Auto-upload batch data to clear storage

.gitattributes

@@ -57,3 +57,69 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
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 *.webm filter=lfs diff=lfs merge=lfs -text
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data/__notebook__.ipynb

@@ -0,0 +1,2591 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "e71279e2",
+   "metadata": {
+    "execution": {
+     "iopub.execute_input": "2026-01-03T05:06:29.218342Z",
+     "iopub.status.busy": "2026-01-03T05:06:29.217998Z"
+    },
+    "papermill": {
+     "duration": null,
+     "end_time": null,
+     "exception": false,
+     "start_time": "2026-01-03T05:06:29.213366",
+     "status": "running"
+    },
+    "tags": []
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> Đã kết nối với Hugging Face Repo: enzosama154/BRCancer\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Đọc file Excel thành công.\n",
+      "Tra cứu UUID cho 1095 IDs...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> Đã tìm thấy 0 file đã xử lý trước đó (sẽ bỏ qua).\n",
+      "Đang lấy danh sách file...\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-> Tổng số file cần xử lý: 10000\n",
+      "[1/10000] (0.00GB) Downloading: 277ef499-3b0f-429e-a5fd-b63b59ce731f.mirbase21.isoforms.quantification.txt (0.26 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[2/10000] (0.00GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_F09_741494.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[3/10000] (0.00GB) Downloading: a3dad6d1-c405-4458-b5d2-63da84596781_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[4/10000] (0.00GB) Downloading: TCGA-BRCA.cdcbf3a0-b1eb-4a63-b669-f7a6438c6902.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[5/10000] (0.00GB) Downloading: TCGA-BRCA.cdcbf3a0-b1eb-4a63-b669-f7a6438c6902.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[6/10000] (0.00GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_C12_741462.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[7/10000] (0.00GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A18H.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[8/10000] (0.00GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A18H.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[9/10000] (0.00GB) Downloading: TCGA-BH-A18H.DF536409-601F-489B-9F8A-A2B372BF9999.PDF (0.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[10/10000] (0.00GB) Downloading: TCGA-BRCA.cdcbf3a0-b1eb-4a63-b669-f7a6438c6902.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[11/10000] (0.00GB) Downloading: nationwidechildrens.org_omf.TCGA-BH-A18H.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[12/10000] (0.00GB) Downloading: 94027f46-390c-4dda-ab89-cb1ac0a291cd.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[13/10000] (0.01GB) Downloading: 277ef499-3b0f-429e-a5fd-b63b59ce731f.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[14/10000] (0.01GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_C12_741462.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[15/10000] (0.01GB) Downloading: TCGA-BRCA.cdcbf3a0-b1eb-4a63-b669-f7a6438c6902.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[16/10000] (0.01GB) Downloading: TCGA-BH-A18H-01A-01-TSA.75dba5a3-f9f5-4ff4-814c-7d2451820e03.svs (207.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[17/10000] (0.21GB) Downloading: a3dad6d1-c405-4458-b5d2-63da84596781.methylation_array.sesame.level3betas.txt (0.73 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[18/10000] (0.22GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A18H.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[19/10000] (0.22GB) Downloading: 01d89297-2636-4115-bfcf-993e9523401e.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[20/10000] (0.22GB) Downloading: TCGA-BRCA.32d3f1cd-077f-43bf-843e-1fe9f0ec0cba.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[21/10000] (0.22GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_A10_741498.nocnv_grch38.seg.v2.txt (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[22/10000] (0.22GB) Downloading: TCGA-BRCA.32d3f1cd-077f-43bf-843e-1fe9f0ec0cba.ascat3.allelic_specific.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[23/10000] (0.22GB) Downloading: TCGA-BRCA.32d3f1cd-077f-43bf-843e-1fe9f0ec0cba.ascat2.allelic_specific.seg.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[24/10000] (0.22GB) Downloading: TCGA-E2-A14P-01Z-00-DX1.663B02FF-C64B-41A6-8685-FD61CD76F9C6.svs (1523.35 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[25/10000] (1.71GB) Downloading: a9c72a75-2d8b-4f11-8af0-8cfed17e0ec4.mirbase21.isoforms.quantification.txt (0.39 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[26/10000] (1.71GB) Downloading: df45fb41-4511-4dab-b865-fcdfcda0400a.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[27/10000] (1.71GB) Downloading: 74b57d2c-a83f-4798-b86b-a533975e4cc0_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[28/10000] (1.71GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A14P.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[29/10000] (1.71GB) Downloading: TCGA-E2-A14P.FD8CDFD9-6DCF-4CE1-9BB1-A7FF568EE53C.PDF (0.26 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[30/10000] (1.71GB) Downloading: TCGA-E2-A14P-01A-31D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.20 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[31/10000] (1.71GB) Downloading: 19d539d7-e9ed-42c4-b374-e8cd4798b30e_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[32/10000] (1.71GB) Downloading: TCGA-E2-A14P-01A-03-TSC.e301fe1e-c75b-4ed2-b304-16a9d63fd835.svs (275.91 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[33/10000] (1.98GB) Downloading: TCGA-E2-A14P-01A-21-A13E-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[34/10000] (1.98GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E2-A14P.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[35/10000] (1.98GB) Downloading: nationwidechildrens.org_ssf.TCGA-E2-A14P.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[36/10000] (1.98GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_A11_741394.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[37/10000] (1.98GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_A11_741394.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[38/10000] (1.98GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_A10_741498.grch38.seg.v2.txt (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[39/10000] (1.98GB) Downloading: TCGA-BRCA.32d3f1cd-077f-43bf-843e-1fe9f0ec0cba.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[40/10000] (1.98GB) Downloading: a9c72a75-2d8b-4f11-8af0-8cfed17e0ec4.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[41/10000] (1.98GB) Downloading: 19d539d7-e9ed-42c4-b374-e8cd4798b30e_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[42/10000] (1.99GB) Downloading: 917569dc-8716-447b-b47f-654a639dfc74.wxs.aliquot_ensemble_masked.maf.gz (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[43/10000] (1.99GB) Downloading: 19d539d7-e9ed-42c4-b374-e8cd4798b30e.methylation_array.sesame.level3betas.txt (0.73 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[44/10000] (1.99GB) Downloading: TCGA-BRCA.32d3f1cd-077f-43bf-843e-1fe9f0ec0cba.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[45/10000] (1.99GB) Downloading: TCGA-AN-A04A-01A-02-BS2.44355b22-95d3-491c-af4c-27225e753d7d.svs (236.18 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[46/10000] (2.22GB) Downloading: TCGA-AN-A04A-01A-21D-A89H-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.16 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[47/10000] (2.22GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_D07_667028.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[48/10000] (2.22GB) Downloading: ee16a10b-11e6-4846-9f8c-59d8d6be9faa_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[49/10000] (2.22GB) Downloading: ee16a10b-11e6-4846-9f8c-59d8d6be9faa_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[50/10000] (2.22GB) Downloading: nationwidechildrens.org_ssf.TCGA-AN-A04A.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[51/10000] (2.22GB) Downloading: TCGA-BRCA.928be25e-9343-4042-a5c0-851465def55b.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[52/10000] (2.22GB) Downloading: TCGA-AN-A04A.6FB7A794-C3E7-4501-A844-CF65B9C3D32C.PDF (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[53/10000] (2.22GB) Downloading: nationwidechildrens.org_clinical.TCGA-AN-A04A.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[54/10000] (2.22GB) Downloading: TCGA-AN-A04A-01A-01-BS1.647f0482-49a8-4794-b9c4-5941b14fd1af.svs (207.28 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[55/10000] (2.42GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B05_666944.grch38.seg.v2.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[56/10000] (2.42GB) Downloading: TCGA-BRCA.928be25e-9343-4042-a5c0-851465def55b.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[57/10000] (2.43GB) Downloading: 6bd02673-dd3f-42ed-9997-e371b09f22ee.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[58/10000] (2.43GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_D07_667028.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[59/10000] (2.43GB) Downloading: TCGA-BRCA.928be25e-9343-4042-a5c0-851465def55b.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[60/10000] (2.43GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B05_666944.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[61/10000] (2.43GB) Downloading: ee16a10b-11e6-4846-9f8c-59d8d6be9faa.methylation_array.sesame.level3betas.txt (0.74 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[62/10000] (2.43GB) Downloading: c33ecc28-d5ba-4416-b93d-445b7883b6e8.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[63/10000] (2.44GB) Downloading: TCGA-AN-A04A-01A-11-A13A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[64/10000] (2.44GB) Downloading: 6bd02673-dd3f-42ed-9997-e371b09f22ee.mirbase21.isoforms.quantification.txt (0.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[65/10000] (2.44GB) Downloading: TCGA-BRCA.928be25e-9343-4042-a5c0-851465def55b.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[66/10000] (2.44GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A04A.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[67/10000] (2.44GB) Downloading: fc2a9d28-f6bd-4b6b-bcc2-05c1eaf56dca.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[68/10000] (2.44GB) Downloading: TCGA-BRCA.928be25e-9343-4042-a5c0-851465def55b.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[69/10000] (2.44GB) Downloading: fe712c27-8dbb-4531-afb3-10999e319a7b.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[70/10000] (2.44GB) Downloading: fe712c27-8dbb-4531-afb3-10999e319a7b.mirbase21.isoforms.quantification.txt (0.36 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[71/10000] (2.44GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_F10_780774.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[72/10000] (2.44GB) Downloading: TCGA-BRCA.6a4af154-27d5-4a5d-9d88-1f4db2dc70d8.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[73/10000] (2.44GB) Downloading: TCGA-BRCA.6a4af154-27d5-4a5d-9d88-1f4db2dc70d8.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[74/10000] (2.44GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A202.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[75/10000] (2.44GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D11_628352.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[76/10000] (2.44GB) Downloading: TCGA-BRCA.23353deb-8af1-474e-8654-70d444529e5e.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[77/10000] (2.44GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_B07_628378.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[78/10000] (2.44GB) Downloading: ac3dbb7f-2ce9-43b7-9f45-1c1521e6bbf5.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[79/10000] (2.44GB) Downloading: d0f46c64-763a-4439-838c-bc95323a9290.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[80/10000] (2.44GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_A06_628440.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[81/10000] (2.44GB) Downloading: 93655b20-9109-4c7e-afd7-7bc76ca61578_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[82/10000] (2.44GB) Downloading: TCGA-A8-A091-01A-01-BS1.e7e9318d-a627-472a-9f2e-10cc917036d3.svs (381.41 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[83/10000] (2.81GB) Downloading: TCGA-A7-A0CD-01Z-00-DX1.F045B9C8-049C-41BF-8432-EF89F236D34D.svs (267.95 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[84/10000] (3.07GB) Downloading: nationwidechildrens.org_clinical.TCGA-LL-A6FP.xml (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[85/10000] (3.07GB) Downloading: TCGA-BRCA.23353deb-8af1-474e-8654-70d444529e5e.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[86/10000] (3.07GB) Downloading: TCGA-BRCA.23353deb-8af1-474e-8654-70d444529e5e.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[87/10000] (3.08GB) Downloading: TCGA-A7-A0CD-01A-01-TSA.8966c3d7-c0d2-47a4-badf-df9412a1e5f0.svs (677.53 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[88/10000] (3.74GB) Downloading: nationwidechildrens.org_ssf.TCGA-LL-A6FP.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[89/10000] (3.74GB) Downloading: 071a05c1-f9df-4e68-b73e-8f6716d75d52_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[90/10000] (3.75GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D09_628270.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[91/10000] (3.75GB) Downloading: 8585afe0-a21f-4093-bd82-269cc8e5698f.mirbase21.isoforms.quantification.txt (0.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[92/10000] (3.75GB) Downloading: 465c6270-2bfa-410a-b282-e7cc7b7b028c_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[93/10000] (3.75GB) Downloading: 37471af4-1248-4dd2-bb13-ebbdcb61c3e3.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[94/10000] (3.75GB) Downloading: 071a05c1-f9df-4e68-b73e-8f6716d75d52.methylation_array.sesame.level3betas.txt (12.41 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[95/10000] (3.76GB) Downloading: TCGA-BRCA.4d7ffa3e-0218-4fc4-b3da-691d56a7df1a.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[96/10000] (3.76GB) Downloading: TCGA-5L-AAT1-01Z-00-DX1.F3449A5B-2AC4-4ED7-BF44-4C8946CDB47D.svs (565.31 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[97/10000] (4.31GB) Downloading: 8585afe0-a21f-4093-bd82-269cc8e5698f.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[98/10000] (4.31GB) Downloading: TCGA-BRCA.4d7ffa3e-0218-4fc4-b3da-691d56a7df1a.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[99/10000] (4.32GB) Downloading: c74a2bd9-ce8c-4d7f-99d5-f8bac92ceaf5.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[100/10000] (4.32GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-5L-AAT1.xml (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[101/10000] (4.32GB) Downloading: TCGA-BRCA.768075b7-62ca-4f16-b1a6-7700c94a146b.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[102/10000] (4.32GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A09K.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[103/10000] (4.32GB) Downloading: nationwidechildrens.org_omf.TCGA-A8-A06T.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[104/10000] (4.32GB) Downloading: TCGA-A8-A09K-01Z-00-DX1.41B2DF5F-C0E1-43BB-BAA5-2946A9EC4650.svs (996.51 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[105/10000] (5.29GB) Downloading: nationwidechildrens.org_clinical.TCGA-5L-AAT1.xml (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[106/10000] (5.29GB) Downloading: nationwidechildrens.org_omf.TCGA-A8-A09K.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[107/10000] (5.29GB) Downloading: TCGA-BRCA.b412fc52-5776-4ff9-b9c4-829efabfb377.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[108/10000] (5.29GB) Downloading: TCGA-BRCA.768075b7-62ca-4f16-b1a6-7700c94a146b.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[109/10000] (5.29GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H09_628554.nocnv_grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[110/10000] (5.29GB) Downloading: fe1694df-4aca-4a23-bbf5-c0c1d24d4c2b.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[111/10000] (5.29GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_H09_628554.grch38.seg.v2.txt (0.32 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[112/10000] (5.30GB) Downloading: e966e65a-f107-47a0-8ae3-649ee2148dbf_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[113/10000] (5.30GB) Downloading: 602e3d24-a45d-4fe4-9b70-a679d93f470d.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[114/10000] (5.30GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G03_628460.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[115/10000] (5.30GB) Downloading: TCGA-BRCA.768075b7-62ca-4f16-b1a6-7700c94a146b.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[116/10000] (5.30GB) Downloading: 69ca2b97-43dd-465a-84f3-ab2265dbd562.wxs.aliquot_ensemble_masked.maf.gz (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[117/10000] (5.30GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09K.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[118/10000] (5.30GB) Downloading: d8c6fdeb-4aba-4a11-b62e-d587dadbcc62_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[119/10000] (5.31GB) Downloading: TCGA-BRCA.d986386e-b0cc-46f5-a9dc-8e0c58178f4a.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[120/10000] (5.31GB) Downloading: TCGA-BRCA.b412fc52-5776-4ff9-b9c4-829efabfb377.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[121/10000] (5.31GB) Downloading: TCGA-AR-A2LR-01A-12D-A89B-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.33 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[122/10000] (5.31GB) Downloading: TCGA-AO-A0J5-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[123/10000] (5.31GB) Downloading: 89c06b7b-8adc-449c-8de5-d8190b0f8c4d_noid_Grn.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[124/10000] (5.31GB) Downloading: 0d4038c9-b069-4b89-8359-b4546aa974c1.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[125/10000] (5.31GB) Downloading: cc383d81-8a72-4071-b69b-9822403ae3d5.mirbase21.isoforms.quantification.txt (0.46 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[126/10000] (5.31GB) Downloading: a4967c46-39b0-4285-ad1d-6c758155017e.mirbase21.isoforms.quantification.txt (0.37 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[127/10000] (5.31GB) Downloading: TCGA-BRCA.d986386e-b0cc-46f5-a9dc-8e0c58178f4a.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[128/10000] (5.32GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_B04_667212.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[129/10000] (5.32GB) Downloading: TCGA-BRCA.d986386e-b0cc-46f5-a9dc-8e0c58178f4a.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[130/10000] (5.32GB) Downloading: d8c6fdeb-4aba-4a11-b62e-d587dadbcc62.methylation_array.sesame.level3betas.txt (12.56 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[131/10000] (5.33GB) Downloading: 61f886ca-c23c-47c9-8f22-05cc18836ee4_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[132/10000] (5.33GB) Downloading: 209d014b-eb5e-4d1d-a4ab-cdf8d9c285b2.mirbase21.isoforms.quantification.txt (0.31 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[133/10000] (5.33GB) Downloading: 9f7e2939-8899-4732-b291-14075f697205.mirbase21.isoforms.quantification.txt (0.38 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[134/10000] (5.33GB) Downloading: bb2942d4-a639-4244-85ba-328d51b50bef.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[135/10000] (5.33GB) Downloading: TCGA-AR-A2LR-01A-21-A24A-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[136/10000] (5.33GB) Downloading: 03d891b3-8faf-4384-94ce-2015f1ca5df0.rna_seq.augmented_star_gene_counts.tsv (4.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[137/10000] (5.34GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A2LR.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[138/10000] (5.34GB) Downloading: TCGA-BRCA.9ba65dff-5f6c-4d9e-8e58-8350a7c1dcbe.ascat2.allelic_specific.seg.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[139/10000] (5.34GB) Downloading: TCGA-BRCA.9ba65dff-5f6c-4d9e-8e58-8350a7c1dcbe.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[140/10000] (5.34GB) Downloading: a4967c46-39b0-4285-ad1d-6c758155017e.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[141/10000] (5.34GB) Downloading: 061a1748-0ede-4380-9d86-fcf4b9713699.wgs.ASCAT.gene_level.copy_number_variation.tsv (3.28 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[142/10000] (5.34GB) Downloading: TCGA-A8-A09I-01A-22D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[143/10000] (5.34GB) Downloading: 2912470e-ef3f-40fa-8a9b-f77aae0afa2d.methylation_array.sesame.level3betas.txt (0.74 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[144/10000] (5.34GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_E01_628368.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[145/10000] (5.34GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_F03_628330.nocnv_grch38.seg.v2.txt (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[146/10000] (5.34GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_B04_667212.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[147/10000] (5.34GB) Downloading: nationwidechildrens.org_clinical.TCGA-AO-A0J5.xml (0.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[148/10000] (5.34GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0BD.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[149/10000] (5.34GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_G04_666952.grch38.seg.v2.txt (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[150/10000] (5.34GB) Downloading: ffc8fa8f-f6f7-4b8a-9773-b29dc0a60410.methylation_array.sesame.level3betas.txt (12.28 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[151/10000] (5.36GB) Downloading: TCGA-BRCA.8cd0933f-c93e-4265-a6c4-6892f407ced9.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[152/10000] (5.36GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_A12_772184.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[153/10000] (5.36GB) Downloading: TCGA-C8-A1HO-01A-11D-A896-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[154/10000] (5.36GB) Downloading: TCGA-A8-A06U-01A-01-BS1.1182603b-20e7-4a0e-a686-055841cf5ca4.svs (179.74 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[155/10000] (5.53GB) Downloading: TCGA-BRCA.bd4d930e-0848-48c1-8b03-c04a986f22d8.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[156/10000] (5.54GB) Downloading: TCGA-BRCA.8cd0933f-c93e-4265-a6c4-6892f407ced9.ascat2.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[157/10000] (5.54GB) Downloading: TCGA-BRCA.89a93ef7-73a7-451f-9c83-251b827f02c6.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[158/10000] (5.54GB) Downloading: TCGA-A8-A06U.A314FB55-F20A-4485-965D-D7894D070A16.PDF (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[159/10000] (5.54GB) Downloading: nationwidechildrens.org_omf.TCGA-A8-A09I.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[160/10000] (5.54GB) Downloading: TCGA-BRCA.714b3b2b-ad91-483d-8754-2afc96067e5e.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[161/10000] (5.54GB) Downloading: TCGA-BRCA.bd4d930e-0848-48c1-8b03-c04a986f22d8.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[162/10000] (5.55GB) Downloading: 29644452-cc56-4895-a959-c7a1c344444a_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[163/10000] (5.56GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_A07_771954.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[164/10000] (5.56GB) Downloading: TCGA-A8-A09I-01A-01-BS1.b0debb62-86b0-459f-b62b-604bb9f17e5d.svs (379.11 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[165/10000] (5.93GB) Downloading: ea37ddc7-e54b-4f05-b60b-489d7252ab09.mirbase21.isoforms.quantification.txt (0.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[166/10000] (5.93GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09I.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[167/10000] (5.93GB) Downloading: 9bc2055b-86f4-4ab7-80db-568b8d65b9f3_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[168/10000] (5.93GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-B6-A1KC.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[169/10000] (5.93GB) Downloading: nationwidechildrens.org_ssf.TCGA-B6-A1KC.xml (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[170/10000] (5.93GB) Downloading: f8ff90c6-3554-4e19-ae56-18f30f51f9b5.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[171/10000] (5.94GB) Downloading: TCGA-BRCA.8cd0933f-c93e-4265-a6c4-6892f407ced9.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[172/10000] (5.94GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_A01_780784.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[173/10000] (5.94GB) Downloading: GAMMA_p_TCGA_b103_104_SNP_N_GenomeWideSNP_6_B04_755920.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[174/10000] (5.94GB) Downloading: nationwidechildrens.org_ssf.TCGA-AO-A0JI.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[175/10000] (5.94GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A07I.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[176/10000] (5.94GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_C04_697074.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[177/10000] (5.94GB) Downloading: TCGA-AQ-A0Y5-01A-01-BSA.0402a8fd-a121-4a86-927e-073a2e4a7e7e.svs (165.44 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[178/10000] (6.10GB) Downloading: TCGA-C8-A1HI-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[179/10000] (6.10GB) Downloading: TCGA-BRCA.fdc086da-5ae1-4600-9039-4ea5c1fb7655.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[180/10000] (6.10GB) Downloading: f7e81ca6-5c0e-4fc1-bdcf-9ddc0749fd01_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[181/10000] (6.11GB) Downloading: d0207ef8-9ffc-4ba5-abb2-57fac81b5c38_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[182/10000] (6.11GB) Downloading: TCGA-AO-A0JI-01A-02-BSB.bfccffbb-dc47-4103-beb9-7799d50af784.svs (333.83 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[183/10000] (6.44GB) Downloading: nationwidechildrens.org_clinical.TCGA-AO-A0JI.xml (0.09 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[184/10000] (6.44GB) Downloading: TCGA-BRCA.8c976a66-2f34-4441-8f79-a13136e1dbe7.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[185/10000] (6.44GB) Downloading: TCGA-BRCA.d8c894f8-3423-401d-9656-65dfd0383fd7.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[186/10000] (6.44GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_F04_628376.nocnv_grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[187/10000] (6.44GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A1HI.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[188/10000] (6.44GB) Downloading: TCGA-BRCA.8c976a66-2f34-4441-8f79-a13136e1dbe7.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[189/10000] (6.44GB) Downloading: TCGA-AO-A0JI-01A-02-TSB.ee965449-b604-4626-83d4-e0b36bb79d9e.svs (245.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[190/10000] (6.68GB) Downloading: TCGA-C8-A1HI-01Z-00-DX1.C6D0F8B8-55ED-477F-BAF7-AA05D0449CC8.svs (890.43 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[191/10000] (7.55GB) Downloading: nationwidechildrens.org_ssf.TCGA-C8-A1HI.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[192/10000] (7.55GB) Downloading: cb3b3878-adfb-41e0-9f1a-971f38df16dd_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[193/10000] (7.56GB) Downloading: TCGA-BRCA.d8c894f8-3423-401d-9656-65dfd0383fd7.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[194/10000] (7.56GB) Downloading: 1a5661df-2a2a-43ad-80fc-1d469d0d9768.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[195/10000] (7.56GB) Downloading: TCGA-A8-A07I.5DA3A8E1-7EE6-45EC-89EC-69423E2B866B.PDF (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[196/10000] (7.56GB) Downloading: TCGA-BRCA.fdc086da-5ae1-4600-9039-4ea5c1fb7655.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[197/10000] (7.57GB) Downloading: TCGA-AQ-A0Y5-01Z-00-DX1.f68f5b49-30fa-4fb6-bec6-5da9f6809d02.svs (844.58 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[198/10000] (8.39GB) Downloading: TCGA-A8-A07I-01A-01-BSA.f3f1a0f0-5e66-4829-aa6d-c692c13a8bf8.svs (306.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[199/10000] (8.69GB) Downloading: 4c6cb929-293d-452e-b7f8-d535b48cf073.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[200/10000] (8.69GB) Downloading: 27fe0b6c-1b76-400b-a0ef-9405f833c482.methylation_array.sesame.level3betas.txt (12.53 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[201/10000] (8.71GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_E02_628380.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[202/10000] (8.71GB) Downloading: nationwidechildrens.org_clinical_nte_brca.txt (0.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[203/10000] (8.71GB) Downloading: TCGA-BRCA.fcd41d63-c0f1-4f8e-ad1f-ea398203a3a4.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[204/10000] (8.71GB) Downloading: 7064608a-0247-45ec-9e62-191721ecc52f.wxs.aliquot_ensemble_masked.maf.gz (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[205/10000] (8.71GB) Downloading: a8e0466b-d106-44b7-b846-c4fb666715f5.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[206/10000] (8.71GB) Downloading: TCGA-BRCA.fcd41d63-c0f1-4f8e-ad1f-ea398203a3a4.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[207/10000] (8.72GB) Downloading: TCGA-BH-A0B1-01A-11D-A890-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[208/10000] (8.72GB) Downloading: TCGA-BH-A0B1-01A-01-BSA.e42c4f30-d738-4366-9d21-0df264e6de0c.svs (316.25 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[209/10000] (9.03GB) Downloading: 5abd7590-46fd-4016-b38a-e334a7066e25_noid_Red.idat (0.69 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[210/10000] (9.03GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A06Q.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[211/10000] (9.03GB) Downloading: a3faa9fb-cbea-4ae5-8bf4-ca9b9f04a55f_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[212/10000] (9.03GB) Downloading: TCGA-AC-A62V-01A-11D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.15 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[213/10000] (9.03GB) Downloading: TCGA-A7-A4SB-01A-02-TSB.C5F241F1-8E0C-46A9-96CF-17AC925C51AC.svs (155.40 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[214/10000] (9.19GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_G04_1365060.nocnv_grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[215/10000] (9.19GB) Downloading: TCGA-AC-A62V.BBA96852-E70C-4D37-A185-611F568BE90C.PDF (0.89 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[216/10000] (9.19GB) Downloading: TCGA-A8-A06Q-01A-01-TS1.6a3caeab-6ec9-4829-b7e2-dbe7a6279a54.svs (151.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[217/10000] (9.33GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B07_666956.nocnv_grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[218/10000] (9.33GB) Downloading: TCGA-AC-A62V-01Z-00-DX1.2D8994FD-58B8-43C1-B99D-AA964E7DFD60.svs (54.86 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[219/10000] (9.39GB) Downloading: a3faa9fb-cbea-4ae5-8bf4-ca9b9f04a55f.methylation_array.sesame.level3betas.txt (12.56 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[220/10000] (9.40GB) Downloading: TCGA-A8-A06Q-01A-01-BS1.3e519802-6b1b-46b6-8e86-0151159873bb.svs (187.88 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[221/10000] (9.58GB) Downloading: TCGA-A2-A0YM-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[222/10000] (9.58GB) Downloading: TCGA-BRCA.938700b3-a62c-4bb7-886f-7b01dc98e33b.ascat2.allelic_specific.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[223/10000] (9.58GB) Downloading: TCGA-AO-A1KQ-01A-21-A17I-20_RPPA_data.tsv (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[224/10000] (9.58GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AO-A1KQ.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[225/10000] (9.58GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_F07_771876.nocnv_grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[226/10000] (9.58GB) Downloading: TCGA-AC-A8OP-01A-01-TS1.E2C52B43-51A4-4AE6-8B11-B7DC7392DCC2.svs (246.76 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[227/10000] (9.82GB) Downloading: eb44c266-8b8f-4012-ad67-f4ac40698391.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[228/10000] (9.83GB) Downloading: 6f51034e-ecfb-44df-9160-fb242d842de8_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[229/10000] (9.84GB) Downloading: TCGA-BRCA.0a7bfa84-8239-4d2b-8320-3d8a9db2a3ef.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[230/10000] (9.84GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_E01_780958.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[231/10000] (9.84GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_C09_1320408.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[232/10000] (9.84GB) Downloading: 82978eff-30b4-48a0-8806-78d3d8f7ad70_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[233/10000] (9.85GB) Downloading: 9e365ec7-4d96-460d-9fed-928f05507fbe.mirbase21.isoforms.quantification.txt (0.42 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[234/10000] (9.85GB) Downloading: TCGA-A2-A0YM-01Z-00-DX1.A48B4C96-2CC5-464C-98B7-F0F92AE56533.svs (823.07 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[235/10000] (10.65GB) Downloading: b03d6309-cf50-4e2c-bb9b-e5630960858b.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[236/10000] (10.65GB) Downloading: TCGA-AC-A8OP-01Z-00-DX1.A2AF501D-7DCD-4BE7-93A4-EBCAF0C0D54E.svs (310.71 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[237/10000] (10.95GB) Downloading: 1c86497b-f3a6-4bc3-a415-3cc2be22793e.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[238/10000] (10.95GB) Downloading: fa1b44dd-3960-4ce1-be3c-2e2e0e7ece66_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[239/10000] (10.96GB) Downloading: fa1b44dd-3960-4ce1-be3c-2e2e0e7ece66.methylation_array.sesame.level3betas.txt (12.53 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[240/10000] (10.97GB) Downloading: HEIGH_p_TCGAb418_19_21_BCR_NSP_GenomeWideSNP_6_G03_1485768.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[241/10000] (10.97GB) Downloading: TCGA-A2-A0YM.E1D8F2CB-25F1-49E0-92D3-132DCA8FD533.PDF (0.24 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[242/10000] (10.97GB) Downloading: 2dd0b954-db3e-402d-9c06-6160e199dedb.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[243/10000] (10.98GB) Downloading: 5cc4350c-416e-4f2c-be73-12af68ad1ee4.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[244/10000] (10.98GB) Downloading: TCGA-AR-A24Q-01Z-00-DX1.69DC7E35-DC0D-4F20-88DA-04C25F28628C.svs (1864.13 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[245/10000] (12.80GB) Downloading: TCGA-AO-A03N.44527CD3-6EC3-4861-8394-CEA005A17A9E.PDF (0.60 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[246/10000] (12.80GB) Downloading: efbe7d9d-d6bd-460f-a13d-73ffdfe5f50a_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[247/10000] (12.81GB) Downloading: efbe7d9d-d6bd-460f-a13d-73ffdfe5f50a_noid_Red.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[248/10000] (12.82GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_F06_697022.grch38.seg.v2.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[249/10000] (12.82GB) Downloading: 0c9e5211-39c9-4969-b962-237ed109069c.wxs.aliquot_ensemble_masked.maf.gz (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[250/10000] (12.82GB) Downloading: nationwidechildrens.org_ssf.TCGA-B6-A0IK.xml (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[251/10000] (12.82GB) Downloading: fb4526f0-ee99-46aa-a0df-f125a460b0a3.wgs.ASCAT.copy_number_variation.seg.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[252/10000] (12.82GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_C05_735300.nocnv_grch38.seg.v2.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[253/10000] (12.82GB) Downloading: TCGA-B6-A0IK-01A-01-TSA.6408a936-e47e-4497-8e83-8b952cbe1fd6.svs (379.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[254/10000] (13.19GB) Downloading: 7c9a2493-5667-48ec-8998-81e13722b4ab.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[255/10000] (13.19GB) Downloading: TCGA-BRCA.2e6cebd3-ce33-4553-a190-ac2dd9bcf91a.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[256/10000] (13.19GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-B6-A0WV.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[257/10000] (13.19GB) Downloading: TCGA-BRCA.82aeac9e-e169-41dc-8580-4165d4ea0ac9.ascat3.allelic_specific.seg.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[258/10000] (13.19GB) Downloading: 76e9cd4b-3d5b-4e4c-b706-a8d15ce8d513_noid_Grn.idat (7.72 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[259/10000] (13.20GB) Downloading: TCGA-A2-A4RW-01A-21D-A89C-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[260/10000] (13.20GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_G08_777668.nocnv_grch38.seg.v2.txt (0.01 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[261/10000] (13.20GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_C09_777692.grch38.seg.v2.txt (0.03 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[262/10000] (13.20GB) Downloading: TCGA-B6-A0WV-01Z-00-DX1.A8B9E114-A8CF-4389-B47C-2E1B842F7FF9.svs (1543.97 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[263/10000] (14.71GB) Downloading: nationwidechildrens.org_clinical.TCGA-A2-A4RW.xml (0.06 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[264/10000] (14.71GB) Downloading: TCGA-BRCA.0eae4d42-893c-48ff-b1a3-52ae7d1220ce.ascat3.allelic_specific.seg.txt (0.00 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[265/10000] (14.71GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A1R2.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[266/10000] (14.71GB) Downloading: 37544806-94ab-49e6-8d36-f8f51baf77eb.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[267/10000] (14.71GB) Downloading: nationwidechildrens.org_clinical_follow_up_v4.0_nte_brca.txt (0.04 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[268/10000] (14.71GB) Downloading: TCGA-BRCA.ba8ff683-777a-4d41-9261-014c89e17791.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[269/10000] (14.71GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A1IO.xml (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[270/10000] (14.71GB) Downloading: d82c50f0-5b73-4e16-aae4-939d595a9471.mirbase21.mirnas.quantification.txt (0.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[271/10000] (14.71GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_G05_778022.grch38.seg.v2.txt (0.08 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[272/10000] (14.71GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_G07_666954.grch38.seg.v2.txt (0.02 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[273/10000] (14.71GB) Downloading: TCGA-BRCA.1123e3e5-8125-432d-9246-195e8114be97.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[274/10000] (14.71GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_C05_778020.nocnv_grch38.seg.v2.txt (0.10 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[275/10000] (14.72GB) Downloading: 88c8a133-1c35-4e23-88d3-042cbca01208.methylation_array.sesame.level3betas.txt (12.56 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[276/10000] (14.73GB) Downloading: 890ccbe0-193d-4c06-ac56-96a2794fa5a4.mirbase21.isoforms.quantification.txt (0.21 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[277/10000] (14.73GB) Downloading: c2e73efe-8112-48fc-9dbd-29b4b5b89ad0.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "[278/10000] (14.73GB) Downloading: TCGA-D8-A1JP-01Z-00-DX1.B02959C4-6AAD-4ACA-9838-61D224D838E4.svs (931.19 MB)... "
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "OK\n",
+      "\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "CẢNH BÁO: Dung lượng đã đạt giới hạn (15.64 GB).\n",
+      "Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\n",
+      "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "It seems you are trying to upload a large folder at once. This might take some time and then fail if the folder is too large. For such cases, it is recommended to upload in smaller batches or to use `HfApi().upload_large_folder(...)`/`hf upload-large-folder` instead. For more details, check out https://huggingface.co/docs/huggingface_hub/main/en/guides/upload#upload-a-large-folder.\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "1a6f72ebbb0c4a39aa3505b3348bb51b",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Processing Files (0 / 0): |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "4674225379ae47518ef7c15ae448df40",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "New Data Upload: |          |  0.00B /  0.00B            "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import pandas as pd\n",
+    "import requests\n",
+    "import os\n",
+    "import shutil\n",
+    "from kaggle_secrets import UserSecretsClient\n",
+    "from huggingface_hub import HfApi, create_repo\n",
+    "\n",
+    "# 1. Lấy Token từ Secrets\n",
+    "user_secrets = UserSecretsClient()\n",
+    "hf_token = user_secrets.get_secret(\"HF_API_PAPER\")\n",
+    "\n",
+    "HF_REPO_ID = \"enzosama154/BRCancer\"\n",
+    "REPO_TYPE = \"dataset\"\n",
+    "\n",
+    "# 3. Khởi tạo API\n",
+    "api = HfApi(token=hf_token)\n",
+    "\n",
+    "# Tạo repo nếu chưa có (private để bảo mật dữ liệu y tế)\n",
+    "try:\n",
+    "    create_repo(repo_id=HF_REPO_ID, repo_type=REPO_TYPE, private=True, exist_ok=True, token=hf_token)\n",
+    "    print(f\"-> Đã kết nối với Hugging Face Repo: {HF_REPO_ID}\")\n",
+    "except Exception as e:\n",
+    "    print(f\"Lỗi kết nối HF: {e}\")\n",
+    "\n",
+    "INPUT_FILE_PATH = '/kaggle/input/databc/brca_clinical_withPAM50.xlsx'\n",
+    "OUTPUT_ROOT_DIR = '/kaggle/working/gdc_data_organized'\n",
+    "TRACKING_FILE = '/kaggle/working/tracking_downloaded.txt' # File lưu lịch sử tránh trùng\n",
+    "LIMIT_SIZE_GB = 15.0 \n",
+    "\n",
+    "def get_folder_size_gb(folder_path):\n",
+    "    \"\"\"Tính tổng dung lượng thư mục (GB).\"\"\"\n",
+    "    total_size = 0\n",
+    "    for dirpath, dirnames, filenames in os.walk(folder_path):\n",
+    "        for f in filenames:\n",
+    "            fp = os.path.join(dirpath, f)\n",
+    "            if not os.path.islink(fp):\n",
+    "                total_size += os.path.getsize(fp)\n",
+    "    return total_size / (1024**3)\n",
+    "\n",
+    "def load_processed_files():\n",
+    "    \"\"\"Đọc danh sách các file ID đã tải xong từ file text.\"\"\"\n",
+    "    if os.path.exists(TRACKING_FILE):\n",
+    "        with open(TRACKING_FILE, 'r') as f:\n",
+    "            return set(line.strip() for line in f)\n",
+    "    return set()\n",
+    "\n",
+    "def save_processed_file(file_id):\n",
+    "    \"\"\"Lưu file ID vào danh sách đã hoàn thành.\"\"\"\n",
+    "    with open(TRACKING_FILE, 'a') as f:\n",
+    "        f.write(f\"{file_id}\\n\")\n",
+    "\n",
+    "def upload_and_clean(current_dir):\n",
+    "    \"\"\"\n",
+    "    Thực hiện đẩy dữ liệu lên HF và xóa dữ liệu local.\n",
+    "    \"\"\"\n",
+    "    print(\"\\n\" + \"!\"*50)\n",
+    "    print(f\"CẢNH BÁO: Dung lượng đã đạt giới hạn ({get_folder_size_gb(current_dir):.2f} GB).\")\n",
+    "    print(\"Đang tiến hành upload lên Hugging Face và giải phóng bộ nhớ...\")\n",
+    "    print(\"!\"*50 + \"\\n\")\n",
+    "    \n",
+    "    # 1. Upload lên Hugging Face\n",
+    "    try:\n",
+    "        api.upload_folder(\n",
+    "            folder_path=current_dir,\n",
+    "            repo_id=HF_REPO_ID,\n",
+    "            repo_type=REPO_TYPE,\n",
+    "            path_in_repo=\"data\", # Lưu vào thư mục 'data' trên HF\n",
+    "            ignore_patterns=[\"tracking_downloaded.txt\"], # Không upload file tracking\n",
+    "            commit_message=f\"Auto-upload batch data to clear storage\"\n",
+    "        )\n",
+    "        print(\"-> Upload thành công!\")\n",
+    "    except Exception as e:\n",
+    "        print(f\"Lỗi khi Upload: {e}\")\n",
+    "        return # Nếu lỗi thì không xóa để tránh mất dữ liệu\n",
+    "\n",
+    "    # 2. Xóa dữ liệu local (giữ lại file tracking)\n",
+    "    print(\"-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\")\n",
+    "    for item in os.listdir(current_dir):\n",
+    "        item_path = os.path.join(current_dir, item)\n",
+    "        # Không xóa file tracking và file CSV kết quả UUID\n",
+    "        if item in [\"tracking_downloaded.txt\", \"brca_clinical_with_uuid.csv\"]:\n",
+    "            continue\n",
+    "        \n",
+    "        try:\n",
+    "            if os.path.isfile(item_path) or os.path.islink(item_path):\n",
+    "                os.unlink(item_path)\n",
+    "            elif os.path.isdir(item_path):\n",
+    "                shutil.rmtree(item_path)\n",
+    "        except Exception as e:\n",
+    "            print(f\"Không thể xóa {item_path}: {e}\")\n",
+    "            \n",
+    "    print(f\"-> Đã làm trống thư mục. Dung lượng hiện tại: {get_folder_size_gb(current_dir):.2f} GB\")\n",
+    "    print(\"-\" * 50)\n",
+    "\n",
+    "# ==============================================================================\n",
+    "# LOGIC CHÍNH: LẤY UUID VÀ DOWNLOAD\n",
+    "# ==============================================================================\n",
+    "\n",
+    "def get_gdc_uuids_from_submitter_ids(submitter_ids):\n",
+    "    url = \"https://api.gdc.cancer.gov/cases\"\n",
+    "    params = {\n",
+    "        \"filters\": {\"op\": \"in\", \"content\": {\"field\": \"submitter_id\", \"value\": submitter_ids}},\n",
+    "        \"fields\": \"submitter_id,case_id\", \"format\": \"json\", \"size\": len(submitter_ids) + 1000\n",
+    "    }\n",
+    "    try:\n",
+    "        response = requests.post(url, json=params)\n",
+    "        response.raise_for_status()\n",
+    "        hits = response.json().get('data', {}).get('hits', [])\n",
+    "        return {item['submitter_id']: item['case_id'] for item in hits}\n",
+    "    except Exception as e:\n",
+    "        print(f\"Lỗi API: {e}\")\n",
+    "        return {}\n",
+    "\n",
+    "def download_smart_loop(case_uuids, root_dir):\n",
+    "    if not os.path.exists(root_dir):\n",
+    "        os.makedirs(root_dir)\n",
+    "\n",
+    "    # Load danh sách các file đã tải trước đó (nếu chạy lại hoặc loop tiếp)\n",
+    "    processed_files = load_processed_files()\n",
+    "    print(f\"-> Đã tìm thấy {len(processed_files)} file đã xử lý trước đó (sẽ bỏ qua).\")\n",
+    "\n",
+    "    # API endpoints\n",
+    "    files_endpt = \"https://api.gdc.cancer.gov/files\"\n",
+    "    data_endpt = \"https://api.gdc.cancer.gov/data\"\n",
+    "\n",
+    "    # Filter lấy tất cả file Open\n",
+    "    filters = {\n",
+    "        \"op\": \"and\",\n",
+    "        \"content\": [\n",
+    "            {\"op\": \"in\", \"content\": {\"field\": \"cases.case_id\", \"value\": case_uuids}},\n",
+    "            {\"op\": \"in\", \"content\": {\"field\": \"access\", \"value\": [\"open\"]}}\n",
+    "        ]\n",
+    "    }\n",
+    "    \n",
+    "    params = {\n",
+    "        \"filters\": filters,\n",
+    "        \"fields\": \"file_id,file_name,file_size,data_format,cases.case_id\",\n",
+    "        \"format\": \"json\",\n",
+    "        \"size\": 10000 \n",
+    "    }\n",
+    "\n",
+    "    print(\"Đang lấy danh sách file...\")\n",
+    "    response = requests.post(files_endpt, json=params)\n",
+    "    files_data = response.json().get('data', {}).get('hits', [])\n",
+    "    print(f\"-> Tổng số file cần xử lý: {len(files_data)}\")\n",
+    "\n",
+    "    for idx, file_info in enumerate(files_data):\n",
+    "        file_id = file_info['file_id']\n",
+    "        file_name = file_info['file_name']\n",
+    "        file_size_mb = file_info['file_size'] / (1024 * 1024)\n",
+    "        \n",
+    "        # 1. KIỂM TRA TRÙNG LẶP\n",
+    "        if file_id in processed_files:\n",
+    "            continue # Bỏ qua nếu đã tải và upload rồi\n",
+    "\n",
+    "        # 2. KIỂM TRA DUNG LƯỢNG TRƯỚC KHI TẢI TIẾP\n",
+    "        current_usage = get_folder_size_gb('/kaggle/working')\n",
+    "        if current_usage >= LIMIT_SIZE_GB:\n",
+    "            upload_and_clean('/kaggle/working')\n",
+    "        \n",
+    "        # 3. TẠO FOLDER VÀ TẢI\n",
+    "        case_id = file_info['cases'][0]['case_id'] if 'cases' in file_info else \"Unknown\"\n",
+    "        case_dir = os.path.join(root_dir, case_id)\n",
+    "        if not os.path.exists(case_dir):\n",
+    "            os.makedirs(case_dir)\n",
+    "            \n",
+    "        save_path = os.path.join(case_dir, file_name)\n",
+    "        \n",
+    "        print(f\"[{idx+1}/{len(files_data)}] ({current_usage:.2f}GB) Downloading: {file_name} ({file_size_mb:.2f} MB)...\", end=\" \")\n",
+    "        \n",
+    "        try:\n",
+    "            with requests.get(f\"{data_endpt}/{file_id}\", stream=True) as r:\n",
+    "                r.raise_for_status()\n",
+    "                with open(save_path, 'wb') as f:\n",
+    "                    for chunk in r.iter_content(chunk_size=1024*1024):\n",
+    "                        if chunk: f.write(chunk)\n",
+    "            print(\"OK\")\n",
+    "            \n",
+    "            # Ghi nhận đã tải xong\n",
+    "            save_processed_file(file_id)\n",
+    "            processed_files.add(file_id)\n",
+    "            \n",
+    "        except Exception as e:\n",
+    "            print(f\"LỖI: {e}\")\n",
+    "\n",
+    "    # Upload lần cuối cùng sau khi chạy hết vòng lặp\n",
+    "    print(\"\\n-> Đã hoàn tất danh sách. Upload phần dữ liệu còn lại...\")\n",
+    "    upload_and_clean('/kaggle/working')\n",
+    "\n",
+    "# ==============================================================================\n",
+    "# MAIN\n",
+    "# ==============================================================================\n",
+    "def main():\n",
+    "    try:\n",
+    "        df = pd.read_excel(INPUT_FILE_PATH)\n",
+    "        print(\"Đọc file Excel thành công.\")\n",
+    "    except Exception as e:\n",
+    "        print(f\"Lỗi đọc file: {e}\")\n",
+    "        return\n",
+    "\n",
+    "    id_col = 'patient_id' if 'patient_id' in df.columns else 'sample_id'\n",
+    "    unique_ids = df[id_col].dropna().unique().tolist()\n",
+    "    \n",
+    "    if unique_ids:\n",
+    "        print(f\"Tra cứu UUID cho {len(unique_ids)} IDs...\")\n",
+    "        uuid_map = get_gdc_uuids_from_submitter_ids(unique_ids)\n",
+    "        valid_uuids = list(set(uuid_map.values()))\n",
+    "        \n",
+    "        # Map và lưu CSV\n",
+    "        df['case_uuid'] = df[id_col].map(uuid_map)\n",
+    "        df.to_csv('/kaggle/working/brca_clinical_with_uuid.csv', index=False)\n",
+    "        \n",
+    "        if valid_uuids:\n",
+    "            download_smart_loop(valid_uuids, OUTPUT_ROOT_DIR)\n",
+    "        else:\n",
+    "            print(\"Không có UUID hợp lệ.\")\n",
+    "    else:\n",
+    "        print(\"File input rỗng.\")\n",
+    "\n",
+    "if __name__ == \"__main__\":\n",
+    "    main()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kaggle": {
+   "accelerator": "none",
+   "dataSources": [
+    {
+     "datasetId": 9181321,
+     "sourceId": 14376718,
+     "sourceType": "datasetVersion"
+    }
+   ],
+   "dockerImageVersionId": 31234,
+   "isGpuEnabled": false,
+   "isInternetEnabled": true,
+   "language": "python",
+   "sourceType": "notebook"
+  },
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
+  },
+  "papermill": {
+   "default_parameters": {},
+   "duration": null,
+   "end_time": null,
+   "environment_variables": {},
+   "exception": null,
+   "input_path": "__notebook__.ipynb",
+   "output_path": "__notebook__.ipynb",
+   "parameters": {},
+   "start_time": "2026-01-03T05:06:25.522693",
+   "version": "2.6.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

data/gdc_data_organized/0491063c-14a7-4104-8002-1459126332f3/0c9e5211-39c9-4969-b962-237ed109069c.wxs.aliquot_ensemble_masked.maf.gz

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+oid sha256:86b8cefd725c787f4ce0418c8d9a4f4d00083a9d5785470b7f31f35fe3bb00cf
+size 53294

data/gdc_data_organized/0491063c-14a7-4104-8002-1459126332f3/BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_F06_697022.grch38.seg.v2.txt

@@ -0,0 +1,604 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
+76923226-7874-406b-8713-5f13b7d34ee2	1	62920	25256850	14015	0.014
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+76923226-7874-406b-8713-5f13b7d34ee2	1	25320253	29116468	1565	0.0037
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+76923226-7874-406b-8713-5f13b7d34ee2	1	29135206	30265585	821	0.0106
+76923226-7874-406b-8713-5f13b7d34ee2	1	30265657	30266949	5	-1.1037
+76923226-7874-406b-8713-5f13b7d34ee2	1	30268649	30670351	336	-0.0212
+76923226-7874-406b-8713-5f13b7d34ee2	1	30670681	30739595	57	0.2647
+76923226-7874-406b-8713-5f13b7d34ee2	1	30742517	34637053	2163	0.0149
+76923226-7874-406b-8713-5f13b7d34ee2	1	34637069	34638890	19	-0.5745
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+76923226-7874-406b-8713-5f13b7d34ee2	1	61648334	61654137	4	-1.4906
+76923226-7874-406b-8713-5f13b7d34ee2	1	61654306	72303233	7296	0.0045
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+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
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+        <admin:batch_number xsd_ver="1.17">61.89.0</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-B6-A0IK</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">0491063c-14a7-4104-8002-1459126332f3</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">B6</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0IK</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">357e1eca-0f5c-49d6-b437-0ed0afe3b178</ssf:bcr_sample_uuid>
+                <shared:days_to_sample_procurement precision="month" xsd_ver="2.3" tier="" cde="" owner="TSS" procurement_status="Completed" preferred_name="" display_order="9999" cde_ver="">-8</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="140110">Excisional Biopsy</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="Not Applicable" restricted="false" source_system_identifier="140111" xsi:nil="true"/>
+                <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="140112">Cassette</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="Not Applicable" restricted="false" source_system_identifier="140113"/>
+                <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="Not Available" restricted="false" source_system_identifier="140114"/>
+                <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="140117">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="140115">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="140116">0</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">5696</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="140187">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="140188">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="140190">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="140189">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="140118">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="140120">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="140192">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="140192">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="140193">Consented</shared:consent_or_death_status>
+                <shared:days_to_consent precision="month" 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">-8</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="Completed" restricted="false" source_system_identifier="740495">United States</shared:country>
+                <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="140103">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="140106">Left</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="140106">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="140106"/>
+                    </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">61f373e1-365f-424a-a39b-ec74b788bda9</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="140151"/>
+                <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="140152"/>
+                <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="Not Available" restricted="false" source_system_identifier="140153"/>
+                <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="Completed" restricted="false" source_system_identifier="140144">0.12</ssf:ncedna_dna_conc>
+                <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="Completed" restricted="false" source_system_identifier="140143">Spect</ssf:ncedna_dna_qm>
+                <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="Completed" restricted="false" source_system_identifier="140142">20</ssf:ncedna_dna_qty>
+                <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="Completed" restricted="false" source_system_identifier="140145">165</ssf:ncedna_dna_vol>
+                <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="Not Available" restricted="false" source_system_identifier="140146"/>
+                        <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="140147"/>
+                    </ssf:normal_control_location>
+                </ssf:normal_control_locations>
+            </ssf:normal_control>
+        </ssf:normal_controls>
+    </ssf:patient>
+</ssf:tcga_bcr>

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data/gdc_data_organized/09765b0a-94f6-47d2-af56-93368084ac3a/CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D11_628352.grch38.seg.v2.txt

@@ -0,0 +1,319 @@
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+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	27112001	27175000	63	0.030340
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+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	27335001	27848000	512	0.035562
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	27848001	27926000	78	0.036963
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	27926001	28317000	391	0.018744
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	28317001	29102000	439	0.026398
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	29102001	31146000	1735	0.024105
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	31146001	31373000	225	0.020359
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	31373001	31639000	265	0.032779
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	31639001	46381000	2403	0.012564
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	46381001	46402000	21	-0.257764
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	46402001	55710000	9275	0.023736
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	55710001	55762000	52	-0.386762
+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	55762001	57124000	1339	-0.362255
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+TCGA-A2-A4RW-01A-21D-A89C-36	chr16	58316001	58321000	5	-0.281673
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data/gdc_data_organized/0d146997-cfdc-4587-888c-e876fc455c80/TCGA-BRCA.82aeac9e-e169-41dc-8580-4165d4ea0ac9.ascat3.allelic_specific.seg.txt

@@ -0,0 +1,110 @@
+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	61735	34903170	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	34903413	37059402	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	37059855	37849142	5	4	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	37849612	43510595	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	43510733	44519510	5	4	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	44522288	45439291	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	45439674	46384885	5	4	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	46393062	47606857	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	47614007	49645545	5	4	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	49648823	54992142	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	54995454	59231559	6	5	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	59232245	63691727	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	63692775	90544055	2	2	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	90544122	106376514	3	3	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	106378429	111220259	4	3	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	111222365	121741181	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	143285278	183431755	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr1	183432535	248930189	4	2	2
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr2	12784	109025001	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr2	109028417	112941846	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr2	112942796	242147305	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr3	18667	36116086	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr3	36118600	89270427	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr3	89270662	191949154	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr3	191949988	198169247	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr4	12281	54338089	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr4	54338326	135392992	2	2	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr4	135398492	190106768	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr5	15532	30931732	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr5	30932238	51088174	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr5	51088637	158624924	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr5	158625642	175634009	2	2	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr5	175637531	181363319	3	3	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	149661	3665219	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	3665339	5210614	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	5214750	7156668	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	7156807	8436105	3	2	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	8436401	8789654	1	1	0
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	8789826	10008724	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	10009830	10723953	4	3	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	10724327	11377924	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	11380158	12746808	5	4	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	12747130	13220183	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	13220487	14029941	4	3	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	14033498	16808406	2	1	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	16809464	17139452	4	3	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	17147207	17516854	7	6	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	17519400	18588718	4	3	1
+82aeac9e-e169-41dc-8580-4165d4ea0ac9	chr6	18588902	21907862	2	1	1
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data/gdc_data_organized/0d146997-cfdc-4587-888c-e876fc455c80/nationwidechildrens.org_clinical.TCGA-A2-A4RW.xml

@@ -0,0 +1,253 @@
+<?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">900C0B48-C293-4066-9A23-B4D8FA785947</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">271.57.0</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="2427246">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="2427157">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="2427153">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="2427160">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">-18060</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">222</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="2427155">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-A2-A4RW</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A2</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A4RW</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">0D146997-CFDC-4587-888C-E876FC455C80</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="2427158">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="2427252">2011</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="2427156">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="2427159">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="2427265">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="2427266">27</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="2427281"/>
+        <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="2427287"/>
+        <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="2427247">Right</clin_shared:anatomic_neoplasm_subdivision>
+            <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="2427247">Right Upper Outer Quadrant</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="2427297"/>
+        <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="2427262">Axillary lymph node dissection alone</brca:axillary_lymph_node_stage_method_type>
+        <brca:axillary_lymph_node_stage_other_method_descriptive_text preferred_name="axillary_staging_method_other" display_order="45" cde="3124496" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2427263"/>
+        <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="2427256">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="2427260" 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="2427259"/>
+        <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="2427257"/>
+        <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="2427248">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="2427249" 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="2427154">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="2427282">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="2427264">NO</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
+        <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2427278">3 Point Scale</brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale>
+        <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="Completed" restricted="false" source_system_identifier="2427279">3+</brca_shared:immunohistochemistry_positive_cell_score>
+        <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2427290">1+</brca_shared:her2_immunohistochemistry_level_result>
+        <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2427261"/>
+        <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="2427258">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="2427254">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="2427255" 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 Evaluated" restricted="false" source_system_identifier="2427293"/>
+        <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="2427276">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="2427288">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="Completed" restricted="false" source_system_identifier="2427268">0</clin_shared:number_of_lymphnodes_positive_by_ihc>
+        <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="2427267">27</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="2427286"/>
+        <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="2427280"/>
+        <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="2427289"/>
+        <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="2427291"/>
+        <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="2427292"/>
+        <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="2427296"/>
+        <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="2427298"/>
+        <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="2427299"/>
+        <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="2427124">YES</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="2427125">NO</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="2427295"/>
+        <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="2427274"/>
+            <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="2427275"/>
+        </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="2427277">80-89%</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="2427283">90-99%</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="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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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="2427294"/>
+        <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="Completed" restricted="false" source_system_identifier="2427284">3 Point Scale</brca:breast_carcinoma_immunohistochemistry_progesterone_receptor_pos_finding_scale>
+        <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="Completed" restricted="false" source_system_identifier="2427285">3+</brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score>
+        <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="2427269">7th</shared_stage:system_version>
+            <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2427273">Stage IIIC</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="2427270">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="2427271">N3a</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="2427272">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="Unknown" restricted="false" source_system_identifier="2427170"/>
+        <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="Unknown" restricted="false" source_system_identifier="2427169"/>
+        <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="2427300">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="2427301"/>
+                <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="2427302"/>
+                <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="2427303"/>
+                <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="2427308"/>
+                <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="2427313"/>
+                <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="2427314"/>
+                <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="2427315"/>
+                <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="2427316"/>
+                <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="2427317"/>
+                <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="2427318"/>
+                <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="2427319"/>
+                <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="2427320"/>
+                <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="2427321"/>
+                <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="2427322"/>
+                <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="2427323"/>
+                <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="2427324"/>
+                <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="2427325"/>
+                <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="2427326"/>
+                <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="2427327"/>
+                <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="2427328"/>
+                <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="2427329"/>
+                <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="2427330"/>
+                <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="2427331"/>
+                <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="2427332"/>
+                <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="2427333"/>
+                <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="2427334"/>
+                <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="2427335"/>
+                <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="2427336"/>
+                <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="2427337"/>
+                <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="2427338"/>
+            </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">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">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>
+        <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-A2-A4RW-F59123</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">33B06046-3374-42DE-8585-2C4E3130E18B</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="3573301">YES</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="Unknown" restricted="false" source_system_identifier="3573302"/>
+                <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="Unknown" restricted="false" source_system_identifier="3573303"/>
+                <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="3573304">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="3573305">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">222</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="Unknown" restricted="false" source_system_identifier="3573314"/>
+                    <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="3573315"/>
+                        <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="3573316"/>
+                        <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="3573317"/>
+                        <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="3573322"/>
+                        <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="3573327"/>
+                        <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="3573328"/>
+                        <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="3573329"/>
+                        <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="3573330"/>
+                        <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="3573331"/>
+                        <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="3573332"/>
+                        <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="3573333"/>
+                        <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="3573334"/>
+                        <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="3573335"/>
+                        <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="3573336"/>
+                        <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="3573337"/>
+                        <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="3573338"/>
+                        <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="3573339"/>
+                        <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="3573340"/>
+                        <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="3573341"/>
+                        <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="3573342"/>
+                        <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="3573343"/>
+                        <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="3573344"/>
+                        <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="3573345"/>
+                        <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="3573346"/>
+                        <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="3573347"/>
+                        <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="3573348"/>
+                        <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="3573349"/>
+                        <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="3573350"/>
+                        <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="3573351"/>
+                        <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="3573352"/>
+                    </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">1</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">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">2014</clin_shared:year_of_form_completion>
+            </follow_up_v4.0:follow_up>
+        </brca:follow_ups>
+        <rx:drugs/>
+        <rad:radiations/>
+    </brca:patient>
+</brca:tcga_bcr>

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data/gdc_data_organized/1502c7d7-1535-4e56-9f34-30623acd50d5/nationwidechildrens.org_biospecimen.TCGA-B6-A1KC.xml

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+        <admin:batch_number xsd_ver="1.17">109.89.0</admin:batch_number>
+        <admin:project_code xsd_ver="">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">1</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">7</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+    </admin:admin>
+    <bio:patient>
+        <admin:additional_studies/>
+        <shared:bcr_patient_barcode cde="2673794" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1502c7d7-1535-4e56-9f34-30623acd50d5</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B6</shared:tissue_source_site>
+        <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A1KC</shared:patient_id>
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+        <bio:days_to_index precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">0</bio:days_to_index>
+        <bio:bcr_canonical_check>
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+        </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=""/>
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+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:initial_weight>
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+                <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">true</bio:oct_embedded>
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+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A</bio:bcr_sample_barcode>
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+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
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+                        <admin:additional_studies/>
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+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
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+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10.00</bio:weight>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">549bfd18-222b-484b-97f3-f95d3b313485</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="">0.15</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.06</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">df6e1936-9666-4303-baa3-94dc8aa3e95e</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="">A13I</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11D-A13I-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b31d6640-b311-49a7-bfd5-3075a0f55933</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.95</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="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100473776</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="">A13J</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11D-A13J-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">89a93ef7-73a7-451f-9c83-251b827f02c6</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108474761</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="">A13K</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11D-A13K-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">bd7cdcd4-59c0-4d7f-9bf9-0d8db021cc73</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100473488</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="">A13L</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11D-A13L-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">34e0baa5-86ed-44b6-812c-18e99d1917e1</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="">2.08</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108474665</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.73</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">941b250d-388e-41fb-b381-d0e0fb1f5d46</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="">A13P</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11R-A13P-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a80486d2-4520-4103-9768-9c145fcd549e</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="">F</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100473385</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="">A13Q</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11R-A13Q-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d9c21c95-9ca3-4ebe-80ab-8f3fd4166c31</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="">4.54</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108475134</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="">1.40</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.40</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-B6-A1KC-01A-11W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0CD2B08B-571B-40D8-9589-4775C0A5FC25</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="">A14Q</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="">03</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01A-11W-A14Q-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d5d6b8fe-a703-4aa2-b29a-5a6a0b85a3aa</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="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100477712</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="Completed" owner="">E1FDF8EB-9D75-4629-9C78-6019DAF8190E</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A1KC.E1FDF8EB-9D75-4629-9C78-6019DAF8190E.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="">4DD3E48B-F434-499F-9FF1-0FFD2883A375</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="">01</bio:sample_type_id>
+                <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B</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="">50</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="">2781</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">018b2eaa-216b-4726-a26e-ac726f4b47d3</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">27</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10.00</bio:weight>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">30c49cd7-4409-420c-8fe7-cefb4b25e58b</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="Completed" owner="">1.83</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1ee032aa-554d-4899-ab05-c3068527fc54</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="">A158</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11D-A158-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">171c222b-a147-4e9f-aeeb-8b51f3dc10ed</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="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100474327</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="">A159</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="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11D-A159-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">fc3e822f-150d-47a7-a346-10919b42aa8c</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.09</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.60</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="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099054644</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="">A160</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="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11D-A160-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">63C1BF52-78E7-48AA-BA7C-ACF89B20B1E0</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="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113421202</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="">A161</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="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11D-A161-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ef33a500-51db-46ba-bd91-84dc598a3ca8</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="">4.54</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113421197</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.83</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ef69b3a8-18b9-43dc-aa5b-ed657de6d0ee</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="">A156</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="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11R-A156-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">17d015b8-b3fb-4957-87ea-791598c19bc6</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="">H</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100477350</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="">A157</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="">17</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11R-A157-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">fe5e5b08-d5c0-4165-ae92-bec6a1d98e60</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="">4.54</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">H</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100477344</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="">1.40</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.10</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-B6-A1KC-01B-11W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B48E1BE7-F9BB-4DDC-9101-98D98CDB5561</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="">A16L</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="">21</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-11W-A16L-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c7887dba-c296-4d95-b965-c762acda00cb</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113421965</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="">100</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">95</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</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="">0</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-01-TS1</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">af22665c-5cc1-4c93-a95c-65580c40e7e1</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A1KC-01B-01-TS1.af22665c-5cc1-4c93-a95c-65580c40e7e1.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="">E1FDF8EB-9D75-4629-9C78-6019DAF8190E</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-B6-A1KC.E1FDF8EB-9D75-4629-9C78-6019DAF8190E.pdf</bio:pathology_report_file_name>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                </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="">2781</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c87025b5-5188-4f26-a73b-00d30ff77188</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="">16</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8fba86db-4edd-4e15-b2aa-ae4771562fd3</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="">0.18</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.44</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f071a83a-f5cf-4039-8013-1d14f8899302</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="">A13M</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01D-A13M-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2fa51a32-2e36-4fbf-bfa5-6f9648b74048</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.34</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="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108475049</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="">A13N</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01D-A13N-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a3787138-8423-4637-8f57-f6f388ce186a</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.20</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108474953</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="">A13O</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="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01D-A13O-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">edea9df4-e636-4be5-9ac8-8f8733d1d4b4</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.09</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.34</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108474377</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="">A188</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="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01D-A188-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">BFB5E574-0807-4E19-A3C7-256F32356D91</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.09</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.68</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">52.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113416483</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="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5AE335CD-3BA8-443B-88A0-1C2E5594C67D</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="">A14R</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="">03</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="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-B6-A1KC-10A-01W-A14R-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1fd8eddb-6c79-4a27-917a-f710225a589d</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="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100479056</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>

data/gdc_data_organized/1502c7d7-1535-4e56-9f34-30623acd50d5/nationwidechildrens.org_ssf.TCGA-B6-A1KC.xml

@@ -0,0 +1,161 @@
+<?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">63B54DE0-1F83-4B34-99B6-B9989A438EAF</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">109.89.0</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-B6-A1KC</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">1502c7d7-1535-4e56-9f34-30623acd50d5</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">B6</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A1KC</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">018b2eaa-216b-4726-a26e-ac726f4b47d3</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="">84</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="599535">Lumpectomy</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="Not Applicable" restricted="false" source_system_identifier="599536" xsi:nil="true"/>
+                <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="599538">Cassette</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="Not Applicable" restricted="false" source_system_identifier="599539"/>
+                <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="Not Available" restricted="false" source_system_identifier="599540"/>
+                <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="599543">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="599541">85</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="599542">0</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">2766</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="599763">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="599764">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="599766">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="599765">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="599544">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="599545">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="599768">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="599769">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="599770">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">84</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="Completed" restricted="false" source_system_identifier="599537">United States</shared:country>
+                <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="599528">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_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="599548">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="599531">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="599531">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="599531"/>
+                    </ssf:tumor_location>
+                    <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="599551">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="599551"/>
+                    </ssf:tumor_location>
+                </ssf:tumor_locations>
+            </ssf:tumor_sample>
+            <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">0cc10a1e-a90a-4c55-87a2-a74d47474a4a</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="">84</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="599555">Lumpectomy</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="Not Applicable" restricted="false" source_system_identifier="599556" xsi:nil="true"/>
+                <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="599558">Cassette</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="Not Applicable" restricted="false" source_system_identifier="599559"/>
+                <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="Not Available" restricted="false" source_system_identifier="599560"/>
+                <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="599563">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="599561">85</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="599562">0</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">2766</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="599763">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="599764">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="599766">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="599765">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="599564">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="599565">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="599768">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="599769">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="599770">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">84</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="Completed" restricted="false" source_system_identifier="599557">United States</shared:country>
+                <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="599528">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_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="599548">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="599531">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="599531">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="599531"/>
+                    </ssf:tumor_location>
+                    <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="599551">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="599551"/>
+                    </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">c87025b5-5188-4f26-a73b-00d30ff77188</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="599652"/>
+                <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="599653"/>
+                <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="Not Available" restricted="false" source_system_identifier="599654"/>
+                <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="Completed" restricted="false" source_system_identifier="599645">0.05</ssf:ncedna_dna_conc>
+                <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="Completed" restricted="false" source_system_identifier="599644">Spect</ssf:ncedna_dna_qm>
+                <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="Completed" restricted="false" source_system_identifier="599643">13</ssf:ncedna_dna_qty>
+                <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="Completed" restricted="false" source_system_identifier="599646">260</ssf:ncedna_dna_vol>
+                <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="Not Available" restricted="false" source_system_identifier="599647"/>
+                        <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="599648"/>
+                    </ssf:normal_control_location>
+                </ssf:normal_control_locations>
+            </ssf:normal_control>
+        </ssf:normal_controls>
+    </ssf:patient>
+</ssf:tcga_bcr>

data/gdc_data_organized/1557183c-aedd-4df6-b98a-3654667f7b69/BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_G04_666952.grch38.seg.v2.txt

@@ -0,0 +1,1238 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
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+815e64f0-821d-4556-b3de-438412c5b356	1	668210	1570600	187	0.0712
+815e64f0-821d-4556-b3de-438412c5b356	1	1570655	1741164	19	-0.5722
+815e64f0-821d-4556-b3de-438412c5b356	1	1756148	13338980	6308	-0.0106
+815e64f0-821d-4556-b3de-438412c5b356	1	13339386	13475857	32	-0.3998
+815e64f0-821d-4556-b3de-438412c5b356	1	13475969	25092208	7338	-0.0198
+815e64f0-821d-4556-b3de-438412c5b356	1	25096910	25097831	2	1.299
+815e64f0-821d-4556-b3de-438412c5b356	1	25098398	25256850	117	-0.0711
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data/gdc_data_organized/1557183c-aedd-4df6-b98a-3654667f7b69/TCGA-A8-A09I-01A-01-BS1.b0debb62-86b0-459f-b62b-604bb9f17e5d.svs

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data/gdc_data_organized/1557183c-aedd-4df6-b98a-3654667f7b69/nationwidechildrens.org_biospecimen.TCGA-A8-A09I.xml

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+        <admin:batch_number xsd_ver="1.17">56.92.0</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">18</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">5</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2022</admin:year_of_dcc_upload>
+        <admin:program xsd_ver="2.7">TCGA</admin:program>
+        <admin:dbgap_registration_code xsd_ver="2.7">000178</admin:dbgap_registration_code>
+    </admin:admin>
+    <bio:patient>
+        <admin:additional_studies/>
+        <shared:bcr_patient_barcode cde="2003301" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1557183c-aedd-4df6-b98a-3654667f7b69</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A8</shared:tissue_source_site>
+        <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A09I</shared:patient_id>
+        <shared:gender cde="2200604" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
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+        <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:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
+                <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">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=""/>
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+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">430</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="">false</bio:oct_embedded>
+                <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
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+                <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
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+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A</bio:bcr_sample_barcode>
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+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
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+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
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+                        <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">22</bio:shipment_portion_day_of_shipment>
+                        <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3</bio:shipment_portion_month_of_shipment>
+                        <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2011</bio:shipment_portion_year_of_shipment>
+                        <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-11-A13A-20</bio:shipment_portion_bcr_aliquot_barcode>
+                        <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">93a8128c-9314-44b7-8737-0c5b08c057f4</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:shipment_portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:portion_number>
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+                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A21V</bio:plate_id>
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+                        <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2012</bio:shipment_portion_year_of_shipment>
+                        <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-13-A21V-30</bio:shipment_portion_bcr_aliquot_barcode>
+                        <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">E510E0E2-CB89-46FC-A4A6-892A17647F49</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="">22</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="">08</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5c14eda1-84eb-4e7f-81da-9be61029f0aa</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="">2</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="Completed" owner="">2.05</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e682be9f-c34c-4d19-935d-06308564ad50</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A032</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A032-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3315363a-a4a7-4034-b616-991b528779a2</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="">4.54</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099049454</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="">A033</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A033-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2ffeb439-cdcd-416d-bf7d-b18e8b8225ef</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="">2.26</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.30</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099050510</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="">A036</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A036-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">bd4d930e-0848-48c1-8b03-c04a986f22d8</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.13</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099049358</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="">A044</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A044-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3a094344-2813-4298-8eaa-b859861caeb9</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="">1.60</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="">C</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="">0100478894</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="">A045</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A045-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b545ff39-9ad0-483b-bbe1-abcd438c4f93</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="">1.07</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0100478318</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="">A19H</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="">02</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">11</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A19H-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">987D41EE-6BAB-490C-B0F2-BF28C0089DE9</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="">2.08</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113385788</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A88Z</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22D-A88Z-36</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3DEDCA56-EAD8-4DA1-9CE6-E564CF9A5F3F</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="">8.50</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112369355</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.80</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6c984e6a-ba63-47c9-833e-ee77d076cb2c</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A034</bio:plate_id>
+                                        <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="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22R-A034-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">433b49ba-949b-4914-985a-be19b3b32502</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099051854</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="">A035</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="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22R-A035-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3e58ba3c-e09a-42f7-9865-b9e88e66c316</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099053390</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="">1.60</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.40</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="">2</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6081C373-1F36-492D-B55F-3123ECC286BA</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A050</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22W-A050-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">96d5070d-1fa9-4fa5-b2c9-472240dfd3b9</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="">C</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="">0100470719</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A051</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22W-A051-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">370f586d-ab33-4704-bbd9-e75dca6e9a6c</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="">C</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="">0100470926</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:subportion_sequence>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">545DBBA8-083A-450B-B516-8036ED719F20</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A048</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22X-A048-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0d9ac7b3-62a5-4782-a5dd-87485a253d22</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="">C</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="">0100471331</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A049</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-22X-A049-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">22500f81-7ab0-4713-b0dc-81d9afda589a</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="">C</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="">0100472270</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G X</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">90</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-01-BS1</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b0debb62-86b0-459f-b62b-604bb9f17e5d</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-01-BS1.b0debb62-86b0-459f-b62b-604bb9f17e5d.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                            <bio:slide>
+                                <admin:additional_studies/>
+                                <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
+                                <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
+                                <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">75</bio:percent_tumor_nuclei>
+                                <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">5</bio:percent_normal_cells>
+                                <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:percent_stromal_cells>
+                                <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">5</bio:percent_lymphocyte_infiltration>
+                                <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
+                                <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
+                                <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-02-BS2</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ca9aacf2-573b-4af2-bc50-5213526eb3a3</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09I-01A-02-BS2.ca9aacf2-573b-4af2-bc50-5213526eb3a3.svs</shared:image_file_name>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                            </bio:slide>
+                        </bio:slides>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">AF12859A-D67A-488D-8BC2-ED28698F2ACA</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09I.AF12859A-D67A-488D-8BC2-ED28698F2ACA.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="">B738E479-8766-4766-B012-B32AC2F27533</bio:ffpe_slide_uuid>
+                </bio:diagnostic_slides>
+            </bio:sample>
+            <bio:sample>
+                <admin:additional_studies/>
+                <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
+                <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
+                <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
+                <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
+                <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
+                <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:days_to_collection precision="month" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">698</bio:days_to_collection>
+                <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c8affd05-3105-4b90-b569-6ec0ad275d30</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a57fb064-5bd1-4be2-9d3a-af27f728958d</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="">0.16</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.94</bio:a260_a280_ratio>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0d276aff-db4a-4c58-bcaa-0c51c96400f3</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A031</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A031-02</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2af1729b-7507-42c1-8d24-56e6b74c4e31</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.13</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.30</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099052430</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="">A037</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">14</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A037-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">815e64f0-821d-4556-b3de-438412c5b356</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0099050702</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="">A046</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A046-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3919af95-3665-4808-979c-29e7ebd2de46</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="">1.60</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="">C</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="">0100491086</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="">A047</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A047-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">54cca86c-ce79-405a-bd0e-2909a5e15770</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="">1.07</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</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="">0100491662</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="">A19H</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="">02</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">11</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A19H-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1EA3BCBF-242F-40FD-840B-FDDB4F65A63F</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="">2.08</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0113389794</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A88Z</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01D-A88Z-36</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E176AA14-5C76-4A9D-A9D5-A6BF9AFAD6A0</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">8.00</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112369356</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01W</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6E60A2EC-9F73-4166-977D-A8ED9C5630AC</bio:bcr_analyte_uuid>
+                                <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                <bio:aliquots>
+                                    <bio:aliquot>
+                                        <admin:additional_studies/>
+                                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A053</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01W-A053-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8053bd51-fa97-466d-9477-c0a132c37a09</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="">C</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="">0100482350</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="">A055</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01W-A055-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ac8bb292-dad8-4f5b-b9d1-8c7aeb24bbac</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="">C</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="">0100485326</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                            <bio:analyte>
+                                <admin:additional_studies/>
+                                <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                                <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
+                                <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
+                                <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
+                                <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01X</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">DF808332-5DA8-4246-9879-8FDC9C5C92E3</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="">A052</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01X-A052-08</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b6438448-80b4-45b7-bae6-696121701777</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="">C</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="">0100480341</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="">A054</bio:plate_id>
+                                        <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
+                                        <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
+                                        <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
+                                        <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09I-10A-01X-A054-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8618d1c6-3f28-47d0-b68c-f4c773dea037</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="">C</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="">0100480814</bio:biospecimen_barcode_bottom>
+                                        <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
+                                        <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
+                                    </bio:aliquot>
+                                </bio:aliquots>
+                                <bio:protocols>
+                                    <bio:protocol>
+                                        <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G X</bio:experimental_protocol_type>
+                                        <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                        <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                                    </bio:protocol>
+                                </bio:protocols>
+                                <bio:dna>
+                                    <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
+                                    <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
+                                </bio:dna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                            </bio:analyte>
+                        </bio:analytes>
+                        <bio:slides/>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                </bio:diagnostic_slides>
+            </bio:sample>
+        </bio:samples>
+    </bio:patient>
+</bio:tcga_bcr>

data/gdc_data_organized/1557183c-aedd-4df6-b98a-3654667f7b69/nationwidechildrens.org_omf.TCGA-A8-A09I.xml

@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<omf:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/omf/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/omf/2.7/TCGA_BCR.Other_Malignancies.xsd" schemaVersion="2.7" xmlns:omf="http://tcga.nci/bcr/xml/clinical/omf/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:omf_v4.0="http://tcga.nci/bcr/xml/clinical/omf/2.7/4.0" xmlns:omf_shared="http://tcga.nci/bcr/xml/clinical/shared/omf/2.7" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7">
+    <admin:admin>
+        <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
+        <admin:file_uuid xsd_ver="2.6">77897DA2-6C08-4E56-A716-0C80687EEAD5</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">56.91.0</admin:batch_number>
+        <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
+        <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
+        <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
+        <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
+        <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
+        <admin:patient_withdrawal>
+            <admin:withdrawn>false</admin:withdrawn>
+        </admin:patient_withdrawal>
+        <admin:program xsi:nil="true" xsd_ver="2.7"/>
+        <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
+    </admin:admin>
+    <omf:patient>
+        <admin:additional_studies/>
+        <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">A09I</shared:patient_id>
+        <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-A09I</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">1557183c-aedd-4df6-b98a-3654667f7b69</shared:bcr_patient_uuid>
+        <omf:omfs>
+            <omf_v4.0:omf>
+                <omf_shared:bcr_omf_barcode xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A09I-O12216</omf_shared:bcr_omf_barcode>
+                <omf_shared:bcr_omf_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">615B5394-299B-4D8C-92E7-4D1539B9553D</omf_shared:bcr_omf_uuid>
+                <omf_shared:malignancy_type preferred_name="malignancy_type" display_order="4" cde="3182890" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961890">Prior Malignancy</omf_shared:malignancy_type>
+                <omf_shared:other_malignancy_anatomic_site preferred_name="" display_order="9999" cde="4122351" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961882">Colon</omf_shared:other_malignancy_anatomic_site>
+                <omf_shared:other_malignancy_anatomic_site_text preferred_name="" display_order="9999" cde="4122371" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="961883" xsi:nil="true"/>
+                <omf_shared:other_malignancy_laterality preferred_name="" display_order="9999" cde="4122391" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961884"/>
+                <omf_shared:other_malignancy_histological_type preferred_name="" display_order="9999" cde="4122411" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961885">Other, specify</omf_shared:other_malignancy_histological_type>
+                <omf_shared:other_malignancy_histological_type_text preferred_name="" display_order="9999" cde="4122431" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961886">malignant neoplasm of colon, unspecified</omf_shared:other_malignancy_histological_type_text>
+                <omf_shared:days_to_other_malignancy_dx precision="day" xsd_ver="2.6" tier="2" cde="3462301" owner="TSS" procurement_status="Not Available" preferred_name="other_malignancy_dx_days_to" display_order="13" cde_ver="1.000"/>
+                <omf_shared:surgery>
+                    <shared:surgery_indicator preferred_name="surgery_indicator" display_order="14" cde="3186538" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <omf_shared:surgery_type preferred_name="other_malignancy_surgery_type" display_order="15" cde="3462300" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <omf_shared:days_to_surgical_resection precision="month" xsd_ver="2.6" tier="2" cde="3462302" owner="TSS" procurement_status="Completed" preferred_name="other_malignancy_surgery_days_to" display_order="19" cde_ver="1.000">-9617</omf_shared:days_to_surgical_resection>
+                </omf_shared:surgery>
+                <omf_shared:drug_tx>
+                    <shared:drug_tx_indicator preferred_name="pharmaceutical_therapy_indicator" display_order="20" cde="3178327" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961891">NO</shared:drug_tx_indicator>
+                    <omf_shared:drug_tx_extent preferred_name="pharmaceutical_therapy_extent" display_order="21" cde="3178365" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961892"/>
+                    <rx:days_to_drug_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Not Available" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000"/>
+                    <omf_shared:administered_drug>
+                        <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="Not Available" restricted="false" source_system_identifier="961893"/>
+                    </omf_shared:administered_drug>
+                </omf_shared:drug_tx>
+                <omf_shared:radiation_tx>
+                    <omf_shared:radiation_tx_indicator preferred_name="radiation_therapy_indicator" display_order="27" cde="3178328" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961897">NO</omf_shared:radiation_tx_indicator>
+                    <omf_shared:radiation_tx_extent preferred_name="radiation_therapy_extent" display_order="28" cde="3178353" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961898"/>
+                    <omf_shared:rad_tx_to_site_of_primary_tumor preferred_name="history_rt_tx_to_site_of_tcga_tumor" display_order="29" cde="2865132" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961899"/>
+                    <rad:days_to_radiation_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3008313" owner="TSS" procurement_status="Not Available" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000"/>
+                </omf_shared:radiation_tx>
+                <omf_shared:omf_staging>
+                    <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
+                    <shared_stage:clinical_stage preferred_name="figo_clinical_tumor_stage" display_order="9999" cde="3225684" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" 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="Not Available" restricted="false" source_system_identifier="961909"/>
+                    <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="Not Available" restricted="false" source_system_identifier="961906"/>
+                        <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="Not Available" restricted="false" source_system_identifier="961907"/>
+                        <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="Not Available" restricted="false" source_system_identifier="961908"/>
+                    </shared_stage:pathologic_categories>
+                </omf_shared:omf_staging>
+                <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="961880">25</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="961879">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="961881">2011</clin_shared:year_of_form_completion>
+            </omf_v4.0:omf>
+        </omf:omfs>
+    </omf:patient>
+</omf:tcga_bcr>

data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/071a05c1-f9df-4e68-b73e-8f6716d75d52.methylation_array.sesame.level3betas.txt

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data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/071a05c1-f9df-4e68-b73e-8f6716d75d52_noid_Red.idat

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data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/TCGA-5L-AAT1-01Z-00-DX1.F3449A5B-2AC4-4ED7-BF44-4C8946CDB47D.svs

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+version https://git-lfs.github.com/spec/v1
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data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/TCGA-BRCA.4d7ffa3e-0218-4fc4-b3da-691d56a7df1a.ascat2.allelic_specific.seg.txt

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+GDC_Aliquot	Chromosome	Start	End	Copy_Number	Major_Copy_Number	Minor_Copy_Number
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	62920	4925709	2	1	1
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	4926246	4941863	5	3	2
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	4941993	53285938	2	1	1
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	53291070	53414255	4	3	1
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	53414567	53428657	2	2	0
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	53431822	72302815	2	1	1
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	72303233	72345465	34	34	0
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	72346221	121705338	2	1	1
+4d7ffa3e-0218-4fc4-b3da-691d56a7df1a	chr1	143541857	152583051	3	2	1
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data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/c74a2bd9-ce8c-4d7f-99d5-f8bac92ceaf5.mirbase21.mirnas.quantification.txt

@@ -0,0 +1,1882 @@
+miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
+hsa-let-7a-1	117580	14927.849784	N
+hsa-let-7a-2	117225	14882.779307	Y
+hsa-let-7a-3	117680	14940.545693	N
+hsa-let-7b	196539	24952.412559	N
+hsa-let-7c	19014	2414.000134	Y
+hsa-let-7d	2504	317.905561	N
+hsa-let-7e	10968	1392.487297	N
+hsa-let-7f-1	44027	5589.627849	N
+hsa-let-7f-2	44725	5678.245293	N
+hsa-let-7g	3627	460.480619	N
+hsa-let-7i	3362	426.836460	N
+hsa-mir-1-1	18	2.285264	N
+hsa-mir-1-2	15	1.904386	N
+hsa-mir-100	17328	2199.947109	N
+hsa-mir-101-1	45575	5786.160520	N
+hsa-mir-101-2	46029	5843.799946	N
+hsa-mir-103a-1	100590	12770.814848	Y
+hsa-mir-103a-2	101287	12859.305333	Y
+hsa-mir-103b-1	0	0.000000	N
+hsa-mir-103b-2	0	0.000000	N
+hsa-mir-105-1	1	0.126959	N
+hsa-mir-105-2	1	0.126959	N
+hsa-mir-106a	94	11.934154	Y
+hsa-mir-106b	2252	285.911870	N
+hsa-mir-107	418	53.068900	Y
+hsa-mir-10a	525233	66683.103637	N
+hsa-mir-10b	403068	51173.146426	N
+hsa-mir-1178	0	0.000000	N
+hsa-mir-1179	0	0.000000	N
+hsa-mir-1180	182	23.106554	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	2	0.253918	N
+hsa-mir-1185-2	2	0.253918	N
+hsa-mir-1193	0	0.000000	N
+hsa-mir-1197	0	0.000000	N
+hsa-mir-1199	0	0.000000	N
+hsa-mir-1200	0	0.000000	N
+hsa-mir-1202	0	0.000000	N
+hsa-mir-1203	0	0.000000	N
+hsa-mir-1204	0	0.000000	N
+hsa-mir-1205	0	0.000000	N
+hsa-mir-1206	0	0.000000	N
+hsa-mir-1207	0	0.000000	N
+hsa-mir-1208	0	0.000000	N
+hsa-mir-122	0	0.000000	N
+hsa-mir-1224	1	0.126959	N
+hsa-mir-1225	0	0.000000	N
+hsa-mir-1226	2	0.253918	N
+hsa-mir-1227	0	0.000000	N
+hsa-mir-1228	6	0.761755	N
+hsa-mir-1229	2	0.253918	N
+hsa-mir-1231	0	0.000000	N
+hsa-mir-1233-1	0	0.000000	N
+hsa-mir-1233-2	0	0.000000	N
+hsa-mir-1234	0	0.000000	N
+hsa-mir-1236	0	0.000000	N
+hsa-mir-1237	0	0.000000	N
+hsa-mir-1238	0	0.000000	N
+hsa-mir-124-1	0	0.000000	N
+hsa-mir-124-2	0	0.000000	N
+hsa-mir-124-3	0	0.000000	N
+hsa-mir-1243	0	0.000000	N
+hsa-mir-1244-1	0	0.000000	N
+hsa-mir-1244-2	0	0.000000	N
+hsa-mir-1244-3	0	0.000000	N
+hsa-mir-1244-4	0	0.000000	N
+hsa-mir-1245a	25	3.173977	N
+hsa-mir-1245b	1	0.126959	N
+hsa-mir-1246	0	0.000000	N
+hsa-mir-1247	128	16.250764	N
+hsa-mir-1248	3	0.380877	N
+hsa-mir-1249	5	0.634795	N
+hsa-mir-1250	1	0.126959	N
+hsa-mir-1251	4	0.507836	N
+hsa-mir-1252	1	0.126959	N
+hsa-mir-1253	0	0.000000	N
+hsa-mir-1254-1	2	0.253918	N
+hsa-mir-1254-2	1	0.126959	N
+hsa-mir-1255a	4	0.507836	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	6	0.761755	N
+hsa-mir-125a	5280	670.343994	N
+hsa-mir-125b-1	2123	269.534148	N
+hsa-mir-125b-2	2239	284.261402	N
+hsa-mir-126	19455	2469.989093	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	0.380877	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	104	13.203745	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	7549	958.414169	N
+hsa-mir-1270	17	2.158305	N
+hsa-mir-1271	18	2.285264	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	2	0.253918	N
+hsa-mir-1275	1	0.126959	N
+hsa-mir-1276	1	0.126959	N
+hsa-mir-1277	4	0.507836	N
+hsa-mir-1278	0	0.000000	N
+hsa-mir-1279	0	0.000000	N
+hsa-mir-128-1	702	89.125281	N
+hsa-mir-128-2	455	57.766386	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	9	1.142632	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	250	31.739772	N
+hsa-mir-1288	1	0.126959	N
+hsa-mir-1289-1	0	0.000000	N
+hsa-mir-1289-2	0	0.000000	N
+hsa-mir-129-1	3	0.380877	N
+hsa-mir-129-2	8	1.015673	N
+hsa-mir-1290	0	0.000000	N
+hsa-mir-1291	4	0.507836	N
+hsa-mir-1292	1	0.126959	N
+hsa-mir-1293	2	0.253918	N
+hsa-mir-1294	5	0.634795	N
+hsa-mir-1295a	1	0.126959	N
+hsa-mir-1295b	0	0.000000	N
+hsa-mir-1296	19	2.412223	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	81	10.283686	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
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+hsa-mir-1304	0	0.000000	N
+hsa-mir-1305	6	0.761755	N
+hsa-mir-1306	25	3.173977	N
+hsa-mir-1307	8013	1017.323187	N
+hsa-mir-130a	518	65.764809	N
+hsa-mir-130b	93	11.807195	N
+hsa-mir-132	670	85.062590	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	1	0.126959	N
+hsa-mir-133a-2	7	0.888714	N
+hsa-mir-133b	0	0.000000	N
+hsa-mir-134	2324	295.052925	N
+hsa-mir-1343	2	0.253918	N
+hsa-mir-135a-1	3	0.380877	N
+hsa-mir-135a-2	4	0.507836	N
+hsa-mir-135b	24	3.047018	N
+hsa-mir-136	244	30.978018	N
+hsa-mir-137	1	0.126959	N
+hsa-mir-138-1	6	0.761755	N
+hsa-mir-138-2	1	0.126959	N
+hsa-mir-139	286	36.310300	N
+hsa-mir-140	7042	894.045911	N
+hsa-mir-141	12804	1625.584186	N
+hsa-mir-142	19964	2534.611270	N
+hsa-mir-143	197093	25022.747895	N
+hsa-mir-144	190	24.122227	N
+hsa-mir-145	4497	570.935027	N
+hsa-mir-1468	24	3.047018	N
+hsa-mir-1469	0	0.000000	N
+hsa-mir-146a	877	111.343122	N
+hsa-mir-146b	7050	895.061583	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	5	0.634795	N
+hsa-mir-148a	235163	29856.080445	N
+hsa-mir-148b	1203	152.731785	N
+hsa-mir-149	46	5.840118	N
+hsa-mir-150	7096	900.901702	N
+hsa-mir-151a	10785	1369.253784	N
+hsa-mir-151b	7	0.888714	N
+hsa-mir-152	1245	158.064067	N
+hsa-mir-153-1	8	1.015673	N
+hsa-mir-153-2	129	16.377723	N
+hsa-mir-1537	3	0.380877	N
+hsa-mir-1538	0	0.000000	N
+hsa-mir-1539	0	0.000000	N
+hsa-mir-154	38	4.824445	N
+hsa-mir-155	3591	455.910092	N
+hsa-mir-1587	0	0.000000	N
+hsa-mir-15a	2107	267.502802	N
+hsa-mir-15b	870	110.454408	N
+hsa-mir-16-1	1793	227.637648	N
+hsa-mir-16-2	1712	217.353962	N
+hsa-mir-17	3133	397.762828	Y
+hsa-mir-181a-1	9083	1153.169413	N
+hsa-mir-181a-2	10660	1353.383898	N
+hsa-mir-181b-1	1316	167.078162	N
+hsa-mir-181b-2	1293	164.158103	N
+hsa-mir-181c	499	63.352586	N
+hsa-mir-181d	96	12.188073	N
+hsa-mir-182	209786	26634.239622	N
+hsa-mir-1825	0	0.000000	N
+hsa-mir-1827	0	0.000000	N
+hsa-mir-183	54983	6980.591637	N
+hsa-mir-184	78	9.902809	N
+hsa-mir-185	674	85.570427	N
+hsa-mir-186	1636	207.705071	N
+hsa-mir-187	8319	1056.172668	N
+hsa-mir-188	4	0.507836	N
+hsa-mir-18a	39	4.951405	N
+hsa-mir-18b	2	0.253918	N
+hsa-mir-1908	0	0.000000	N
+hsa-mir-1909	0	0.000000	N
+hsa-mir-190a	39	4.951405	N
+hsa-mir-190b	68	8.633218	N
+hsa-mir-191	5783	734.204417	N
+hsa-mir-1910	1	0.126959	N
+hsa-mir-1911	0	0.000000	N
+hsa-mir-1912	0	0.000000	N
+hsa-mir-1913	0	0.000000	N
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+hsa-mir-1915	0	0.000000	N
+hsa-mir-192	3123	396.493238	Y
+hsa-mir-193a	1507	191.327348	N
+hsa-mir-193b	248	31.485854	N
+hsa-mir-194-1	803	101.948149	N
+hsa-mir-194-2	884	112.231835	N
+hsa-mir-195	175	22.217841	N
+hsa-mir-196a-1	7823	993.200960	N
+hsa-mir-196a-2	8806	1118.001745	N
+hsa-mir-196b	1741	221.035775	N
+hsa-mir-197	1348	171.140853	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	78	9.902809	N
+hsa-mir-198	0	0.000000	N
+hsa-mir-199a-1	18399	2335.920294	Y
+hsa-mir-199a-2	27864	3537.588079	Y
+hsa-mir-199b	31160	3956.045240	Y
+hsa-mir-19a	119	15.108132	N
+hsa-mir-19b-1	316	40.119072	N
+hsa-mir-19b-2	285	36.183341	N
+hsa-mir-200a	7609	966.031715	N
+hsa-mir-200b	4630	587.820586	N
+hsa-mir-200c	90335	11468.849381	N
+hsa-mir-202	2	0.253918	N
+hsa-mir-203a	29003	3682.194483	N
+hsa-mir-203b	187	23.741350	N
+hsa-mir-204	21	2.666141	N
+hsa-mir-205	5727	727.094708	N
+hsa-mir-2052	0	0.000000	N
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+hsa-mir-2054	0	0.000000	N
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+hsa-mir-208a	0	0.000000	N
+hsa-mir-208b	0	0.000000	N
+hsa-mir-20a	1914	242.999698	N
+hsa-mir-20b	251	31.866732	N
+hsa-mir-21	2763806	350890.294270	N
+hsa-mir-210	1772	224.971507	N
+hsa-mir-211	0	0.000000	N
+hsa-mir-2110	8	1.015673	N
+hsa-mir-2113	0	0.000000	N
+hsa-mir-2114	13	1.650468	N
+hsa-mir-2115	7	0.888714	N
+hsa-mir-2116	3	0.380877	N
+hsa-mir-2117	1	0.126959	N
+hsa-mir-212	24	3.047018	N
+hsa-mir-214	250	31.739772	N
+hsa-mir-215	14	1.777427	Y
+hsa-mir-216a	1	0.126959	N
+hsa-mir-216b	1	0.126959	N
+hsa-mir-217	56	7.109709	N
+hsa-mir-218-1	137	17.393395	N
+hsa-mir-218-2	130	16.504682	N
+hsa-mir-219a-1	16	2.031345	N
+hsa-mir-219a-2	1	0.126959	N
+hsa-mir-219b	2	0.253918	N
+hsa-mir-22	733223	93089.324734	N
+hsa-mir-221	749	95.092358	N
+hsa-mir-222	287	36.437259	N
+hsa-mir-223	1073	136.227103	N
+hsa-mir-224	44	5.586200	N
+hsa-mir-2276	1	0.126959	N
+hsa-mir-2277	7	0.888714	N
+hsa-mir-2278	0	0.000000	N
+hsa-mir-2355	327	41.515622	N
+hsa-mir-2392	0	0.000000	N
+hsa-mir-23a	10911	1385.250629	Y
+hsa-mir-23b	1972	250.363325	Y
+hsa-mir-23c	0	0.000000	N
+hsa-mir-24-1	2052	260.520052	N
+hsa-mir-24-2	2192	278.294325	N
+hsa-mir-2467	0	0.000000	N
+hsa-mir-25	51836	6581.051381	N
+hsa-mir-2681	0	0.000000	N
+hsa-mir-2682	0	0.000000	N
+hsa-mir-26a-1	6053	768.483371	N
+hsa-mir-26a-2	5950	755.406585	N
+hsa-mir-26b	4182	530.942914	N
+hsa-mir-27a	5075	644.317381	Y
+hsa-mir-27b	2453	311.430647	Y
+hsa-mir-28	22415	2845.787999	N
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+hsa-mir-2909	0	0.000000	N
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+hsa-mir-298	0	0.000000	N
+hsa-mir-299	21	2.666141	N
+hsa-mir-29a	31628	4015.462094	N
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+hsa-mir-29b-2	2131	270.549820	N
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+hsa-mir-3064	1	0.126959	N
+hsa-mir-3065	57	7.236668	N
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+hsa-mir-30a	536570	68122.438838	Y
+hsa-mir-30b	2092	265.598416	Y
+hsa-mir-30c-1	2286	290.228479	N
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+hsa-mir-30d	37165	4718.434574	N
+hsa-mir-30e	67401	8557.169615	Y
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+hsa-mir-3128	0	0.000000	N
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+hsa-mir-3613	73	9.268014	N
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+hsa-mir-3618	0	0.000000	N
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+hsa-mir-362	64	8.125382	N
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+hsa-mir-3622a	1	0.126959	N
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+hsa-mir-363	83	10.537604	N
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+hsa-mir-3651	2	0.253918	N
+hsa-mir-3652	2	0.253918	N
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+hsa-mir-3661	0	0.000000	N
+hsa-mir-3662	2	0.253918	N
+hsa-mir-3663	0	0.000000	N
+hsa-mir-3664	6	0.761755	N
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+hsa-mir-3672	0	0.000000	N
+hsa-mir-3674	0	0.000000	N
+hsa-mir-3675	0	0.000000	N
+hsa-mir-3677	15	1.904386	N
+hsa-mir-3678	3	0.380877	N
+hsa-mir-3679	0	0.000000	N
+hsa-mir-3680-1	1	0.126959	N
+hsa-mir-3680-2	0	0.000000	N
+hsa-mir-3681	0	0.000000	N
+hsa-mir-3682	6	0.761755	N
+hsa-mir-3683	0	0.000000	N
+hsa-mir-3684	0	0.000000	N
+hsa-mir-3685	0	0.000000	N
+hsa-mir-3686	0	0.000000	N
+hsa-mir-3687-1	0	0.000000	N
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+hsa-mir-4726	0	0.000000	N
+hsa-mir-4727	0	0.000000	N
+hsa-mir-4728	6	0.761755	N
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+hsa-mir-4732	1	0.126959	N
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+hsa-mir-4736	0	0.000000	N
+hsa-mir-4737	0	0.000000	N
+hsa-mir-4738	1	0.126959	N
+hsa-mir-4739	1	0.126959	N
+hsa-mir-4740	0	0.000000	N
+hsa-mir-4741	2	0.253918	N
+hsa-mir-4742	6	0.761755	N
+hsa-mir-4743	0	0.000000	N
+hsa-mir-4744	0	0.000000	N
+hsa-mir-4745	0	0.000000	N
+hsa-mir-4746	11	1.396550	N
+hsa-mir-4747	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	2	0.253918	N
+hsa-mir-4754	0	0.000000	N
+hsa-mir-4755	0	0.000000	N
+hsa-mir-4756	0	0.000000	N
+hsa-mir-4757	1	0.126959	N
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+hsa-mir-4760	0	0.000000	N
+hsa-mir-4761	0	0.000000	N
+hsa-mir-4762	2	0.253918	N
+hsa-mir-4763	0	0.000000	N
+hsa-mir-4764	0	0.000000	N
+hsa-mir-4765	0	0.000000	N
+hsa-mir-4766	3	0.380877	N
+hsa-mir-4767	0	0.000000	N
+hsa-mir-4768	0	0.000000	N
+hsa-mir-4769	1	0.126959	N
+hsa-mir-4770	0	0.000000	N
+hsa-mir-4771-1	0	0.000000	N
+hsa-mir-4771-2	0	0.000000	N
+hsa-mir-4772	68	8.633218	N
+hsa-mir-4773-1	0	0.000000	N
+hsa-mir-4773-2	0	0.000000	N
+hsa-mir-4774	0	0.000000	N
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+hsa-mir-4776-2	0	0.000000	N
+hsa-mir-4777	4	0.507836	N
+hsa-mir-4778	0	0.000000	N
+hsa-mir-4779	0	0.000000	N
+hsa-mir-4780	0	0.000000	N
+hsa-mir-4781	5	0.634795	N
+hsa-mir-4782	0	0.000000	N
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+hsa-mir-4784	2	0.253918	N
+hsa-mir-4785	0	0.000000	N
+hsa-mir-4786	5	0.634795	N
+hsa-mir-4787	1	0.126959	N
+hsa-mir-4788	2	0.253918	N
+hsa-mir-4789	1	0.126959	N
+hsa-mir-4790	0	0.000000	N
+hsa-mir-4791	0	0.000000	N
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+hsa-mir-4797	1	0.126959	N
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+hsa-mir-4802	4	0.507836	N
+hsa-mir-4803	0	0.000000	N
+hsa-mir-4804	0	0.000000	N
+hsa-mir-483	24	3.047018	N
+hsa-mir-484	270	34.278954	N
+hsa-mir-485	34	4.316609	N
+hsa-mir-486-1	85	10.791523	N
+hsa-mir-486-2	67	8.506259	N
+hsa-mir-487a	9	1.142632	N
+hsa-mir-487b	31	3.935732	N
+hsa-mir-488	2	0.253918	N
+hsa-mir-489	1	0.126959	N
+hsa-mir-490	0	0.000000	N
+hsa-mir-491	18	2.285264	N
+hsa-mir-492	0	0.000000	N
+hsa-mir-493	132	16.758600	N
+hsa-mir-494	7	0.888714	N
+hsa-mir-495	62	7.871464	N
+hsa-mir-496	28	3.554855	N
+hsa-mir-497	65	8.252341	N
+hsa-mir-498	0	0.000000	N
+hsa-mir-4999	4	0.507836	N
+hsa-mir-499a	3	0.380877	N
+hsa-mir-499b	0	0.000000	N
+hsa-mir-5000	14	1.777427	N
+hsa-mir-5001	1	0.126959	N
+hsa-mir-5002	0	0.000000	N
+hsa-mir-5003	1	0.126959	N
+hsa-mir-5004	0	0.000000	N
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+hsa-mir-5007	0	0.000000	N
+hsa-mir-5008	0	0.000000	N
+hsa-mir-5009	1	0.126959	N
+hsa-mir-500a	1841	233.731684	Y
+hsa-mir-500b	21	2.666141	Y
+hsa-mir-501	273	34.659832	N
+hsa-mir-5010	1	0.126959	N
+hsa-mir-5011	0	0.000000	N
+hsa-mir-502	40	5.078364	Y
+hsa-mir-503	131	16.631641	N
+hsa-mir-504	2	0.253918	N
+hsa-mir-5047	0	0.000000	N
+hsa-mir-505	128	16.250764	N
+hsa-mir-506	0	0.000000	N
+hsa-mir-507	0	0.000000	N
+hsa-mir-508	3	0.380877	N
+hsa-mir-5087	0	0.000000	N
+hsa-mir-5088	0	0.000000	N
+hsa-mir-5089	2	0.253918	N
+hsa-mir-509-1	0	0.000000	N
+hsa-mir-509-2	2	0.253918	N
+hsa-mir-509-3	1	0.126959	N
+hsa-mir-5090	1	0.126959	N
+hsa-mir-5091	0	0.000000	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	39	4.951405	N
+hsa-mir-512-1	1	0.126959	N
+hsa-mir-512-2	1	0.126959	N
+hsa-mir-513a-1	0	0.000000	N
+hsa-mir-513a-2	0	0.000000	N
+hsa-mir-513b	0	0.000000	N
+hsa-mir-513c	0	0.000000	N
+hsa-mir-514a-1	2	0.253918	N
+hsa-mir-514a-2	0	0.000000	N
+hsa-mir-514a-3	2	0.253918	N
+hsa-mir-514b	0	0.000000	N
+hsa-mir-515-1	1	0.126959	N
+hsa-mir-515-2	1	0.126959	N
+hsa-mir-516a-1	2	0.253918	N
+hsa-mir-516a-2	0	0.000000	N
+hsa-mir-516b-1	0	0.000000	N
+hsa-mir-516b-2	0	0.000000	N
+hsa-mir-517a	0	0.000000	N
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+hsa-mir-517c	0	0.000000	N
+hsa-mir-5186	0	0.000000	N
+hsa-mir-5187	4	0.507836	N
+hsa-mir-5188	0	0.000000	N
+hsa-mir-5189	1	0.126959	N
+hsa-mir-518a-1	0	0.000000	N
+hsa-mir-518a-2	0	0.000000	N
+hsa-mir-518b	1	0.126959	N
+hsa-mir-518c	3	0.380877	N
+hsa-mir-518d	0	0.000000	N
+hsa-mir-518e	0	0.000000	N
+hsa-mir-518f	0	0.000000	N
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+hsa-mir-5197	0	0.000000	N
+hsa-mir-519a-1	2	0.253918	N
+hsa-mir-519a-2	1	0.126959	N
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+hsa-mir-519c	0	0.000000	N
+hsa-mir-519d	0	0.000000	N
+hsa-mir-519e	0	0.000000	N
+hsa-mir-520a	4	0.507836	N
+hsa-mir-520b	1	0.126959	Y
+hsa-mir-520c	1	0.126959	Y
+hsa-mir-520d	2	0.253918	N
+hsa-mir-520e	0	0.000000	N
+hsa-mir-520f	0	0.000000	N
+hsa-mir-520g	0	0.000000	N
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+hsa-mir-521-2	0	0.000000	N
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+hsa-mir-524	0	0.000000	N
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+hsa-mir-532	5305	673.517972	N
+hsa-mir-539	48	6.094036	N
+hsa-mir-541	4	0.507836	N
+hsa-mir-542	3486	442.579387	N
+hsa-mir-543	14	1.777427	N
+hsa-mir-544a	0	0.000000	N
+hsa-mir-544b	0	0.000000	N
+hsa-mir-545	5	0.634795	N
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+hsa-mir-548a-2	0	0.000000	N
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+hsa-mir-548ae-1	0	0.000000	N
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+hsa-mir-548ag-2	1	0.126959	N
+hsa-mir-548ah	0	0.000000	N
+hsa-mir-548ai	1	0.126959	N
+hsa-mir-548aj-1	0	0.000000	N
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+hsa-mir-548au	3	0.380877	N
+hsa-mir-548av	0	0.000000	N
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+hsa-mir-548ax	0	0.000000	N
+hsa-mir-548ay	1	0.126959	N
+hsa-mir-548az	0	0.000000	N
+hsa-mir-548b	3	0.380877	N
+hsa-mir-548ba	0	0.000000	N
+hsa-mir-548bb	0	0.000000	N
+hsa-mir-548c	0	0.000000	N
+hsa-mir-548d-1	1	0.126959	N
+hsa-mir-548d-2	0	0.000000	N
+hsa-mir-548e	6	0.761755	N
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+hsa-mir-548f-2	0	0.000000	N
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+hsa-mir-548f-4	0	0.000000	N
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+hsa-mir-548i-1	0	0.000000	N
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+hsa-mir-548j	1	0.126959	N
+hsa-mir-548k	0	0.000000	N
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+hsa-mir-548m	0	0.000000	N
+hsa-mir-548n	1	0.126959	N
+hsa-mir-548o	3	0.380877	N
+hsa-mir-548o-2	2	0.253918	N
+hsa-mir-548p	0	0.000000	N
+hsa-mir-548q	1	0.126959	N
+hsa-mir-548s	2	0.253918	N
+hsa-mir-548t	1	0.126959	N
+hsa-mir-548u	0	0.000000	N
+hsa-mir-548v	7	0.888714	N
+hsa-mir-548w	0	0.000000	N
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+hsa-mir-549a	0	0.000000	N
+hsa-mir-550a-1	10	1.269591	N
+hsa-mir-550a-2	4	0.507836	N
+hsa-mir-550a-3	5	0.634795	N
+hsa-mir-550b-1	0	0.000000	N
+hsa-mir-550b-2	0	0.000000	N
+hsa-mir-551a	1	0.126959	N
+hsa-mir-551b	6	0.761755	N
+hsa-mir-552	2	0.253918	N
+hsa-mir-553	0	0.000000	N
+hsa-mir-554	0	0.000000	N
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+hsa-mir-557	0	0.000000	N
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+hsa-mir-5586	38	4.824445	N
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+hsa-mir-5684	7	0.888714	N
+hsa-mir-5685	0	0.000000	N
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+hsa-mir-5688	0	0.000000	N
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+hsa-mir-5691	0	0.000000	N
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+hsa-mir-5692c-2	0	0.000000	N
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+hsa-mir-5694	3	0.380877	N
+hsa-mir-5695	1	0.126959	N
+hsa-mir-5696	3	0.380877	N
+hsa-mir-5697	1	0.126959	N
+hsa-mir-5698	3	0.380877	N
+hsa-mir-5699	2	0.253918	N
+hsa-mir-570	3	0.380877	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	1	0.126959	N
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+hsa-mir-573	0	0.000000	N
+hsa-mir-5739	0	0.000000	N
+hsa-mir-574	357	45.324395	N
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+hsa-mir-576	122	15.489009	N
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+hsa-mir-5787	0	0.000000	N
+hsa-mir-579	3	0.380877	N
+hsa-mir-580	5	0.634795	N
+hsa-mir-581	3	0.380877	N
+hsa-mir-582	353	44.816559	N
+hsa-mir-583	0	0.000000	N
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+hsa-mir-585	2	0.253918	N
+hsa-mir-586	0	0.000000	N
+hsa-mir-587	0	0.000000	N
+hsa-mir-588	1	0.126959	N
+hsa-mir-589	322	40.880827	N
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+hsa-mir-591	0	0.000000	N
+hsa-mir-592	21	2.666141	N
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+hsa-mir-596	0	0.000000	N
+hsa-mir-597	0	0.000000	N
+hsa-mir-598	30	3.808773	N
+hsa-mir-599	1	0.126959	N
+hsa-mir-600	0	0.000000	N
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+hsa-mir-606	0	0.000000	N
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+hsa-mir-6069	0	0.000000	N
+hsa-mir-607	0	0.000000	N
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+hsa-mir-6078	0	0.000000	N
+hsa-mir-6079	0	0.000000	N
+hsa-mir-608	0	0.000000	N
+hsa-mir-6080	0	0.000000	N
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+hsa-mir-6082	0	0.000000	N
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+hsa-mir-6087	0	0.000000	N
+hsa-mir-6088	0	0.000000	N
+hsa-mir-6089-1	0	0.000000	N
+hsa-mir-6089-2	0	0.000000	N
+hsa-mir-609	0	0.000000	N
+hsa-mir-6090	0	0.000000	N
+hsa-mir-610	0	0.000000	N
+hsa-mir-611	0	0.000000	N
+hsa-mir-612	0	0.000000	N
+hsa-mir-6124	0	0.000000	N
+hsa-mir-6125	0	0.000000	N
+hsa-mir-6126	0	0.000000	N
+hsa-mir-6127	0	0.000000	N
+hsa-mir-6128	0	0.000000	N
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+hsa-mir-96	216	27.423163	N
+hsa-mir-98	475	60.305568	N
+hsa-mir-99a	4876	619.052522	N
+hsa-mir-99b	182185	23130.041784	N

data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/nationwidechildrens.org_biospecimen.TCGA-5L-AAT1.xml

@@ -0,0 +1,371 @@
+<?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">2C9767BE-FFD2-449A-911D-C5E4C34C19AF</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">379.35.0</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-5L-AAT1</shared:bcr_patient_barcode>
+        <shared:bcr_patient_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">16FC3677-0393-4ED1-AD3F-C8355F056369</shared:bcr_patient_uuid>
+        <shared:tissue_source_site cde="" xsd_ver="2.4" procurement_status="Completed" owner="">5L</shared:tissue_source_site>
+        <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">AAT1</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="">130</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="">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="">1259</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-5L-AAT1-01A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A31DEC9B-3626-4CB0-8265-1425D5CE1C1E</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="">21</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                        <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A43F</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="">24</bio:shipment_portion_day_of_shipment>
+                        <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">6</bio:shipment_portion_month_of_shipment>
+                        <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2014</bio:shipment_portion_year_of_shipment>
+                        <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-21-A43F-20</bio:shipment_portion_bcr_aliquot_barcode>
+                        <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">047431B7-6180-49AB-9DD0-D23D794F2953</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="">12</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2014</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-5L-AAT1-01A-12</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3810CA85-7372-466B-9F59-5AEB9199E5E3</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="">2</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="">0.14</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-5L-AAT1-01A-12D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1705B81C-5621-4F09-85CD-995179F07D02</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="">A41E</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-12D-A41E-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4D7FFA3E-0218-4FC4-B3DA-691D56A7DF1A</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="">G</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="">0174189699</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="">A41F</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-12D-A41F-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">AF6872D5-0475-437F-B4D6-5115E71C442E</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="">G</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="">0174191290</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="">A41Q</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-12D-A41Q-05</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B53BCCF1-44AA-4E79-BFA7-75522DB25A37</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
+                                        <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
+                                        <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</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="">0174190260</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="">2</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="">0.18</bio:concentration>
+                                <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.86</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-5L-AAT1-01A-12R</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7C3DAE3F-025A-492E-A583-E550692C6E1F</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="">A41B</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-12R-A41B-07</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">34DFA8C6-6445-4EF8-BC3B-B2BA600B5808</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.34</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="">G</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="">0174191546</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="">A41G</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-12R-A41G-13</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E19D0664-9A68-4F3B-9645-72096CFCDFA5</bio:bcr_aliquot_uuid>
+                                        <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
+                                        <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.60</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="">G</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="">0174189815</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="">1.88</bio:ratio_28s_18s>
+                                    <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.20</bio:rinvalue>
+                                </bio:rna>
+                                <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
+                            </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="">5</bio:percent_necrosis>
+                                <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">35</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="">20</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="">20</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-5L-AAT1-01A-01-TS1</shared:bcr_slide_barcode>
+                                <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">140261A5-268A-4C22-9E3E-066B47697DCB</shared:bcr_slide_uuid>
+                                <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-5L-AAT1-01A-01-TS1.140261A5-268A-4C22-9E3E-066B47697DCB.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="">B5CA42BB-9514-42C6-9FB0-C8889C1DC51A</bio:pathology_report_uuid>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-5L-AAT1.B5CA42BB-9514-42C6-9FB0-C8889C1DC51A.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="">F3449A5B-2AC4-4ED7-BF44-4C8946CDB47D</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="">1259</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-5L-AAT1-10A</bio:bcr_sample_barcode>
+                <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5D4B9024-0F9B-4688-91B8-417BC20ADC43</bio:bcr_sample_uuid>
+                <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
+                <bio:portions>
+                    <bio:portion>
+                        <admin:additional_studies/>
+                        <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
+                        <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                        <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:day_of_creation>
+                        <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
+                        <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2014</bio:year_of_creation>
+                        <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.00</bio:weight>
+                        <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-10A-01</bio:bcr_portion_barcode>
+                        <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">56A0416E-E4CF-4878-ACBD-80F0ABD210B0</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-5L-AAT1-10A-01D</bio:bcr_analyte_barcode>
+                                <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">AA12DBC0-0FB6-4904-8101-D1F898987F0B</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="">A41E</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-10A-01D-A41E-01</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2B364D27-181A-4123-BC26-D0C9F1DF05CE</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="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0174189704</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="">A41F</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="">28</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="">2014</bio:year_of_shipment>
+                                        <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-5L-AAT1-10A-01D-A41F-09</bio:bcr_aliquot_barcode>
+                                        <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9DB372B8-F687-49C1-844A-53D3E1246EF4</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="">G</bio:plate_row>
+                                        <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6</bio:plate_column>
+                                        <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0174191265</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:analytes>
+                        <bio:slides/>
+                        <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
+                    </bio:portion>
+                </bio:portions>
+                <bio:tumor_pathology/>
+                <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
+                <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
+                <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
+                <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
+                <bio:diagnostic_slides>
+                    <admin:additional_studies/>
+                </bio:diagnostic_slides>
+            </bio:sample>
+        </bio:samples>
+    </bio:patient>
+</bio:tcga_bcr>

data/gdc_data_organized/16fc3677-0393-4ed1-ad3f-c8355f056369/nationwidechildrens.org_clinical.TCGA-5L-AAT1.xml

@@ -0,0 +1,230 @@
+<?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: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">4E94CDFB-858B-4345-9064-7BE3CD0F75F5</admin:file_uuid>
+        <admin:batch_number xsd_ver="1.17">379.35.0</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="3798674">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="3798642">Yes</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="3798638">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="3798645">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">-23225</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">1471</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="3798640">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-5L-AAT1</shared:bcr_patient_barcode>
+        <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">5L</shared:tissue_source_site>
+        <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">AAT1</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">16FC3677-0393-4ED1-AD3F-C8355F056369</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="3798643">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">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="3798680">2010</clin_shared:year_of_initial_pathologic_diagnosis>
+        <clin_shared:ethnicity preferred_name="ethnicity" display_order="13" cde="2192217" cde_ver="2.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="3798641">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="3798644">WITH TUMOR</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="3798693">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="3798694">1</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="3798709"/>
+        <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="3798715"/>
+        <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="3798675">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="3798725"/>
+        <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="3798690">Other (specify)</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="Completed" restricted="false" source_system_identifier="3798691">Level 1 clearance</brca:axillary_lymph_node_stage_other_method_descriptive_text>
+        <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="3798684">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="3798688" 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="3798687"/>
+        <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="3798685"/>
+        <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="3798676">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="3798677" 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="3798639">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="3798710">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="3798692">NO</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
+        <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="3798706"/>
+        <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="3798707"/>
+        <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="3798718">2+</brca_shared:her2_immunohistochemistry_level_result>
+        <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="3798689"/>
+        <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="3798686">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="3798682">Tumor resection</clin_shared:initial_pathologic_diagnosis_method>
+        <clin_shared:init_pathology_dx_method_other preferred_name="method_initial_path_dx_other" display_order="37" cde="2757948" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="3798683" 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 Evaluated" restricted="false" source_system_identifier="3798721"/>
+        <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="3798704">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="3798716">Equivocal</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
+        <clin_shared:number_of_lymphnodes_positive_by_ihc preferred_name="lymph_nodes_examined_ihc_count" display_order="50" cde="3086383" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="3798696"/>
+        <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="3798695">0</clin_shared:number_of_lymphnodes_positive_by_he>
+        <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="3798714"/>
+        <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="3798708"/>
+        <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="3798717"/>
+        <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="Completed" restricted="false" source_system_identifier="3798719">CISH</brca_shared:pos_finding_her2_erbb2_other_measurement_scale_text>
+        <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="Completed" restricted="false" source_system_identifier="3798720">CISH</brca_shared:her2_erbb_method_calculation_method_text>
+        <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="3798724"/>
+        <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="3798726"/>
+        <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="3798727"/>
+        <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="3798632">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="3798633">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="3798723"/>
+        <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="Completed" restricted="false" source_system_identifier="3798702">Bone</clin_shared:metastatic_site_at_diagnosis>
+            <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="3798703"/>
+        </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="3798705">80-89%</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="3798711">10-19%</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="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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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"/>
+        <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="3798722"/>
+        <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="3798712"/>
+        <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="3798713"/>
+        <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="3798697">7th</shared_stage:system_version>
+            <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
+            <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="3798701">Stage IV</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="3798698">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="3798699">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="3798700">M1</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="Completed" restricted="false" source_system_identifier="3798655">YES</clin_shared:postoperative_rx_tx>
+        <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="3798654">NO</clin_shared:radiation_therapy>
+        <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="3798728">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="3798729"/>
+                <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="3798730"/>
+                <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="3798731"/>
+                <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="3798736"/>
+                <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="3798741"/>
+                <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="3798742"/>
+                <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="3798743"/>
+                <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="3798744"/>
+                <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="3798745"/>
+                <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="3798746"/>
+                <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="3798747"/>
+                <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="3798748"/>
+                <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="3798749"/>
+                <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="3798750"/>
+                <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="3798751"/>
+                <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="3798752"/>
+                <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="3798753"/>
+                <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="3798754"/>
+                <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="3798755"/>
+                <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="3798756"/>
+                <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="3798757"/>
+                <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="3798758"/>
+                <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="3798759"/>
+                <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="3798760"/>
+                <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="3798761"/>
+                <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="3798762"/>
+                <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="3798763"/>
+                <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="3798764"/>
+                <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="3798765"/>
+                <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="3798766"/>
+            </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">15</clin_shared:day_of_form_completion>
+        <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">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">2014</clin_shared:year_of_form_completion>
+        <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="3798885">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-5L-AAT1-D63716</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">747059AE-DC7B-409F-9178-2DD683C19A6F</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">46</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="3798888">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="3798886">Letrozol</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="3798887"/>
+                <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="3798893">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="3798898" 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">15</clin_shared:day_of_form_completion>
+                <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">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">2014</clin_shared:year_of_form_completion>
+            </rx:drug>
+        </rx:drugs>
+        <rad:radiations/>
+    </brca:patient>
+</brca:tcga_bcr>

data/gdc_data_organized/1c40b84e-a0e3-429f-a48c-21566cf881c0/GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_C05_735300.nocnv_grch38.seg.v2.txt

@@ -0,0 +1,38 @@
+GDC_Aliquot	Chromosome	Start	End	Num_Probes	Segment_Mean
+a932959b-407f-4062-8e7e-9d82bc8da663	1	3301765	247650984	129572	0.0094
+a932959b-407f-4062-8e7e-9d82bc8da663	2	480597	241537572	131968	0.0017
+a932959b-407f-4062-8e7e-9d82bc8da663	3	2170634	197812401	107002	0.0081
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data/gdc_data_organized/281f70c5-876f-44b3-84fb-f2302f85e74c/BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B07_666956.nocnv_grch38.seg.v2.txt

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