1633	AB3314P	Set163	MCT4	-0.07786011
+AGID00175	1164	3521	Set163	MDM2_pS166	-0.228265
+AGID00044	417	1235-1/ab32576	Old	MEK1	0.036435
+AGID00143	1076	9154	Old	MEK1_pS217S221	-0.029856
+AGID00201	1243	9125	Set163	MEK2	0.08666955
+AGID00361	2118	ab51061	Set163	MelanA	-0.125975
+AGID00362	2119	ab137078	Set163	Melanoma-gp100	-0.1489301
+AGID00337	1951	12711	Set163	MERIT40	0.08550439
+AGID00338	1952	12110	Set163	MERIT40_pS29	0.08607003
+AGID02212	2574	ab195352	Set163	METTL3	0.19783
+AGID00225	1323	sc-20121	Set163	MIF	-0.15057
+AGID00137	1062	WH0054206M1	Old	MIG6	-0.1348
+AGID00403	2117	ab20663	Set163	MITF	0.1194346
+AGID00503	1067	ab3298	Old	MITOCHONDRIA	NA
+AGID00321	1809	14739	Set163	Mitofusin-1	1.442341
+AGID00322	1810	11925	Set163	Mitofusin-2	-0.0698001
+AGID00389	2324	3515	Set163	MLH1	0.02238988
+AGID00312	1780	14993	Set163	MLKL	-0.4292601
+AGID00402	2359	MAB3328	Set163	MMP14	0.02287997
+AGID00045	435	4022	Set163	MMP2	0.3052872
+AGID00122	1005	2195	Set163	Mnk1	-0.3204912
+AGID00331	1899	sc-377312	Set163	MR1	0.1419248
+AGID00273	1589	ab103319	Set163	MRAP	0.07594003
+AGID00530	440	4847	Old	MRE11	0.31864
+AGID00390	905	2850	Old	MSH2	-0.33781
+AGID00138	1063	22030002	Old	MSH6	-0.70678
+AGID00299	1675	ab76148	Set163	MSI2	0.395275
+AGID00232	1344	ab14705	Set163	MTCO1	-0.5261217
+AGID00046	444	2983	Old	MTOR	-0.056459
+AGID00047	446	2971	Old	MTOR_pS2448	0.14828
+AGID00204	1247	H00009788-M01A	Set163	MTSS1	0.2462949
+AGID00401	1139	21370002	Old	MYH11	3.283
+AGID00291	1647	3403	Old	MYOSINIIA	0.29826
+AGID00173	1160	5026	Old	MYOSINIIA_pS1943	0.38847
+AGID00318	1803	4282	Set163	Myt1	0.04373977
+AGID00216	1274	5795-1/ab129189	Old	NAPSINA	NA
+AGID00418	452	4061	Old	NCADHERIN	0.38589
+AGID00156	1126	3217	Old	NDRG1_pT346	-0.46481
+AGID02133	2436	PA5-45913	Set163	NDUFB4	-0.19167
+AGID00134	1046	22710002	Old	NF2	-0.54923
+AGID00048	457	3033	Old	NFKBP65_pS536	0.80529
+AGID02155	2461	3608	Old	NOTCH1	-0.16728
+AGID00340	1969	4147	Set163	Notch1-cleaved	0.2094648
+AGID00087	767	sc-5593	Set163	Notch3	0.16481
+AGID00258	1420	3187	Set163	NQO1	1.568485
+AGID00162	1136	sc-31	Old	NRAS	0.018821
+AGID00257	1419	12721	Old	NRF2	NA
+AGID00297	1669	2750	Set163	Oct-4	0.203895
+AGID00420	466	1712-1/ab40803	Old	P16INK4A	0.60393
+AGID00384	470	sc-6246	Old	P21	-0.027068
+AGID00105	897	1591-1/ab32034	Old	P27	0.61095
+AGID00096	842	AF1555	Old	P27_pT157	0.047241
+AGID00099	878	ab64949	Old	P27_pT198	-0.20261
+AGID00181	1175	9228	Set163	p38-a	0.1037089
+AGID00098	479	9211	Old	P38_pT180Y182	0.59712
+AGID00049	478	9212	Old	P38MAPK	0.11117
+AGID00151	1119	4695	Set163	p44-42-MAPK	-0.193795
+AGID00050	481	9282	Old	P53	0.01459
+AGID00490	1187	610833	Old	P62LCKLIGAND	0.95195
+AGID00545	1415	ab53039	Old	P63	NA
+AGID00052	494	9205	Old	P70S6K_pT389	-0.18012
+AGID00051	493	1494-1/ab32529	Old	P70S6K1	-0.33408
+AGID00085	759	9347	Old	P90RSK	-0.075478
+AGID00531	770	9344	Old	P90RSK_pT359S363	0.067074
+AGID00182	1178	9346	Set163	p90RSK_pT573	-0.2429201
+AGID00053	499	612024	Old	PAI1	0.47567
+AGID00224	1322	HPA035895	Set163	PAICS	-0.62394
+AGID00323	1811	2602	Set163	PAK1	-0.2462104
+AGID02199	2517	PA5-69540	Set163	PAK4	0.1335349
+AGID00245	1370	4336-BPC-100	Set163	PAR	0.1006796
+AGID00374	2209	66564	Set163	PARG	-0.1955302
+AGID00370	1372	sc-7150	Old	PARP1	-0.27264
+AGID00468	501	9546	Old	PARPCLEAVED	0.010755
+AGID00274	1591	ab53715	Set163	Patched	0.34946
+AGID00513	2486	60433	Set163	PAX6	-0.1449801
+AGID00441	1621	9857	Set163	PAX8	-0.3199064
+AGID00054	504	2542	Old	PAXILLIN	-0.34489
+AGID00055	509	2130	Old	PCADHERIN	-0.010606
+AGID00248	511	ab29	Old	PCNA	-0.32779
+AGID00413	2095	43248	Old	PDCD1	NA
+AGID00094	816	600-401-965	Old	PDCD4	-0.039437
+AGID00385	1225	3169	Set163	PDGFRB	0.449645
+AGID00210	1258	ab110332	Set163	PDH	0.2468539
+AGID00324	1817	3205	Set163	PDHA1	-0.1718656
+AGID00280	1622	3820	Set163	PDHK1	0.1513
+AGID00056	515	3062	Old	PDK1	0.062489
+AGID00057	516	3061	Old	PDK1_pS241	-0.10907
+AGID00300	1234	sc-19090	Old	PDL1	0.034348
+AGID00124	1017	2780	Old	PEA15	-0.091642
+AGID00125	1018	44-836G	Old	PEA15_pS116	-0.22086
+AGID00440	2429	3192	Set163	PERK	-0.4793006
+AGID02207	2569	ab192876	Set163	PGM1	0.2316894
+AGID00281	1623	13428	Set163	PHGDH	0.4217294
+AGID00425	2399	22789-1-AP	Set163	PHLPP	-0.34407
+AGID00226	1330	sc-376412	Set163	PI3K-p110-b	0.25714
+AGID00093	808	4255	Old	PI3KP110ALPHA	0.70639
+AGID00058	523	06-195	Old	PI3KP85	0.19122
+AGID00296	1667	5675	Set163	PKA-a	0.2493549
+AGID00259	1426	9375	Set163	PKC-a-b-II_pT638_T641	0.24105
+AGID00172	529	05-154	Old	PKCALPHA	-0.45101
+AGID00460	530	06-822	Old	PKCALPHA_pS657	-0.019352
+AGID00114	932	07-875	Old	PKCDELTA_pS664	-0.015887
+AGID00163	1137	9371	Old	PKCPANBETAII_pS660	-0.73034
+AGID00126	1025	4053	Old	PKM2	NA
+AGID00512	2489	5690	Set163	PLC-gamma1	-0.4773708
+AGID02138	2441	GTX133463	Set163	PLC-gamma2_pY759	-0.02350514
+AGID00084	754	4513	Set163	PLK1	-1.24186
+AGID00203	1246	22510002	Set163	PMS2	-0.4608
+AGID00207	1254	ab14734	Set163	Porin	0.25677
+AGID00381	549	1483-1/ab32085	Old	PR	0.11999
+AGID00081	738	AHO1031	Set163	PRAS40	0.02096003
+AGID00082	739	44-1100G	Old	PRAS40_pT246	-0.14037
+AGID00424	2398	OAAF05458	Set163	PRC1_pT481	-0.34126
+AGID00492	1205	HPA007730	Old	PRDX1	0.17063
+AGID00190	1204	ab102739	Old	PREX1	0.41081
+AGID00061	566	9552	Old	PTEN	0.040717
+AGID00364	2154	ab76942	Set163	PTPN12	-0.3907101
+AGID00218	1290	4976	Set163	Puma	-0.05054497
+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	0.3845744
+AGID00145	1083	3539	Old	RAB11	0.067332
+AGID00169	1150	4314	Old	RAB25	0.20976
+AGID00342	1979	24555	Set163	Rad23A	0.3244949
+AGID00261	987	05-525	Old	RAD50	-0.10456
+AGID00360	579	NA71	Old	RAD51	-0.16564
+AGID00158	1128	2280	Old	RAPTOR	0.2315
+AGID00059	552	9309	Old	RB	-0.016021
+AGID00060	557	9308	Old	RB_pS807S811	-0.99085
+AGID00164	1138	21390002	Old	RBM15	-1.275
+AGID00547	735	3221	Old	RET_pY905	NA
+AGID00097	847	MAB3426	Set163	Rheb	0.5404899
+AGID00159	1129	2114	Old	RICTOR	1.1897
+AGID00160	1130	3806	Old	RICTOR_pT1135	0.28587
+AGID00282	1624	4926	Set163	RIP	0.186395
+AGID00283	1625	13526	Set163	RIP3	0.2358893
+AGID00416	1368	2208	Set163	RPA32	0.435365
+AGID00246	1375	A300-245A	Set163	RPA32_pS4_S8	0.04010893
+AGID00341	1978	3388	Set163	RRM1	0.1799248
+AGID00344	1981	PA5-27856	Set163	RRM2	-0.04430663
+AGID00554	2425	8408	Set163	RSK1	0.1105522
+AGID00353	2031	13018	Set163	S100A4	-0.005724979
+AGID00330	1874	2317	Old	S6	-0.68246
+AGID00062	600	2211	Old	S6_pS235S236	-1.3172
+AGID00063	601	2215	Old	S6_pS240S244	-1.1049
+AGID00157	1127	sc-58420	Old	SCD1	0.074629
+AGID00230	1339	11998	Set163	SDHA	0.39157
+AGID00294	1039	ab69836	Old	SETD2	0.027197
+AGID00161	1131	32-4500	Old	SF2	-0.051602
+AGID02179	2495	3534	Set163	SFRP1	0.352504
+AGID00431	2411	12103	Set163	SGK1	-0.2650607
+AGID00430	2409	8156	Set163	SGK3	-0.447865
+AGID02168	2476	bs-3413R	Old	SHC_pY317	0.44952
+AGID00376	2241	3397	Set163	SHP2	-0.06740023
+AGID00183	1180	3751	Old	SHP2_pY542	0.66411
+AGID02208	2570	ab8120	Set163	SIRP-alpha	-0.5048556
+AGID00222	1133	sc-99002	Old	SLC1A5	-0.10949
+AGID00255	1411	sc-136891	Set163	Slfn11	0.6149399
+AGID00064	610	2954	Old	SMAC	-0.12982
+AGID00113	922	1649-1/ab33902	Old	SMAD1	0.97383
+AGID00091	796	1735-1/ab40854	Old	SMAD3	-0.34156
+AGID02160	2467	46535	Old	SMAD4	-0.091838
+AGID00065	616	3895	Old	SNAIL	0.064118
+AGID00325	1818	4266	Set163	SOD1	0.1735085
+AGID00380	1328	13141	Set163	SOD2	0.1858348
+AGID00298	1670	2748	Set163	Sox2	0.2878098
+AGID00066	621	05-184	Old	SRC	-0.11262
+AGID02157	2463	6943	Old	SRC_pY416	-0.013762
+AGID00068	626	2105	Old	SRC_pY527	0.39334
+AGID00185	1197	4904	Set163	Stat3	0.1365969
+AGID00388	637	9131	Old	STAT3_pY705	0.35245
+AGID00069	638	1289-1/ab32043	Old	STAT5ALPHA	-0.29323
+AGID00077	718	1972-1/ab52630	Old	STATHMIN	0.13504
+AGID00357	2099	13647	Set163	STING	-0.603875
+AGID00128	1033	sc-1240	Old	SYK	-0.67428
+AGID00070	646	05-348	Set163	Tau	-0.145735
+AGID00327	777	2149	Old	TAZ	0.41389
+AGID00228	1333	7495	Set163	TFAM	0.4290437
+AGID00165	1140	22500002	Old	TFRC	0.14846
+AGID00149	1107	S1711/ab137573	Old	TIGAR	-0.11869
+AGID00109	908	MS-224-P1	Old	TRANSGLUTAMINASE	-0.49815
+AGID00406	2370	612344	Set163	TRAP1	-0.1267
+AGID00559	2537	PA5-34561	Set163	TRIM24	0.08451278
+AGID00306	1756	ab167154	Set163	TRIM25	-0.1071757
+AGID00426	2400	PA5-52193	Set163	TRIP13	-0.349915
+AGID00155	1125	4906	Old	TSC1	-0.19934
+AGID00144	1081	2044-1/ab76013	Old	TTF1	NA
+AGID00071	670	1613-1/ab32554	Old	TUBERIN	-0.26127
+AGID02194	2511	ab109403	Old	TUBERIN_pT1462	-0.0058078
+AGID00417	1842	ab173300	Set163	TUFM	0.00706
+AGID00238	1353	sc-81417	Set163	Twist	0.18192
+AGID00436	1080	5585	Set163	Tyro3	-0.05780051
+AGID00295	1662	5546	Set163	U-Histone-H2B	0.6053649
+AGID00214	1270	HPA005651	Set163	UBAC1	0.1229749
+AGID00351	2020	sc-136145	Set163	UBQLN4	0.06091001
+AGID00213	1267	sc-271268	Set163	UGT1A	0.167765
+AGID00284	1626	6888	Set163	ULK1_pS757	-0.1058379
+AGID00208	1256	MS304/ab14745	Set163	UQCRC2	0.14883
+AGID00313	1781	13115	Set163	UVRAG	0.23306
+AGID00073	678	3112	Set163	VASP	-0.1312103
+AGID00184	1181	2502	Set163	VAV1	-0.7130259
+AGID00074	688	2479	Old	VEGFR2	0.39892
+AGID00421	2394	68547	Set163	VHL	-0.49555
+AGID00231	1343	SAB4200080	Set163	Vinculin	0.6813796
+AGID00317	1802	4936	Set163	Wee1	-0.1243762
+AGID00354	2058	4910	Set163	Wee1_pS642	-0.05141022
+AGID00285	1627	12124	Set163	WIPI1	-0.05078999
+AGID00286	1628	8567	Set163	WIPI2	0.306745
+AGID02214	2576	ab195380	Set163	WTAP	0.07992932
+AGID00133	1044	sc-32136	Old	XBP1	0.16895
+AGID00076	699	2042	Set163	XIAP	-0.2856505
+AGID00241	1359	sc-56813	Set163	XPA	0.07088503
+AGID00349	1354	ab3299	Set163	XPF	-0.0750726
+AGID02137	2440	PA5-29359	Old	XRCC1	-0.16942
+AGID00088	780	sc-15407	Old	YAP	0.13244
+AGID00089	782	4911	Old	YAP_pS127	0.032392
+AGID00504	700	17250002	Old	YB1	0.017455
+AGID00095	835	2900	Old	YB1_pS102	-0.1608
+AGID02217	2579	ab220163	Set163	YTHDF2	-0.087295
+AGID02210	2572	ab220161	Set163	YTHDF3	-0.42447
+AGID00326	1828	2705	Set163	ZAP-70	-0.3260671
+AGID00432	2244	sc-25388	Set163	ZEB1	-0.0560617

data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/TCGA-BH-A0DI-11A-02-TSB.07e1b819-2663-42a7-a85d-ea27aa3669d0.svs

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data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/TCGA-BRCA.dd174335-cc95-4d3d-a25b-9abaaaa432a2.ascat2.allelic_specific.seg.txt

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+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	62920	30056287	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	30056442	30058066	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	30058192	112354983	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	112356018	112384683	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	112385183	160268299	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	160270643	160703576	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	160703989	163217034	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	163218794	164844202	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	164845546	172048306	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	172048912	173903663	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	173904921	175762369	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	175765148	248930189	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr2	12784	522617	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr2	522921	242147305	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	20930	90200333	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	90203297	161640080	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	161640906	162200870	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	162201550	162568526	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	162568569	163335921	5	3	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	163338633	167490049	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	167494552	167950316	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	167950357	168418902	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	168418915	169834467	8	7	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	169834593	170208667	13	12	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	170214703	170527206	21	20	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	170527322	171508945	12	11	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	171509190	171908838	21	20	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	171913882	172405681	12	11	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	172406798	173036832	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	173037156	173832823	11	10	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	173835947	174666487	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	174669395	175111897	15	14	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	175112560	177150790	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	177157836	178231984	14	13	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	178237407	178668350	8	7	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	178668533	181143482	22	21	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	181144394	181889140	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	181889874	182187691	4	3	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	182197432	183058822	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	183061011	183948156	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	183950977	185155227	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185157318	185202792	6	4	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185205817	185917897	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185923795	185980858	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185986556	186288037	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	186291844	186698441	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	186699982	187371932	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	187376772	193156958	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	193160113	193165114	26	26	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	193168646	198169247	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	68929	10208766	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	10212536	10227178	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	10227193	69424538	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	69424683	103877830	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	103879184	104350516	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	104351077	112739280	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	112739669	113001595	6	5	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	113003702	115679516	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	115680119	116431547	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	116432785	118414420	6	5	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	118415482	122918872	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	122918909	122959597	8	6	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	122960435	135731038	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	135732439	135764238	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	135764369	135777648	3	2	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	136431289	136913680	6	5	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	150743708	153430427	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	153432302	153719405	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	153719700	156149409	1	1	0
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	156784399	190106768	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	15532	59972144	3	2	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	171654902	177452694	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	177463415	181363319	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	149661	60395828	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	78285868	83253510	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	83254076	87330681	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	87333654	90651637	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	90651798	95562546	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	95564032	96031145	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	96032663	96840605	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	96840788	97549013	4	3	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	97549456	110722651	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	122891131	127401647	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	117592169	120587419	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	120587468	124524073	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	124524582	127791286	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	127798179	127978547	10	8	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	127980044	132683568	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	132683710	142007745	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	142008825	142613247	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	142613305	142912583	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	142912817	144976790	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	144977426	145757651	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	145758075	146981903	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	146981994	147581427	4	3	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	147581780	148357730	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	148360510	149450101	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	149450192	149738097	4	3	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	149740738	151025883	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	151026178	151800882	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	151801616	152312842	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	152320139	153993293	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	154002202	157286892	4	3	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	157288706	158243769	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	158244763	158657442	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr7	158661963	159334314	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	81254	31469500	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	31469533	32402366	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	32404066	32444900	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	32445797	32932871	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	32938756	32954900	9	9	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	32955985	33276530	13	11	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	33277317	34453268	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	34462222	34574584	24	19	5
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	34584165	34761549	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	34762638	34872345	8	6	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	34872413	34889743	9	6	3
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	34896015	36633719	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	36640718	37273772	12	11	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	37274389	37368206	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	37370213	38761314	25	23	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	38763462	39537590	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	39538338	40609356	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	40609497	53087916	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	53088433	53119366	5	3	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	53119424	105195178	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	105196650	107744952	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	107745365	111773048	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	111773547	137858162	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	137858643	137870935	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr8	137871229	145072769	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	46587	41741113	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	60863881	83290105	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	83290145	83296891	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	83297027	102111018	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	102112478	102277464	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr9	102278981	138200944	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr10	45792	95105427	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr10	95105451	95116202	18	18	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr10	95116218	133102328	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr10	133102617	133654968	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	198510	50000581	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	50001495	50085543	3	3	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	50088070	50475455	13	10	3
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	50479468	50810146	14	14	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	54952548	56347137	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	56350479	66877907	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	66878680	69236833	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	69241110	69674395	11	10	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	69675578	70202349	18	17	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	70207381	70354488	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	70354796	71121768	10	9	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	73640259	74342716	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	74343378	74367350	5	5	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	74369062	80971331	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	80976191	81418555	8	7	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	81419208	87634916	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	87635019	90256074	6	5	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr11	90256319	135074876	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr12	51460	97337476	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr12	97338152	97442715	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr12	97444476	133201603	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr13	18452809	114342922	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr14	18239283	21986046	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr14	21987373	22558476	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr14	22560379	105733039	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr14	106321086	106877229	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	19811075	27687756	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	27687774	36409751	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	36409832	37236196	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	37241857	37833473	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	37834341	38441646	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	38442921	47350513	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	47350566	47355320	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	47355558	71279075	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr15	71282607	71366925	3	2	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr17	49211095	56083553	3	2	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr18	48133	80257174	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr19	55858227	58586487	2	1	1
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+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr20	14940893	15309055	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr20	15310906	64324800	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr21	12973348	29830106	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr21	29830158	29858385	0	0	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr21	29858821	46677045	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr22	16392123	29978339	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr22	29979545	50796027	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chrX	251810	152874018	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chrX	152877879	156004181	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chrY	2782397	56872112	0	0	0

data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/TCGA-BRCA.dd174335-cc95-4d3d-a25b-9abaaaa432a2.ascat3.allelic_specific.seg.txt

@@ -0,0 +1,152 @@
+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	61735	163319781	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	163320198	164853962	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	164855770	172116091	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	172117958	173665550	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	173667915	175911302	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr1	175917134	248930189	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr2	12784	242147305	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	18667	90187614	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	90197950	161635132	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	161635856	163339133	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	163351638	168418915	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	168421786	169834467	8	7	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	169834593	171510899	14	13	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	171512107	171914539	23	22	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	171915129	172405681	13	12	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	172406798	173036832	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	173037156	173841783	12	11	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	173845902	174666353	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	174666487	175111897	16	15	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	175112560	177150790	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	177157836	178210690	15	14	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	178210729	178668533	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	178668607	181138665	22	21	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	181142061	181910133	10	9	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	181910676	183058822	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	183061011	183108528	4	4	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	183110356	183936149	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	183940178	185199880	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185202792	185923795	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185924102	185980858	2	2	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	185986556	186288037	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	186291844	186698441	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	186699982	187371932	7	6	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr3	187376772	198169247	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	12281	69432905	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	69433003	112739669	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	112743148	113001595	8	6	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	113003702	115711744	2	1	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	115713568	116430348	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	116431547	118720855	6	5	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	118724784	122959597	5	4	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	122960435	135767791	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	135770028	136419418	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	136419937	136920976	6	5	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	136924257	148661459	9	8	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	148665220	150708987	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	150712994	153430427	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	153432302	153720486	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	153720538	156168453	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	156168553	156781100	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr4	156784399	190106768	1	1	0
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	15532	72544135	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	72544643	75065564	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	75067918	171674890	3	2	1
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr5	171675159	181363319	4	2	2
+dd174335-cc95-4d3d-a25b-9abaaaa432a2	chr6	149661	60358475	2	1	1
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data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/nationwidechildrens.org_clinical.TCGA-BH-A0DI.xml

@@ -0,0 +1,367 @@
+<?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">9BBD979B-95F5-4F1E-9E06-B2A941CA5D75</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">96.80.0</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="1166604">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="1166594">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="1166590">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="1166596">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">-23327</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">673</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="1166592">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-BH-A0DI</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">BH</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0DI</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">27ba717a-5cd8-440a-9345-4ae086f6efca</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="1166595">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="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">63</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="1166610">2009</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="1166593">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="1166603">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="1166622">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="1166623">28</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="Not Available" restricted="false" source_system_identifier="1166638"/>
+        <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="1166644"/>
+        <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="1166605">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="1166654"/>
+        <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="1166619"/>
+        <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="1166620"/>
+        <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="1166613">Modified Radical 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="1166617" 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="1166616"/>
+        <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="1166614"/>
+        <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="1166606">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="1166607" 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="1166591">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="1166639">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="1166621"/>
+        <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="1166635"/>
+        <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="1166636"/>
+        <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="1166647"/>
+        <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="1166618"/>
+        <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="1166615">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="1166611">Core needle biopsy</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="1166612" 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="Not Available" restricted="false" source_system_identifier="1166650"/>
+        <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="1166633">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="1166645">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="1166625"/>
+        <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="1166624">3</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="1166643"/>
+        <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="1166637"/>
+        <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="1166646"/>
+        <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="1166648"/>
+        <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="1166649"/>
+        <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="1166653"/>
+        <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="1166655"/>
+        <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="1166656"/>
+        <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="1165753">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="1165754">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="1166652"/>
+        <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="1166631"/>
+            <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="1166632"/>
+        </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="1166634"/>
+        <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="1166640"/>
+        <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="1166657">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="1166658"/>
+        <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="1166659"/>
+        <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="1166661"/>
+        <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="1166662"/>
+        <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="1166663"/>
+        <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="1166664"/>
+        <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="1166670"/>
+        <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="1166665"/>
+        <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="1166667"/>
+        <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="1166668"/>
+        <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="1166669"/>
+        <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="1166671"/>
+        <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="1166672"/>
+        <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="1166673"/>
+        <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="1166674"/>
+        <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="1166675"/>
+        <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="1166677"/>
+        <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="1166678"/>
+        <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="1166679"/>
+        <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="1166680"/>
+        <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="1166681"/>
+        <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="1166676"/>
+        <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="1166651"/>
+        <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="1166641"/>
+        <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="1166642"/>
+        <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="1166626">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="1166630">Stage IIB</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="1166627">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="1166628">N1a</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="1166629">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="1165751">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" source_system_identifier="1165750">8</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="1165752">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-BH-A0DI-F58698</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">31AD28DA-0E4B-4F0D-95BF-E74BE74D8070</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="3555286">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="3555442">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="3555443">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="3555444">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="3555445">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">912</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="3555454">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="3555455"/>
+                        <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="3555456"/>
+                        <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="3555457"/>
+                        <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="3555462"/>
+                        <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="3555467"/>
+                        <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="3555468"/>
+                        <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="3555469"/>
+                        <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="3555470"/>
+                        <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="3555471"/>
+                        <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="3555472"/>
+                        <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="3555473"/>
+                        <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="3555474"/>
+                        <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="3555475"/>
+                        <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="3555476"/>
+                        <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="3555477"/>
+                        <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="3555478"/>
+                        <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="3555479"/>
+                        <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="3555480"/>
+                        <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="3555481"/>
+                        <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="3555482"/>
+                        <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="3555483"/>
+                        <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="3555484"/>
+                        <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="3555485"/>
+                        <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="3555486"/>
+                        <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="3555487"/>
+                        <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="3555488"/>
+                        <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="3555489"/>
+                        <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="3555490"/>
+                        <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="3555491"/>
+                        <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="3555492"/>
+                    </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">22</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">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">2014</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="3556119">YES</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-BH-A0DI-D58707</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">062DAD22-5616-49FF-9EE5-1C0763405FEE</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="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">131</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">194</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="3556122">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="3556120">Adriamycin</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" source_system_identifier="3556121"/>
+                <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="3556127">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="3556132">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">22</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">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">2014</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="3556136">YES</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-BH-A0DI-D58708</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">CD0C2F47-0F49-4143-8B90-4DD1AEF83C03</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="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">131</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">194</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="3556139">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="3556137">Cytoxan</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" source_system_identifier="3556138"/>
+                <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="3556144">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="3556149">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">22</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">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">2014</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="3556153">YES</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-BH-A0DI-D58709</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">443925EA-94E1-4E24-96E1-9D9EAC2A280A</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="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">215</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="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">319</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="3556156">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="3556154">Taxol</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" source_system_identifier="3556155"/>
+                <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="3556161">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="3556166">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">22</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">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">2014</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-BH-A0DI-R58701</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">F056AB35-31BF-4599-ABE9-440E2C255424</rad:bcr_radiation_uuid>
+                <rad:days_to_radiation_therapy_start precision="day" 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">362</rad:days_to_radiation_therapy_start>
+                <rad:days_to_radiation_therapy_end precision="day" 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">402</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="3555755">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="Completed" restricted="false" source_system_identifier="3555757">50</rad:radiation_dosage>
+                <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="3555758">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="Completed" restricted="false" source_system_identifier="3555759">28</rad:numfractions>
+                <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="3555756">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="3555764">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="3555769">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">22</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">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">2014</clin_shared:year_of_form_completion>
+            </rad:radiation>
+            <rad:radiation>
+                <rad:bcr_radiation_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-BH-A0DI-R58704</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">67811850-0D4F-4182-8CBF-45970A1F7B64</rad:bcr_radiation_uuid>
+                <rad:days_to_radiation_therapy_start precision="day" 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">322</rad:days_to_radiation_therapy_start>
+                <rad:days_to_radiation_therapy_end precision="day" 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">357</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="3556083">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="Completed" restricted="false" source_system_identifier="3556085">45</rad:radiation_dosage>
+                <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="3556086">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="Completed" restricted="false" source_system_identifier="3556087">25</rad:numfractions>
+                <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="3556084">Regional site</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="3556092">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="3556097">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">22</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">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">2014</clin_shared:year_of_form_completion>
+            </rad:radiation>
+            <rad:radiation>
+                <rad:bcr_radiation_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-BH-A0DI-R58706</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">638AB258-DB1B-4910-9106-5FA88FB73D59</rad:bcr_radiation_uuid>
+                <rad:days_to_radiation_therapy_start precision="day" 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">363</rad:days_to_radiation_therapy_start>
+                <rad:days_to_radiation_therapy_end precision="day" 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">369</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="3556101">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="Completed" restricted="false" source_system_identifier="3556103">10</rad:radiation_dosage>
+                <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="3556104">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="Completed" restricted="false" source_system_identifier="3556105">5</rad:numfractions>
+                <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="3556102">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="3556110">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="3556115">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">22</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">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">2014</clin_shared:year_of_form_completion>
+            </rad:radiation>
+        </rad:radiations>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/27ba717a-5cd8-440a-9345-4ae086f6efca/nationwidechildrens.org_ssf.TCGA-BH-A0DI.xml

@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ssf:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/ssf/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/ssf/2.7/TCGA_BCR.SSF.xsd" schemaVersion="2.7" xmlns:ssf="http://tcga.nci/bcr/xml/ssf/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:ssf_disease="http://tcga.nci/bcr/xml/ssf_disease/2.7">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">8A25DBA6-DDC0-4989-8455-6BE47648873C</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">96.80.0</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>
+    <ssf:patient>
+        <admin:additional_studies/>
+        <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-BH-A0DI</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">27ba717a-5cd8-440a-9345-4ae086f6efca</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">BH</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0DI</shared:patient_id>
+        <shared:hiv_status preferred_name="hiv_status" display_order="9999" cde="2180464" cde_ver="1.000" xsd_ver="2.5" tier="" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
+        <ssf:tumor_samples>
+            <ssf:tumor_sample>
+                <ssf:bcr_sample_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false">3f33a14d-7797-4ade-85f7-1dbec18f774f</ssf:bcr_sample_uuid>
+                <shared:days_to_sample_procurement precision="day" xsd_ver="2.3" tier="" cde="" owner="TSS" procurement_status="Completed" preferred_name="" display_order="9999" cde_ver="">27</shared:days_to_sample_procurement>
+                <shared:method_of_sample_procurement preferred_name="tumor_sample_procurement_method" display_order="11" cde="3103514" cde_ver="1.000" xsd_ver="2.3" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143526">Other Method, specify</shared:method_of_sample_procurement>
+                <shared:other_method_of_sample_procurement preferred_name="cancer_procurement_method_other" display_order="12" cde="2006730" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143527">MODIFIED RADICAL MASTECTOMY</shared:other_method_of_sample_procurement>
+                <ssf:vessel_used preferred_name="tumor_sample_vessel_used" display_order="16" cde="3081940" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143528">Other</ssf:vessel_used>
+                <ssf:other_vessel_used preferred_name="tumor_sample_ship_vessel_other" display_order="17" cde="3288137" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143529">SPECIMEN STORAGE BAGS</ssf:other_vessel_used>
+                <shared:maximum_tumor_dimension preferred_name="tumor_resected_max_dimension" display_order="9999" cde="64215" cde_ver="3.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
+                <ssf:tumor_weight preferred_name="tumor_sample_weight" display_order="23" cde="3081946" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143530">200</ssf:tumor_weight>
+                <ssf:sample_prescreened preferred_name="tumor_sample_prescreened_at_tss" display_order="19" cde="3081942" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143533">YES</ssf:sample_prescreened>
+                <shared:tumor_nuclei_percent preferred_name="tumor_nuclei_percent" display_order="24" cde="2841225" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143531">70</shared:tumor_nuclei_percent>
+                <shared:tumor_necrosis_percent preferred_name="necrosis_percent" display_order="25" cde="2841237" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143532">30</shared:tumor_necrosis_percent>
+                <ssf:days_to_pathology_review precision="day" xsd_ver="2.5" tier="2" cde="3288497" owner="TSS" procurement_status="Completed" preferred_name="tss_pathology_review_days_to" display_order="63" cde_ver="1.000">264</ssf:days_to_pathology_review>
+                <ssf:path_confirm_tumor_nuclei_metrics preferred_name="tumor_nuclei_requirements_indicator" display_order="64" cde="3288520" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143603">YES</ssf:path_confirm_tumor_nuclei_metrics>
+                <ssf:path_confirm_tumor_necrosis_metrics preferred_name="necrosis_requirements_indicator" display_order="65" cde="3288524" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143604">YES</ssf:path_confirm_tumor_necrosis_metrics>
+                <ssf:path_confirm_report_attached preferred_name="tss_pathology_submitted" display_order="66" cde="3288292" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143606">YES</ssf:path_confirm_report_attached>
+                <ssf:path_confirm_diagnosis_matching preferred_name="histologic_dx_consistent" display_order="68" cde="3288300" cde_ver="1.000" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143605">YES</ssf:path_confirm_diagnosis_matching>
+                <ssf:reason_path_confirm_diagnosis_not_matching preferred_name="histologic_dx_inconsistent_reason" display_order="69" cde="3288315" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <ssf:top_slide_submitted preferred_name="tumor_sample_top_slide_submitted" display_order="999" cde="3081944" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143534">YES</ssf:top_slide_submitted>
+                <ssf:digital_image_submitted preferred_name="tumor_sample_image_submitted" display_order="999" cde="3081948" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143536">NO</ssf:digital_image_submitted>
+                <ssf:ffpe_tumor_slide_submitted preferred_name="ffpe_slide_submitted_indicator" display_order="9999" cde="3295811" cde_ver="1.000" xsd_ver="2.5" tier="" owner="TSS" procurement_status="Completed" restricted="false">NO</ssf:ffpe_tumor_slide_submitted>
+                <ssf:submitted_for_lce preferred_name="tumor_sample_bcr_macrodissection" display_order="9999" cde="3288488" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                <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="143608">No</shared:other_dx>
+                <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="143608">No</shared:history_of_neoadjuvant_treatment>
+                <shared:consent_or_death_status preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143609">Consented</shared:consent_or_death_status>
+                <shared:days_to_consent precision="day" xsd_ver="2.5" tier="1" cde="3288498" owner="TSS" procurement_status="Completed" preferred_name="patient_consent_days_to" display_order="76" cde_ver="1.000">15</shared:days_to_consent>
+                <shared:country preferred_name="tumor_sample_procurement_country" display_order="13" cde="3203072" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="740588"/>
+                <ssf_disease:disease_details/>
+                <ssf:tumor_histologies>
+                    <ssf:tumor_histology>
+                        <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="143519">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" xsi:nil="true"/>
+                        <shared:histological_percentage preferred_name="histologic_diagnosis_percent" display_order="9999" cde="3729998" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                        <shared:tumor_morphology_percentage preferred_name="" display_order="9999" cde="3729984" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
+                    </ssf:tumor_histology>
+                </ssf:tumor_histologies>
+                <ssf:tumor_locations>
+                    <ssf:tumor_focality preferred_name="tumor_focality" display_order="9999" cde="3174022" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+                    <ssf:laterality preferred_name="" display_order="9999" cde="4742852" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143522">Right</ssf:laterality>
+                    <ssf:tumor_location>
+                        <ssf:site_of_disease preferred_name="" display_order="9999" cde="4742851" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143522">Breast</ssf:site_of_disease>
+                        <ssf:site_of_disease_text preferred_name="" display_order="9999" cde="4742871" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                        <ssf:site_of_disease_description preferred_name="" display_order="9999" cde="4742918" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143522"/>
+                    </ssf:tumor_location>
+                </ssf:tumor_locations>
+            </ssf:tumor_sample>
+        </ssf:tumor_samples>
+        <ssf:normal_controls>
+            <ssf:normal_control>
+                <ssf:bcr_sample_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false">00eb938e-8d64-4103-8782-ce13f24cd2a6</ssf:bcr_sample_uuid>
+                <ssf:method_of_normal_sample_procurement preferred_name="normal_control_method" display_order="50" cde="3288147" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143567"/>
+                <ssf:other_method_of_normal_sample_procurement preferred_name="normal_control_method_other" display_order="51" cde="3288151" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="143568"/>
+                <ssf:days_to_normal_sample_procurement precision="day" xsd_ver="2.3" tier="1" cde="3288496" owner="TSS" procurement_status="Not Available" preferred_name="normal_control_procurement_days_to" display_order="55" cde_ver="1.000"/>
+                <ssf:normal_sample_site_proximity_to_tumor preferred_name="normal_control_proximity_to_tumor" display_order="59" cde="3088708" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143569">Distal (>2cm)</ssf:normal_sample_site_proximity_to_tumor>
+                <ssf:ncedna_dna_conc preferred_name="normal_control_DNA_concentration" display_order="48" cde="3288187" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143560"/>
+                <ssf:ncedna_dna_qm preferred_name="normal_control_DNA_quant_method" display_order="47" cde="3288186" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143559"/>
+                <ssf:ncedna_dna_qty preferred_name="normal_control_DNA_quantity" display_order="46" cde="3288185" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143558"/>
+                <ssf:ncedna_dna_vol preferred_name="normal_control_DNA_volume" display_order="49" cde="3288188" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="143561"/>
+                <ssf:normal_control_locations>
+                    <ssf:normal_control_location>
+                        <ssf:normal_tissue_anatomic_site preferred_name="" display_order="57" cde="4132152" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="143562">Breast</ssf:normal_tissue_anatomic_site>
+                        <ssf:other_anatomic_site_normal_tissue preferred_name="normal_control_site_other" display_order="58" cde="3288189" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="143563"/>
+                    </ssf:normal_control_location>
+                </ssf:normal_control_locations>
+            </ssf:normal_control>
+        </ssf:normal_controls>
+    </ssf:patient>
+</ssf:tcga_bcr>

data/gdc_data_organized/2b22db1d-54a1-4b9e-a86e-a174cf51d95c/1b8fc655-8f38-4d99-9945-131af673f31e.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	66863	23219.576635	N
+hsa-let-7a-2	67120	23308.825266	Y
+hsa-let-7a-3	67382	23399.810251	N
+hsa-let-7b	193371	67152.128285	N
+hsa-let-7c	34969	12143.717383	Y
+hsa-let-7d	1752	608.418681	N
+hsa-let-7e	3523	1223.435510	N
+hsa-let-7f-1	17459	6063.003282	N
+hsa-let-7f-2	17664	6134.193824	N
+hsa-let-7g	2596	901.515351	N
+hsa-let-7i	1625	564.315272	N
+hsa-mir-1-1	4	1.389084	N
+hsa-mir-1-2	9	3.125438	N
+hsa-mir-100	47960	16655.114120	Y
+hsa-mir-101-1	20269	7038.834614	N
+hsa-mir-101-2	20263	7036.750989	N
+hsa-mir-103a-1	9925	3446.664046	Y
+hsa-mir-103a-2	10095	3505.700105	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	20	6.945419	Y
+hsa-mir-106b	1038	360.467232	N
+hsa-mir-107	100	34.727094	Y
+hsa-mir-10a	119438	41477.346128	N
+hsa-mir-10b	739395	256770.394180	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	1	0.347271	N
+hsa-mir-1180	11	3.819980	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	1	0.347271	N
+hsa-mir-1224	0	0.000000	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	2	0.694542	N
+hsa-mir-1227	1	0.347271	N
+hsa-mir-1228	2	0.694542	N
+hsa-mir-1229	2	0.694542	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	1	0.347271	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	8	2.778167	N
+hsa-mir-1245b	1	0.347271	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	217	75.357793	N
+hsa-mir-1248	6	2.083626	N
+hsa-mir-1249	39	13.543567	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	0	0.000000	N
+hsa-mir-1255a	1	0.347271	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	11	3.819980	N
+hsa-mir-125a	9180	3187.947198	N
+hsa-mir-125b-1	10218	3548.414430	N
+hsa-mir-125b-2	10424	3619.952243	N
+hsa-mir-126	18235	6332.485529	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	9	3.125438	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	23	7.987232	N
+hsa-mir-1267	0	0.000000	N
+hsa-mir-1268a	0	0.000000	N
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+hsa-mir-1269a	0	0.000000	N
+hsa-mir-1269b	0	0.000000	N
+hsa-mir-127	2784	966.802288	N
+hsa-mir-1270	7	2.430897	N
+hsa-mir-1271	37	12.849025	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
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+hsa-mir-1273g	0	0.000000	N
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+hsa-mir-1275	2	0.694542	N
+hsa-mir-1276	1	0.347271	N
+hsa-mir-1277	0	0.000000	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	119	41.325241	N
+hsa-mir-128-2	79	27.434404	N
+hsa-mir-1281	0	0.000000	N
+hsa-mir-1282	0	0.000000	N
+hsa-mir-1283-1	0	0.000000	N
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+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	102	35.421636	N
+hsa-mir-1288	1	0.347271	N
+hsa-mir-1289-1	0	0.000000	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	17	5.903606	N
+hsa-mir-129-2	21	7.292690	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	4	1.389084	N
+hsa-mir-1292	0	0.000000	N
+hsa-mir-1293	0	0.000000	N
+hsa-mir-1294	1	0.347271	N
+hsa-mir-1295a	17	5.903606	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	39	13.543567	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	14	4.861793	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
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+hsa-mir-1303	0	0.000000	N
+hsa-mir-1304	2	0.694542	N
+hsa-mir-1305	0	0.000000	N
+hsa-mir-1306	30	10.418128	N
+hsa-mir-1307	821	285.109439	N
+hsa-mir-130a	907	314.974740	N
+hsa-mir-130b	27	9.376315	N
+hsa-mir-132	203	70.496000	N
+hsa-mir-1321	0	0.000000	N
+hsa-mir-1322	0	0.000000	N
+hsa-mir-1323	1	0.347271	N
+hsa-mir-1324	0	0.000000	N
+hsa-mir-133a-1	6	2.083626	Y
+hsa-mir-133a-2	3	1.041813	N
+hsa-mir-133b	1	0.347271	Y
+hsa-mir-134	1443	501.111962	N
+hsa-mir-1343	4	1.389084	N
+hsa-mir-135a-1	0	0.000000	N
+hsa-mir-135a-2	4	1.389084	N
+hsa-mir-135b	17	5.903606	N
+hsa-mir-136	98	34.032552	N
+hsa-mir-137	0	0.000000	N
+hsa-mir-138-1	0	0.000000	N
+hsa-mir-138-2	1	0.347271	N
+hsa-mir-139	930	322.961971	N
+hsa-mir-140	4486	1557.857422	N
+hsa-mir-141	1464	508.404651	N
+hsa-mir-142	3003	1042.854623	N
+hsa-mir-143	267286	92820.659565	N
+hsa-mir-144	167	57.994246	N
+hsa-mir-145	33700	11703.030564	N
+hsa-mir-1468	67	23.267153	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	490	170.162759	N
+hsa-mir-146b	1045	362.898129	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	139336	48387.343225	N
+hsa-mir-148b	199	69.106916	N
+hsa-mir-149	295	102.444926	N
+hsa-mir-150	4391	1524.866683	N
+hsa-mir-151a	4671	1622.102545	N
+hsa-mir-151b	19	6.598148	N
+hsa-mir-152	566	196.555350	N
+hsa-mir-153-1	5	1.736355	N
+hsa-mir-153-2	100	34.727094	N
+hsa-mir-1537	0	0.000000	N
+hsa-mir-1538	1	0.347271	N
+hsa-mir-1539	0	0.000000	N
+hsa-mir-154	40	13.890837	N
+hsa-mir-155	546	189.609931	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	145	50.354286	N
+hsa-mir-15b	414	143.770168	N
+hsa-mir-16-1	509	176.760907	N
+hsa-mir-16-2	536	186.137222	N
+hsa-mir-17	937	325.392868	Y
+hsa-mir-181a-1	1672	580.637006	N
+hsa-mir-181a-2	3180	1104.321578	N
+hsa-mir-181b-1	191	66.328749	N
+hsa-mir-181b-2	198	68.759645	N
+hsa-mir-181c	214	74.315980	N
+hsa-mir-181d	61	21.183527	N
+hsa-mir-182	12126	4211.007377	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	3030	1052.230938	N
+hsa-mir-184	6	2.083626	N
+hsa-mir-185	87	30.212571	N
+hsa-mir-186	987	342.756414	N
+hsa-mir-187	10	3.472709	N
+hsa-mir-188	5	1.736355	N
+hsa-mir-18a	11	3.819980	N
+hsa-mir-18b	0	0.000000	N
+hsa-mir-1908	0	0.000000	N
+hsa-mir-1909	0	0.000000	N
+hsa-mir-190a	20	6.945419	N
+hsa-mir-190b	6	2.083626	N
+hsa-mir-191	2227	773.372376	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	991	344.145498	Y
+hsa-mir-193a	3025	1050.494583	N
+hsa-mir-193b	238	82.650483	N
+hsa-mir-194-1	230	79.872315	N
+hsa-mir-194-2	256	88.901360	N
+hsa-mir-195	523	181.622700	N
+hsa-mir-196a-1	185	64.245123	N
+hsa-mir-196a-2	225	78.135961	N
+hsa-mir-196b	1932	670.927450	N
+hsa-mir-197	1352	469.510306	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	14	4.861793	N
+hsa-mir-198	0	0.000000	N
+hsa-mir-199a-1	8398	2916.381326	Y
+hsa-mir-199a-2	13765	4780.184443	Y
+hsa-mir-199b	18928	6573.144288	Y
+hsa-mir-19a	34	11.807212	N
+hsa-mir-19b-1	270	93.763153	N
+hsa-mir-19b-2	298	103.486739	N
+hsa-mir-200a	840	291.707587	N
+hsa-mir-200b	1038	360.467232	N
+hsa-mir-200c	15088	5239.623892	N
+hsa-mir-202	10	3.472709	N
+hsa-mir-203a	7470	2594.113897	N
+hsa-mir-203b	34	11.807212	N
+hsa-mir-204	103	35.768906	N
+hsa-mir-205	51265	17802.844566	N
+hsa-mir-2052	0	0.000000	N
+hsa-mir-2053	0	0.000000	N
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+hsa-mir-206	0	0.000000	N
+hsa-mir-208a	0	0.000000	N
+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	425	147.590148	N
+hsa-mir-20b	20	6.945419	N
+hsa-mir-21	94359	32768.138308	N
+hsa-mir-210	225	78.135961	N
+hsa-mir-211	0	0.000000	N
+hsa-mir-2110	7	2.430897	N
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+hsa-mir-2114	0	0.000000	N
+hsa-mir-2115	1	0.347271	N
+hsa-mir-2116	2	0.694542	N
+hsa-mir-2117	1	0.347271	N
+hsa-mir-212	11	3.819980	N
+hsa-mir-214	116	40.283429	N
+hsa-mir-215	15	5.209064	Y
+hsa-mir-216a	1	0.347271	N
+hsa-mir-216b	0	0.000000	N
+hsa-mir-217	32	11.112670	N
+hsa-mir-218-1	110	38.199803	N
+hsa-mir-218-2	97	33.685281	N
+hsa-mir-219a-1	4	1.389084	N
+hsa-mir-219a-2	1	0.347271	N
+hsa-mir-219b	3	1.041813	N
+hsa-mir-22	112016	38899.901236	N
+hsa-mir-221	323	112.168513	N
+hsa-mir-222	200	69.454187	N
+hsa-mir-223	302	104.875823	N
+hsa-mir-224	175	60.772414	N
+hsa-mir-2276	0	0.000000	N
+hsa-mir-2277	2	0.694542	N
+hsa-mir-2278	0	0.000000	N
+hsa-mir-2355	87	30.212571	N
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+hsa-mir-23a	12438	4319.355910	Y
+hsa-mir-23b	3369	1169.955785	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	1660	576.469755	N
+hsa-mir-24-2	1669	579.595193	N
+hsa-mir-2467	0	0.000000	N
+hsa-mir-25	19500	6771.783264	N
+hsa-mir-2681	0	0.000000	N
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+hsa-mir-26a-1	5711	1983.264319	N
+hsa-mir-26a-2	5524	1918.324654	N
+hsa-mir-26b	3753	1303.307825	N
+hsa-mir-27a	1941	674.052888	Y
+hsa-mir-27b	1571	545.562641	Y
+hsa-mir-28	19200	6667.601983	N
+hsa-mir-2861	0	0.000000	N
+hsa-mir-2909	0	0.000000	N
+hsa-mir-296	55	19.099902	N
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+hsa-mir-298	0	0.000000	N
+hsa-mir-299	28	9.723586	N
+hsa-mir-29a	25740	8938.753909	N
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+hsa-mir-29b-2	869	301.778444	N
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+hsa-mir-30c-1	1758	610.502307	Y
+hsa-mir-30c-2	1951	677.525597	Y
+hsa-mir-30d	18825	6537.375382	N
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+hsa-mir-3130-2	4	1.389084	N
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+hsa-mir-3152	2	0.694542	N
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+hsa-mir-320d-2	5	1.736355	N
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+hsa-mir-330	58	20.141714	N
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+hsa-mir-335	716	248.645991	N
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+hsa-mir-338	362	125.712079	N
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+hsa-mir-33b	4	1.389084	N
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+hsa-mir-342	652	226.420651	N
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+hsa-mir-346	2	0.694542	N
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+hsa-mir-3591	0	0.000000	N
+hsa-mir-3605	25	8.681773	N
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+hsa-mir-3607	487	169.120946	N
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+hsa-mir-361	1121	389.290720	N
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+hsa-mir-3611	0	0.000000	N
+hsa-mir-3612	2	0.694542	N
+hsa-mir-3613	18	6.250877	N
+hsa-mir-3614	5	1.736355	N
+hsa-mir-3615	2	0.694542	N
+hsa-mir-3616	0	0.000000	N
+hsa-mir-3617	0	0.000000	N
+hsa-mir-3618	1	0.347271	N
+hsa-mir-3619	0	0.000000	N
+hsa-mir-362	19	6.598148	N
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+hsa-mir-3926-2	5	1.736355	N
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+hsa-mir-424	564	195.860808	N
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+hsa-mir-4676	2	0.694542	N
+hsa-mir-4677	17	5.903606	N
+hsa-mir-4678	0	0.000000	N
+hsa-mir-4679-1	1	0.347271	N
+hsa-mir-4679-2	0	0.000000	N
+hsa-mir-4680	0	0.000000	N
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+hsa-mir-4682	0	0.000000	N
+hsa-mir-4683	1	0.347271	N
+hsa-mir-4684	0	0.000000	N
+hsa-mir-4685	0	0.000000	N
+hsa-mir-4686	0	0.000000	N
+hsa-mir-4687	0	0.000000	N
+hsa-mir-4688	0	0.000000	N
+hsa-mir-4689	0	0.000000	N
+hsa-mir-4690	0	0.000000	N
+hsa-mir-4691	0	0.000000	N
+hsa-mir-4692	0	0.000000	N
+hsa-mir-4693	0	0.000000	N
+hsa-mir-4694	0	0.000000	N
+hsa-mir-4695	0	0.000000	N
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+hsa-mir-4699	1	0.347271	N
+hsa-mir-4700	0	0.000000	N
+hsa-mir-4701	0	0.000000	N
+hsa-mir-4703	0	0.000000	N
+hsa-mir-4704	0	0.000000	N
+hsa-mir-4705	1	0.347271	N
+hsa-mir-4706	0	0.000000	N
+hsa-mir-4707	1	0.347271	N
+hsa-mir-4708	0	0.000000	N
+hsa-mir-4709	0	0.000000	N
+hsa-mir-4710	0	0.000000	N
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+hsa-mir-4712	0	0.000000	N
+hsa-mir-4713	0	0.000000	N
+hsa-mir-4714	3	1.041813	N
+hsa-mir-4715	0	0.000000	N
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+hsa-mir-4718	0	0.000000	N
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+hsa-mir-4726	1	0.347271	N
+hsa-mir-4727	0	0.000000	N
+hsa-mir-4728	3	1.041813	N
+hsa-mir-4729	0	0.000000	N
+hsa-mir-4730	0	0.000000	N
+hsa-mir-4731	0	0.000000	N
+hsa-mir-4732	3	1.041813	N
+hsa-mir-4733	0	0.000000	N
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+hsa-mir-4735	0	0.000000	N
+hsa-mir-4736	0	0.000000	N
+hsa-mir-4737	0	0.000000	N
+hsa-mir-4738	2	0.694542	N
+hsa-mir-4739	0	0.000000	N
+hsa-mir-4740	1	0.347271	N
+hsa-mir-4741	0	0.000000	N
+hsa-mir-4742	2	0.694542	N
+hsa-mir-4743	0	0.000000	N
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+hsa-mir-4745	0	0.000000	N
+hsa-mir-4746	0	0.000000	N
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+hsa-mir-4751	0	0.000000	N
+hsa-mir-4752	0	0.000000	N
+hsa-mir-4753	0	0.000000	N
+hsa-mir-4754	0	0.000000	N
+hsa-mir-4755	1	0.347271	N
+hsa-mir-4756	0	0.000000	N
+hsa-mir-4757	1	0.347271	N
+hsa-mir-4758	0	0.000000	N
+hsa-mir-4759	1	0.347271	N
+hsa-mir-4760	0	0.000000	N
+hsa-mir-4761	0	0.000000	N
+hsa-mir-4762	1	0.347271	N
+hsa-mir-4763	0	0.000000	N
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+hsa-mir-4766	1	0.347271	N
+hsa-mir-4767	0	0.000000	N
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+hsa-mir-4769	0	0.000000	N
+hsa-mir-4770	2	0.694542	N
+hsa-mir-4771-1	0	0.000000	N
+hsa-mir-4771-2	0	0.000000	N
+hsa-mir-4772	17	5.903606	N
+hsa-mir-4773-1	0	0.000000	N
+hsa-mir-4773-2	0	0.000000	N
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+hsa-mir-4775	0	0.000000	N
+hsa-mir-4776-1	0	0.000000	N
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+hsa-mir-4778	0	0.000000	N
+hsa-mir-4779	0	0.000000	N
+hsa-mir-4780	1	0.347271	N
+hsa-mir-4781	1	0.347271	N
+hsa-mir-4782	0	0.000000	N
+hsa-mir-4783	0	0.000000	N
+hsa-mir-4784	0	0.000000	N
+hsa-mir-4785	0	0.000000	N
+hsa-mir-4786	0	0.000000	N
+hsa-mir-4787	2	0.694542	N
+hsa-mir-4788	1	0.347271	N
+hsa-mir-4789	0	0.000000	N
+hsa-mir-4790	0	0.000000	N
+hsa-mir-4791	0	0.000000	N
+hsa-mir-4792	0	0.000000	N
+hsa-mir-4793	0	0.000000	N
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+hsa-mir-4797	1	0.347271	N
+hsa-mir-4798	0	0.000000	N
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+hsa-mir-4801	0	0.000000	N
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+hsa-mir-4803	0	0.000000	N
+hsa-mir-4804	1	0.347271	N
+hsa-mir-483	57	19.794443	N
+hsa-mir-484	121	42.019783	N
+hsa-mir-485	10	3.472709	N
+hsa-mir-486-1	456	158.355547	N
+hsa-mir-486-2	422	146.548335	N
+hsa-mir-487a	3	1.041813	N
+hsa-mir-487b	24	8.334502	N
+hsa-mir-488	4	1.389084	N
+hsa-mir-489	0	0.000000	N
+hsa-mir-490	1	0.347271	N
+hsa-mir-491	26	9.029044	N
+hsa-mir-492	0	0.000000	N
+hsa-mir-493	8	2.778167	N
+hsa-mir-494	11	3.819980	N
+hsa-mir-495	32	11.112670	N
+hsa-mir-496	5	1.736355	N
+hsa-mir-497	295	102.444926	N
+hsa-mir-498	0	0.000000	N
+hsa-mir-4999	0	0.000000	N
+hsa-mir-499a	1	0.347271	N
+hsa-mir-499b	0	0.000000	N
+hsa-mir-5000	6	2.083626	N
+hsa-mir-5001	1	0.347271	N
+hsa-mir-5002	0	0.000000	N
+hsa-mir-5003	0	0.000000	N
+hsa-mir-5004	0	0.000000	N
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+hsa-mir-5007	0	0.000000	N
+hsa-mir-5008	1	0.347271	N
+hsa-mir-5009	0	0.000000	N
+hsa-mir-500a	237	82.303212	Y
+hsa-mir-500b	9	3.125438	Y
+hsa-mir-501	41	14.238108	N
+hsa-mir-5010	1	0.347271	N
+hsa-mir-5011	0	0.000000	N
+hsa-mir-502	14	4.861793	Y
+hsa-mir-503	8	2.778167	N
+hsa-mir-504	4	1.389084	N
+hsa-mir-5047	0	0.000000	N
+hsa-mir-505	176	61.119685	N
+hsa-mir-506	0	0.000000	N
+hsa-mir-507	0	0.000000	N
+hsa-mir-508	6	2.083626	N
+hsa-mir-5087	0	0.000000	N
+hsa-mir-5088	0	0.000000	N
+hsa-mir-5089	1	0.347271	N
+hsa-mir-509-1	1	0.347271	N
+hsa-mir-509-2	2	0.694542	N
+hsa-mir-509-3	8	2.778167	N
+hsa-mir-5090	0	0.000000	N
+hsa-mir-5091	3	1.041813	N
+hsa-mir-5092	0	0.000000	N
+hsa-mir-5093	0	0.000000	N
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+hsa-mir-5095	0	0.000000	N
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+hsa-mir-510	0	0.000000	N
+hsa-mir-5100	0	0.000000	N
+hsa-mir-511	36	12.501754	N
+hsa-mir-512-1	0	0.000000	N
+hsa-mir-512-2	0	0.000000	N
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+hsa-mir-514a-3	1	0.347271	N
+hsa-mir-514b	0	0.000000	N
+hsa-mir-515-1	0	0.000000	N
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+hsa-mir-516a-1	1	0.347271	N
+hsa-mir-516a-2	0	0.000000	N
+hsa-mir-516b-1	1	0.347271	N
+hsa-mir-516b-2	0	0.000000	N
+hsa-mir-517a	2	0.694542	Y
+hsa-mir-517b	2	0.694542	Y
+hsa-mir-517c	0	0.000000	N
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+hsa-mir-5188	0	0.000000	N
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+hsa-mir-518f	0	0.000000	N
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+hsa-mir-519b	0	0.000000	N
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+hsa-mir-519d	0	0.000000	N
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+hsa-mir-520h	1	0.347271	Y
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+hsa-mir-527	0	0.000000	N
+hsa-mir-532	1325	460.133991	N
+hsa-mir-539	37	12.849025	N
+hsa-mir-541	0	0.000000	N
+hsa-mir-542	287	99.666759	N
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+hsa-mir-550a-2	5	1.736355	N
+hsa-mir-550a-3	2	0.694542	N
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+hsa-mir-551b	12	4.167251	N
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+hsa-mir-558	0	0.000000	N
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+hsa-mir-5587	0	0.000000	N
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+hsa-mir-5590	0	0.000000	N
+hsa-mir-5591	0	0.000000	N
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+hsa-mir-562	0	0.000000	N
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+hsa-mir-564	0	0.000000	N
+hsa-mir-566	0	0.000000	N
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+hsa-mir-5680	2	0.694542	N
+hsa-mir-5681a	0	0.000000	N
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+hsa-mir-5683	30	10.418128	N
+hsa-mir-5684	1	0.347271	N
+hsa-mir-5685	0	0.000000	N
+hsa-mir-5687	1	0.347271	N
+hsa-mir-5688	0	0.000000	N
+hsa-mir-5689	0	0.000000	N
+hsa-mir-569	0	0.000000	N
+hsa-mir-5690	0	0.000000	N
+hsa-mir-5691	1	0.347271	N
+hsa-mir-5692a-1	0	0.000000	N
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+hsa-mir-5692c-2	0	0.000000	N
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+hsa-mir-5696	1	0.347271	N
+hsa-mir-5697	0	0.000000	N
+hsa-mir-5698	2	0.694542	N
+hsa-mir-5699	1	0.347271	N
+hsa-mir-570	3	1.041813	N
+hsa-mir-5700	0	0.000000	N
+hsa-mir-5701-1	0	0.000000	N
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+hsa-mir-5707	0	0.000000	N
+hsa-mir-5708	0	0.000000	N
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+hsa-mir-573	0	0.000000	N
+hsa-mir-5739	0	0.000000	N
+hsa-mir-574	700	243.089656	N
+hsa-mir-575	0	0.000000	N
+hsa-mir-576	31	10.765399	N
+hsa-mir-577	6	2.083626	N
+hsa-mir-578	0	0.000000	N
+hsa-mir-5787	0	0.000000	N
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+hsa-mir-580	1	0.347271	N
+hsa-mir-581	0	0.000000	N
+hsa-mir-582	191	66.328749	N
+hsa-mir-583	0	0.000000	N
+hsa-mir-584	151	52.437911	N
+hsa-mir-585	9	3.125438	N
+hsa-mir-586	0	0.000000	N
+hsa-mir-587	0	0.000000	N
+hsa-mir-588	1	0.347271	N
+hsa-mir-589	106	36.810719	N
+hsa-mir-590	28	9.723586	N
+hsa-mir-591	0	0.000000	N
+hsa-mir-592	1	0.347271	N
+hsa-mir-593	0	0.000000	N
+hsa-mir-595	0	0.000000	N
+hsa-mir-596	0	0.000000	N
+hsa-mir-597	0	0.000000	N
+hsa-mir-598	36	12.501754	N
+hsa-mir-599	0	0.000000	N
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data/gdc_data_organized/2b22db1d-54a1-4b9e-a86e-a174cf51d95c/JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_A06_747912.nocnv_grch38.seg.v2.txt

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data/gdc_data_organized/2b22db1d-54a1-4b9e-a86e-a174cf51d95c/JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_B11_747940.grch38.seg.v2.txt

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data/gdc_data_organized/2b22db1d-54a1-4b9e-a86e-a174cf51d95c/TCGA-BH-A0BS-01A-11D-A890-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt

@@ -0,0 +1,359 @@
+GDC_Aliquot_ID	Chromosome	Start	End	Num_Probes	Segment_Mean
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	17001	16534000	15133	-0.000626
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	16534001	16645000	79	0.177000
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	16645001	16722000	37	0.198458
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	16722001	16730000	8	0.440026
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	16730001	16949000	119	-0.008542
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	16949001	103561000	85944	-0.001205
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	103561001	103761000	43	0.541744
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	103761001	120574000	16005	0.000214
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	120671001	120947000	32	-0.698394
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	120947001	125168000	811	-0.002440
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	125168001	143772000	311	0.528125
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	143775001	158254000	10469	0.456799
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	158254001	172713000	14287	0.454147
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	172713001	175459000	2712	0.455812
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	175459001	181567000	6070	0.448414
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	181567001	184210000	2637	0.453138
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	184210001	184479000	269	0.451250
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	184479001	191182000	6655	0.449954
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	191182001	206019000	14687	0.451916
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	206019001	206440000	193	0.449665
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	206440001	217939000	11406	0.449638
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	217939001	224730000	6620	0.448341
+TCGA-BH-A0BS-01A-11D-A890-36	chr1	224730001	229381000	4532	0.448856
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