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Auto-upload batch data to clear storage

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  1. .gitattributes +76 -0
  2. data/__notebook__.ipynb +2713 -0
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+ "text": [
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+ "OK\n",
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+ },
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+ "name": "stdout",
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+ "text": [
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ "OK\n",
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9087/10000] (0.02GB) Downloading: 099445c1-bd35-43ac-ab7e-9a8a9999c9a7.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9088/10000] (0.03GB) Downloading: nationwidechildrens.org_ssf.TCGA-AC-A3QQ.xml (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9089/10000] (0.03GB) Downloading: nationwidechildrens.org_ssf.TCGA-OL-A66J.xml (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9090/10000] (0.03GB) Downloading: TCGA-AC-A3QQ-01Z-00-DX1.86463263-AB12-49FB-8967-D5FD1F7D221A.svs (188.28 MB)... "
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9091/10000] (0.21GB) Downloading: nationwidechildrens.org_ssf.TCGA-A2-A0CU.xml (0.02 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9092/10000] (0.21GB) Downloading: 88e8a65d-5575-41e9-a3a0-9743d830e2eb_noid_Grn.idat (7.72 MB)... "
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+ ]
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+ },
75058
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9093/10000] (0.22GB) Downloading: 3ae8416a-b546-462d-b821-75883bea825a.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9094/10000] (0.22GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-OL-A66J.xml (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9095/10000] (0.22GB) Downloading: TCGA-BRCA.25dbaee9-17b6-4279-94ec-99b5b97e14e9.ascat3.allelic_specific.seg.txt (0.00 MB)... "
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+ ]
75081
+ },
75082
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9096/10000] (0.22GB) Downloading: TCGA-BRCA.415eb849-be66-47d3-a813-100c1eed8345.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
75088
+ ]
75089
+ },
75090
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9097/10000] (0.22GB) Downloading: TCGA-BRCA.25dbaee9-17b6-4279-94ec-99b5b97e14e9.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
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+ ]
75097
+ },
75098
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9098/10000] (0.23GB) Downloading: 88e8a65d-5575-41e9-a3a0-9743d830e2eb_noid_Red.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9099/10000] (0.23GB) Downloading: 40f6614e-332e-449c-9615-0710f0dffbee_noid_Red.idat (0.69 MB)... "
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+ ]
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+ },
75114
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9100/10000] (0.23GB) Downloading: ecedae95-8eee-4fc9-bc46-38ae50262772.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
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+ },
75122
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9101/10000] (0.23GB) Downloading: ecedae95-8eee-4fc9-bc46-38ae50262772.mirbase21.isoforms.quantification.txt (0.33 MB)... "
75128
+ ]
75129
+ },
75130
+ {
75131
+ "name": "stdout",
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+ "output_type": "stream",
75133
+ "text": [
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+ "OK\n",
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+ "[9102/10000] (0.23GB) Downloading: nationwidechildrens.org_clinical.TCGA-A2-A0CU.xml (0.05 MB)... "
75136
+ ]
75137
+ },
75138
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75141
+ "text": [
75142
+ "OK\n",
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+ "[9103/10000] (0.23GB) Downloading: TCGA-BRCA.a527543f-fdc1-44a9-a00e-bfb45cbb15b8.gene_level_copy_number.v36.tsv (3.29 MB)... "
75144
+ ]
75145
+ },
75146
+ {
75147
+ "name": "stdout",
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+ "output_type": "stream",
75149
+ "text": [
75150
+ "OK\n",
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+ "[9104/10000] (0.24GB) Downloading: TCGA-BRCA.846ab0bd-1c82-48a3-a25a-8a3af1f2bfa0.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75152
+ ]
75153
+ },
75154
+ {
75155
+ "name": "stdout",
75156
+ "output_type": "stream",
75157
+ "text": [
75158
+ "OK\n",
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+ "[9105/10000] (0.24GB) Downloading: TCGA-D8-A73U-01A-21-A43F-20_RPPA_data.tsv (0.02 MB)... "
75160
+ ]
75161
+ },
75162
+ {
75163
+ "name": "stdout",
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+ "output_type": "stream",
75165
+ "text": [
75166
+ "OK\n",
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+ "[9106/10000] (0.24GB) Downloading: TCGA-BRCA.b90d3cc1-678c-414a-b57f-864f8b6951eb.ascat2.allelic_specific.seg.txt (0.01 MB)... "
75168
+ ]
75169
+ },
75170
+ {
75171
+ "name": "stdout",
75172
+ "output_type": "stream",
75173
+ "text": [
75174
+ "OK\n",
75175
+ "[9107/10000] (0.24GB) Downloading: TCGA-D8-A73U-01A-11D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.02 MB)... "
75176
+ ]
75177
+ },
75178
+ {
75179
+ "name": "stdout",
75180
+ "output_type": "stream",
75181
+ "text": [
75182
+ "OK\n",
75183
+ "[9108/10000] (0.24GB) Downloading: 40f6614e-332e-449c-9615-0710f0dffbee_noid_Grn.idat (0.69 MB)... "
75184
+ ]
75185
+ },
75186
+ {
75187
+ "name": "stdout",
75188
+ "output_type": "stream",
75189
+ "text": [
75190
+ "OK\n",
75191
+ "[9109/10000] (0.24GB) Downloading: TCGA-A2-A0CU.D503E73D-8B94-46A0-A24F-93069A56DC7D.PDF (0.12 MB)... "
75192
+ ]
75193
+ },
75194
+ {
75195
+ "name": "stdout",
75196
+ "output_type": "stream",
75197
+ "text": [
75198
+ "OK\n",
75199
+ "[9110/10000] (0.24GB) Downloading: TCGA-BRCA.a527543f-fdc1-44a9-a00e-bfb45cbb15b8.ascat3.allelic_specific.seg.txt (0.00 MB)... "
75200
+ ]
75201
+ },
75202
+ {
75203
+ "name": "stdout",
75204
+ "output_type": "stream",
75205
+ "text": [
75206
+ "OK\n",
75207
+ "[9111/10000] (0.24GB) Downloading: e8a76a4e-ee9e-43be-ae99-04cfbfaa6d53.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
75208
+ ]
75209
+ },
75210
+ {
75211
+ "name": "stdout",
75212
+ "output_type": "stream",
75213
+ "text": [
75214
+ "OK\n",
75215
+ "[9112/10000] (0.24GB) Downloading: TCGA-BRCA.846ab0bd-1c82-48a3-a25a-8a3af1f2bfa0.ascat2.allelic_specific.seg.txt (0.01 MB)... "
75216
+ ]
75217
+ },
75218
+ {
75219
+ "name": "stdout",
75220
+ "output_type": "stream",
75221
+ "text": [
75222
+ "OK\n",
75223
+ "[9113/10000] (0.24GB) Downloading: 77e4a7c3-f2cd-4b5e-8c18-bfa3ce91cf56.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
75224
+ ]
75225
+ },
75226
+ {
75227
+ "name": "stdout",
75228
+ "output_type": "stream",
75229
+ "text": [
75230
+ "OK\n",
75231
+ "[9114/10000] (0.24GB) Downloading: TCGA-BRCA.a527543f-fdc1-44a9-a00e-bfb45cbb15b8.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
75232
+ ]
75233
+ },
75234
+ {
75235
+ "name": "stdout",
75236
+ "output_type": "stream",
75237
+ "text": [
75238
+ "OK\n",
75239
+ "[9115/10000] (0.25GB) Downloading: TCGA-AN-A0XS.D5C9D3FF-3799-4773-8A86-B000DBE42BD8.PDF (0.04 MB)... "
75240
+ ]
75241
+ },
75242
+ {
75243
+ "name": "stdout",
75244
+ "output_type": "stream",
75245
+ "text": [
75246
+ "OK\n",
75247
+ "[9116/10000] (0.25GB) Downloading: TCGA-D8-A73U-01Z-00-DX2.91F571C8-303C-463D-952C-263FAA5097DF.svs (933.09 MB)... "
75248
+ ]
75249
+ },
75250
+ {
75251
+ "name": "stdout",
75252
+ "output_type": "stream",
75253
+ "text": [
75254
+ "OK\n",
75255
+ "[9117/10000] (1.16GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_A10_730924.nocnv_grch38.seg.v2.txt (0.00 MB)... "
75256
+ ]
75257
+ },
75258
+ {
75259
+ "name": "stdout",
75260
+ "output_type": "stream",
75261
+ "text": [
75262
+ "OK\n",
75263
+ "[9118/10000] (1.16GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_E08_628562.grch38.seg.v2.txt (0.02 MB)... "
75264
+ ]
75265
+ },
75266
+ {
75267
+ "name": "stdout",
75268
+ "output_type": "stream",
75269
+ "text": [
75270
+ "OK\n",
75271
+ "[9119/10000] (1.16GB) Downloading: TCGA-A8-A09N-01Z-00-DX1.A0E4EF10-5BFF-46A0-94C7-578EA3A88599.svs (605.78 MB)... "
75272
+ ]
75273
+ },
75274
+ {
75275
+ "name": "stdout",
75276
+ "output_type": "stream",
75277
+ "text": [
75278
+ "OK\n",
75279
+ "[9120/10000] (1.75GB) Downloading: 078f75c2-6d13-47b9-8a5b-1ce4c99b67c0_noid_Red.idat (0.69 MB)... "
75280
+ ]
75281
+ },
75282
+ {
75283
+ "name": "stdout",
75284
+ "output_type": "stream",
75285
+ "text": [
75286
+ "OK\n",
75287
+ "[9121/10000] (1.75GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_F03_1373632.nocnv_grch38.seg.v2.txt (0.00 MB)... "
75288
+ ]
75289
+ },
75290
+ {
75291
+ "name": "stdout",
75292
+ "output_type": "stream",
75293
+ "text": [
75294
+ "OK\n",
75295
+ "[9122/10000] (1.75GB) Downloading: 9f189237-a9bf-4c6c-bc0c-94a730bb1b30_noid_Grn.idat (7.72 MB)... "
75296
+ ]
75297
+ },
75298
+ {
75299
+ "name": "stdout",
75300
+ "output_type": "stream",
75301
+ "text": [
75302
+ "OK\n",
75303
+ "[9123/10000] (1.76GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A0XS.xml (0.06 MB)... "
75304
+ ]
75305
+ },
75306
+ {
75307
+ "name": "stdout",
75308
+ "output_type": "stream",
75309
+ "text": [
75310
+ "OK\n",
75311
+ "[9124/10000] (1.76GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A09N.xml (0.01 MB)... "
75312
+ ]
75313
+ },
75314
+ {
75315
+ "name": "stdout",
75316
+ "output_type": "stream",
75317
+ "text": [
75318
+ "OK\n",
75319
+ "[9125/10000] (1.76GB) Downloading: f303bc85-e1fc-451e-9833-0392b9ca0529.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
75320
+ ]
75321
+ },
75322
+ {
75323
+ "name": "stdout",
75324
+ "output_type": "stream",
75325
+ "text": [
75326
+ "OK\n",
75327
+ "[9126/10000] (1.76GB) Downloading: d99e16ae-7815-4b80-ac00-ff1c28bb08ec.mirbase21.isoforms.quantification.txt (0.26 MB)... "
75328
+ ]
75329
+ },
75330
+ {
75331
+ "name": "stdout",
75332
+ "output_type": "stream",
75333
+ "text": [
75334
+ "OK\n",
75335
+ "[9127/10000] (1.76GB) Downloading: TCGA-AC-A5XU-01A-01-TSA.53BFAB63-FB19-4F47-B71C-C93645D58BBB.svs (130.29 MB)... "
75336
+ ]
75337
+ },
75338
+ {
75339
+ "name": "stdout",
75340
+ "output_type": "stream",
75341
+ "text": [
75342
+ "OK\n",
75343
+ "[9128/10000] (1.89GB) Downloading: TCGA-BRCA.bdf230f7-71c7-4ee8-b1ed-b29015b40f57.gene_level_copy_number.v36.tsv (3.29 MB)... "
75344
+ ]
75345
+ },
75346
+ {
75347
+ "name": "stdout",
75348
+ "output_type": "stream",
75349
+ "text": [
75350
+ "OK\n",
75351
+ "[9129/10000] (1.89GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_E01_1343820.grch38.seg.v2.txt (0.07 MB)... "
75352
+ ]
75353
+ },
75354
+ {
75355
+ "name": "stdout",
75356
+ "output_type": "stream",
75357
+ "text": [
75358
+ "OK\n",
75359
+ "[9130/10000] (1.89GB) Downloading: be0d9a28-8d20-4d26-bc0e-ed066de3e8d9.methylation_array.sesame.level3betas.txt (12.50 MB)... "
75360
+ ]
75361
+ },
75362
+ {
75363
+ "name": "stdout",
75364
+ "output_type": "stream",
75365
+ "text": [
75366
+ "OK\n",
75367
+ "[9131/10000] (1.90GB) Downloading: be0d9a28-8d20-4d26-bc0e-ed066de3e8d9_noid_Grn.idat (7.72 MB)... "
75368
+ ]
75369
+ },
75370
+ {
75371
+ "name": "stdout",
75372
+ "output_type": "stream",
75373
+ "text": [
75374
+ "OK\n",
75375
+ "[9132/10000] (1.91GB) Downloading: TCGA-BRCA.513f5d19-3ff2-436a-adeb-817f9ac828d6.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
75376
+ ]
75377
+ },
75378
+ {
75379
+ "name": "stdout",
75380
+ "output_type": "stream",
75381
+ "text": [
75382
+ "OK\n",
75383
+ "[9133/10000] (1.91GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AC-A5XU.xml (0.05 MB)... "
75384
+ ]
75385
+ },
75386
+ {
75387
+ "name": "stdout",
75388
+ "output_type": "stream",
75389
+ "text": [
75390
+ "OK\n",
75391
+ "[9134/10000] (1.91GB) Downloading: TCGA-BRCA.bdf230f7-71c7-4ee8-b1ed-b29015b40f57.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75392
+ ]
75393
+ },
75394
+ {
75395
+ "name": "stdout",
75396
+ "output_type": "stream",
75397
+ "text": [
75398
+ "OK\n",
75399
+ "[9135/10000] (1.92GB) Downloading: TCGA-BRCA.513f5d19-3ff2-436a-adeb-817f9ac828d6.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75400
+ ]
75401
+ },
75402
+ {
75403
+ "name": "stdout",
75404
+ "output_type": "stream",
75405
+ "text": [
75406
+ "OK\n",
75407
+ "[9136/10000] (1.92GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09N.xml (0.09 MB)... "
75408
+ ]
75409
+ },
75410
+ {
75411
+ "name": "stdout",
75412
+ "output_type": "stream",
75413
+ "text": [
75414
+ "OK\n",
75415
+ "[9137/10000] (1.92GB) Downloading: TCGA-A8-A09N.F5A97F05-4B5C-4B10-BF10-5DDE7D412BCF.PDF (0.05 MB)... "
75416
+ ]
75417
+ },
75418
+ {
75419
+ "name": "stdout",
75420
+ "output_type": "stream",
75421
+ "text": [
75422
+ "OK\n",
75423
+ "[9138/10000] (1.92GB) Downloading: ce09de27-a89e-4b64-ba7c-5d9c21667a61.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
75424
+ ]
75425
+ },
75426
+ {
75427
+ "name": "stdout",
75428
+ "output_type": "stream",
75429
+ "text": [
75430
+ "OK\n",
75431
+ "[9139/10000] (1.92GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_E12_628474.nocnv_grch38.seg.v2.txt (0.04 MB)... "
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+ ]
75433
+ },
75434
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
75441
+ },
75442
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9141/10000] (1.92GB) Downloading: TCGA-C8-A135-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
75448
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9142/10000] (1.92GB) Downloading: 1edf23dc-f89a-40ed-8a3f-fc916ed30c9b.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
75456
+ ]
75457
+ },
75458
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75461
+ "text": [
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+ "OK\n",
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+ "[9143/10000] (1.92GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-EW-A6SC.xml (0.05 MB)... "
75464
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9144/10000] (1.92GB) Downloading: fa512622-dbc8-4eed-9862-e070c95cde56_noid_Red.idat (0.69 MB)... "
75472
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9145/10000] (1.92GB) Downloading: TCGA-BRCA.71796d70-39a8-4fa4-894e-2e19953dd94d.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
75481
+ },
75482
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9146/10000] (1.92GB) Downloading: a651873b-1137-4c5f-ba89-3a16a47cf9d9.mirbase21.isoforms.quantification.txt (0.40 MB)... "
75488
+ ]
75489
+ },
75490
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9147/10000] (1.92GB) Downloading: TCGA-EW-A6SC-01A-21-A43F-20_RPPA_data.tsv (0.02 MB)... "
75496
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9148/10000] (1.92GB) Downloading: TCGA-C8-A135-01A-01-BSA.4871792f-d00b-4541-815b-7aaa44c43f94.svs (230.26 MB)... "
75504
+ ]
75505
+ },
75506
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9149/10000] (2.15GB) Downloading: TCGA-BRCA.71796d70-39a8-4fa4-894e-2e19953dd94d.ascat3.allelic_specific.seg.txt (0.01 MB)... "
75512
+ ]
75513
+ },
75514
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75517
+ "text": [
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+ "OK\n",
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+ "[9150/10000] (2.15GB) Downloading: TCGA-BRCA.dc5b229b-a3c1-4e91-a28a-809ce6035c0c.gene_level_copy_number.v36.tsv (3.29 MB)... "
75520
+ ]
75521
+ },
75522
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75525
+ "text": [
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+ "OK\n",
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+ "[9151/10000] (2.15GB) Downloading: 4fa35f20-e26e-4bb0-811d-b307e3927904.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
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+ ]
75529
+ },
75530
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75533
+ "text": [
75534
+ "OK\n",
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+ "[9152/10000] (2.16GB) Downloading: fa512622-dbc8-4eed-9862-e070c95cde56.methylation_array.sesame.level3betas.txt (0.73 MB)... "
75536
+ ]
75537
+ },
75538
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9153/10000] (2.16GB) Downloading: TCGA-BRCA.dc5b229b-a3c1-4e91-a28a-809ce6035c0c.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75544
+ ]
75545
+ },
75546
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75549
+ "text": [
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+ "OK\n",
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+ "[9154/10000] (2.16GB) Downloading: TCGA-C8-A135-01Z-00-DX1.B69A605E-B577-4F43-9471-2C95312B05D9.svs (1242.62 MB)... "
75552
+ ]
75553
+ },
75554
+ {
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+ "name": "stdout",
75556
+ "output_type": "stream",
75557
+ "text": [
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+ "OK\n",
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+ "[9155/10000] (3.37GB) Downloading: FENCE_p_TCGAb_332_333_334_NSP_GenomeWideSNP_6_F09_1367368.grch38.seg.v2.txt (0.04 MB)... "
75560
+ ]
75561
+ },
75562
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9156/10000] (3.37GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-C8-A135.xml (0.06 MB)... "
75568
+ ]
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+ },
75570
+ {
75571
+ "name": "stdout",
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+ "output_type": "stream",
75573
+ "text": [
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+ "OK\n",
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+ "[9157/10000] (3.37GB) Downloading: nationwidechildrens.org_clinical.TCGA-C8-A135.xml (0.08 MB)... "
75576
+ ]
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+ },
75578
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9158/10000] (3.37GB) Downloading: 58478a9c-229e-4bcd-a031-18385ab39d02_noid_Red.idat (7.72 MB)... "
75584
+ ]
75585
+ },
75586
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75589
+ "text": [
75590
+ "OK\n",
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+ "[9159/10000] (3.38GB) Downloading: TCGA-C8-A135-01A-11D-A894-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.08 MB)... "
75592
+ ]
75593
+ },
75594
+ {
75595
+ "name": "stdout",
75596
+ "output_type": "stream",
75597
+ "text": [
75598
+ "OK\n",
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+ "[9160/10000] (3.38GB) Downloading: TCGA-EW-A6SC.315A77B4-1A2E-468D-9E44-FF0B07697943.PDF (0.23 MB)... "
75600
+ ]
75601
+ },
75602
+ {
75603
+ "name": "stdout",
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+ "output_type": "stream",
75605
+ "text": [
75606
+ "OK\n",
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+ "[9161/10000] (3.38GB) Downloading: TCGA-BRCA.dc5b229b-a3c1-4e91-a28a-809ce6035c0c.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
75608
+ ]
75609
+ },
75610
+ {
75611
+ "name": "stdout",
75612
+ "output_type": "stream",
75613
+ "text": [
75614
+ "OK\n",
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+ "[9162/10000] (3.38GB) Downloading: TCGA-BRCA.71796d70-39a8-4fa4-894e-2e19953dd94d.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75616
+ ]
75617
+ },
75618
+ {
75619
+ "name": "stdout",
75620
+ "output_type": "stream",
75621
+ "text": [
75622
+ "OK\n",
75623
+ "[9163/10000] (3.39GB) Downloading: 183b24a1-dc9a-4078-bf01-4633823704d0.mirbase21.isoforms.quantification.txt (0.32 MB)... "
75624
+ ]
75625
+ },
75626
+ {
75627
+ "name": "stdout",
75628
+ "output_type": "stream",
75629
+ "text": [
75630
+ "OK\n",
75631
+ "[9164/10000] (3.39GB) Downloading: TCGA-C8-A135-01A-01-TSA.c03f75de-8d25-4f74-8ca4-498db35d5df9.svs (335.27 MB)... "
75632
+ ]
75633
+ },
75634
+ {
75635
+ "name": "stdout",
75636
+ "output_type": "stream",
75637
+ "text": [
75638
+ "OK\n",
75639
+ "[9165/10000] (3.72GB) Downloading: TCGA-BRCA.87fe6581-eab6-4755-8837-75771304741f.ascat3.allelic_specific.seg.txt (0.01 MB)... "
75640
+ ]
75641
+ },
75642
+ {
75643
+ "name": "stdout",
75644
+ "output_type": "stream",
75645
+ "text": [
75646
+ "OK\n",
75647
+ "[9166/10000] (3.72GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_G01_787490.nocnv_grch38.seg.v2.txt (0.00 MB)... "
75648
+ ]
75649
+ },
75650
+ {
75651
+ "name": "stdout",
75652
+ "output_type": "stream",
75653
+ "text": [
75654
+ "OK\n",
75655
+ "[9167/10000] (3.72GB) Downloading: 26bfb542-c5db-46cf-bacb-cedfd98596d9_noid_Grn.idat (7.72 MB)... "
75656
+ ]
75657
+ },
75658
+ {
75659
+ "name": "stdout",
75660
+ "output_type": "stream",
75661
+ "text": [
75662
+ "OK\n",
75663
+ "[9168/10000] (3.72GB) Downloading: 72c27793-2913-4e0a-9e49-527660e52cf6.methylation_array.sesame.level3betas.txt (12.47 MB)... "
75664
+ ]
75665
+ },
75666
+ {
75667
+ "name": "stdout",
75668
+ "output_type": "stream",
75669
+ "text": [
75670
+ "OK\n",
75671
+ "[9169/10000] (3.74GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_E02_780876.grch38.seg.v2.txt (0.02 MB)... "
75672
+ ]
75673
+ },
75674
+ {
75675
+ "name": "stdout",
75676
+ "output_type": "stream",
75677
+ "text": [
75678
+ "OK\n",
75679
+ "[9170/10000] (3.74GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_F11_787638.grch38.seg.v2.txt (0.05 MB)... "
75680
+ ]
75681
+ },
75682
+ {
75683
+ "name": "stdout",
75684
+ "output_type": "stream",
75685
+ "text": [
75686
+ "OK\n",
75687
+ "[9171/10000] (3.74GB) Downloading: 26bfb542-c5db-46cf-bacb-cedfd98596d9_noid_Red.idat (7.72 MB)... "
75688
+ ]
75689
+ },
75690
+ {
75691
+ "name": "stdout",
75692
+ "output_type": "stream",
75693
+ "text": [
75694
+ "OK\n",
75695
+ "[9172/10000] (3.74GB) Downloading: TCGA-BRCA.97f9770c-3539-4578-84f4-bb63a7463900.ascat3.allelic_specific.seg.txt (0.01 MB)... "
75696
+ ]
75697
+ },
75698
+ {
75699
+ "name": "stdout",
75700
+ "output_type": "stream",
75701
+ "text": [
75702
+ "OK\n",
75703
+ "[9173/10000] (3.74GB) Downloading: 5362c264-ef43-498f-b6aa-362f127a8e94.mirbase21.mirnas.quantification.txt (0.05 MB)... "
75704
+ ]
75705
+ },
75706
+ {
75707
+ "name": "stdout",
75708
+ "output_type": "stream",
75709
+ "text": [
75710
+ "OK\n",
75711
+ "[9174/10000] (3.74GB) Downloading: 72c27793-2913-4e0a-9e49-527660e52cf6_noid_Red.idat (7.72 MB)... "
75712
+ ]
75713
+ },
75714
+ {
75715
+ "name": "stdout",
75716
+ "output_type": "stream",
75717
+ "text": [
75718
+ "OK\n",
75719
+ "[9175/10000] (3.75GB) Downloading: TCGA-D8-A1XK.B3DB4F9E-C91B-4913-93E8-F18FF22CBA7C.PDF (0.07 MB)... "
75720
+ ]
75721
+ },
75722
+ {
75723
+ "name": "stdout",
75724
+ "output_type": "stream",
75725
+ "text": [
75726
+ "OK\n",
75727
+ "[9176/10000] (3.75GB) Downloading: TCGA-BRCA.b3f1bdd3-a76f-4ab7-9c8c-c02c36f1ecee.gene_level_copy_number.v36.tsv (3.29 MB)... "
75728
+ ]
75729
+ },
75730
+ {
75731
+ "name": "stdout",
75732
+ "output_type": "stream",
75733
+ "text": [
75734
+ "OK\n",
75735
+ "[9177/10000] (3.75GB) Downloading: 72c27793-2913-4e0a-9e49-527660e52cf6_noid_Grn.idat (7.72 MB)... "
75736
+ ]
75737
+ },
75738
+ {
75739
+ "name": "stdout",
75740
+ "output_type": "stream",
75741
+ "text": [
75742
+ "OK\n",
75743
+ "[9178/10000] (3.76GB) Downloading: TCGA-BRCA.97f9770c-3539-4578-84f4-bb63a7463900.ascat2.allelic_specific.seg.txt (0.02 MB)... "
75744
+ ]
75745
+ },
75746
+ {
75747
+ "name": "stdout",
75748
+ "output_type": "stream",
75749
+ "text": [
75750
+ "OK\n",
75751
+ "[9179/10000] (3.76GB) Downloading: TCGA-OL-A5RW-01A-21-A321-20_RPPA_data.tsv (0.02 MB)... "
75752
+ ]
75753
+ },
75754
+ {
75755
+ "name": "stdout",
75756
+ "output_type": "stream",
75757
+ "text": [
75758
+ "OK\n",
75759
+ "[9180/10000] (3.76GB) Downloading: 0a6f0619-8092-4742-aa17-b6788694142d.wxs.aliquot_ensemble_masked.maf.gz (0.06 MB)... "
75760
+ ]
75761
+ },
75762
+ {
75763
+ "name": "stdout",
75764
+ "output_type": "stream",
75765
+ "text": [
75766
+ "OK\n",
75767
+ "[9181/10000] (3.76GB) Downloading: TCGA-D8-A1X9-01A-12D-A898-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.20 MB)... "
75768
+ ]
75769
+ },
75770
+ {
75771
+ "name": "stdout",
75772
+ "output_type": "stream",
75773
+ "text": [
75774
+ "OK\n",
75775
+ "[9182/10000] (3.76GB) Downloading: TCGA-OL-A5RW.86B06754-B000-4F8B-9037-95E7A0BD4D20.PDF (0.69 MB)... "
75776
+ ]
75777
+ },
75778
+ {
75779
+ "name": "stdout",
75780
+ "output_type": "stream",
75781
+ "text": [
75782
+ "OK\n",
75783
+ "[9183/10000] (3.76GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A1XK.xml (0.01 MB)... "
75784
+ ]
75785
+ },
75786
+ {
75787
+ "name": "stdout",
75788
+ "output_type": "stream",
75789
+ "text": [
75790
+ "OK\n",
75791
+ "[9184/10000] (3.76GB) Downloading: 00574710-29e7-4df3-a26d-7cdfd19aef31.mirbase21.mirnas.quantification.txt (0.05 MB)... "
75792
+ ]
75793
+ },
75794
+ {
75795
+ "name": "stdout",
75796
+ "output_type": "stream",
75797
+ "text": [
75798
+ "OK\n",
75799
+ "[9185/10000] (3.76GB) Downloading: nationwidechildrens.org_clinical.TCGA-OL-A5RW.xml (0.08 MB)... "
75800
+ ]
75801
+ },
75802
+ {
75803
+ "name": "stdout",
75804
+ "output_type": "stream",
75805
+ "text": [
75806
+ "OK\n",
75807
+ "[9186/10000] (3.76GB) Downloading: TCGA-BRCA.87fe6581-eab6-4755-8837-75771304741f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
75808
+ ]
75809
+ },
75810
+ {
75811
+ "name": "stdout",
75812
+ "output_type": "stream",
75813
+ "text": [
75814
+ "OK\n",
75815
+ "[9187/10000] (3.77GB) Downloading: TCGA-D8-A1X9-01A-01-TS1.5e0a9a6f-7590-4912-be93-23dac19f12f0.svs (183.95 MB)... "
75816
+ ]
75817
+ },
75818
+ {
75819
+ "name": "stdout",
75820
+ "output_type": "stream",
75821
+ "text": [
75822
+ "OK\n",
75823
+ "[9188/10000] (3.95GB) Downloading: TCGA-D8-A1X9-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
75824
+ ]
75825
+ },
75826
+ {
75827
+ "name": "stdout",
75828
+ "output_type": "stream",
75829
+ "text": [
75830
+ "OK\n",
75831
+ "[9189/10000] (3.95GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_F06_780932.grch38.seg.v2.txt (0.07 MB)... "
75832
+ ]
75833
+ },
75834
+ {
75835
+ "name": "stdout",
75836
+ "output_type": "stream",
75837
+ "text": [
75838
+ "OK\n",
75839
+ "[9190/10000] (3.95GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_H02_1343848.nocnv_grch38.seg.v2.txt (0.01 MB)... "
75840
+ ]
75841
+ },
75842
+ {
75843
+ "name": "stdout",
75844
+ "output_type": "stream",
75845
+ "text": [
75846
+ "OK\n",
75847
+ "[9191/10000] (3.95GB) Downloading: TCGA-A2-A0CU-01A-12D-A890-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.08 MB)... "
75848
+ ]
75849
+ },
75850
+ {
75851
+ "name": "stdout",
75852
+ "output_type": "stream",
75853
+ "text": [
75854
+ "OK\n",
75855
+ "[9192/10000] (3.95GB) Downloading: TCGA-BRCA.87fe6581-eab6-4755-8837-75771304741f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
75856
+ ]
75857
+ },
75858
+ {
75859
+ "name": "stdout",
75860
+ "output_type": "stream",
75861
+ "text": [
75862
+ "OK\n",
75863
+ "[9193/10000] (3.95GB) Downloading: TCGA-BH-A0DQ-11A-01-TSA.14a71136-c42e-4c8e-9ef8-a88c247ed5b4.svs (67.53 MB)... "
75864
+ ]
75865
+ },
75866
+ {
75867
+ "name": "stdout",
75868
+ "output_type": "stream",
75869
+ "text": [
75870
+ "OK\n",
75871
+ "[9194/10000] (4.01GB) Downloading: 86f15dc2-5cd0-4c70-ab8a-31c039a964fc.mirbase21.isoforms.quantification.txt (0.33 MB)... "
75872
+ ]
75873
+ },
75874
+ {
75875
+ "name": "stdout",
75876
+ "output_type": "stream",
75877
+ "text": [
75878
+ "OK\n",
75879
+ "[9195/10000] (4.02GB) Downloading: 3d2c22a8-c817-4470-8145-c9cf79ed1368_noid_Red.idat (0.69 MB)... "
75880
+ ]
75881
+ },
75882
+ {
75883
+ "name": "stdout",
75884
+ "output_type": "stream",
75885
+ "text": [
75886
+ "OK\n",
75887
+ "[9196/10000] (4.02GB) Downloading: 281a89c1-e817-49d4-afa1-2894c2747919.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
75888
+ ]
75889
+ },
75890
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
75893
+ "text": [
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+ "OK\n",
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9200/10000] (4.02GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0DQ.xml (0.11 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9201/10000] (4.02GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_C06_667230.nocnv_grch38.seg.v2.txt (0.06 MB)... "
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+ ]
75929
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9202/10000] (4.02GB) Downloading: TCGA-BRCA.9c3fcdbc-c563-416e-8cd4-b95d15b9bee9.ascat3.allelic_specific.seg.txt (0.01 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9203/10000] (4.02GB) Downloading: df199db6-cd07-4832-a7d1-a88e5a3182f4.methylation_array.sesame.level3betas.txt (12.52 MB)... "
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+ ]
75945
+ },
75946
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9204/10000] (4.04GB) Downloading: df199db6-cd07-4832-a7d1-a88e5a3182f4_noid_Grn.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9205/10000] (4.04GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A1AU.xml (0.01 MB)... "
75960
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9206/10000] (4.04GB) Downloading: TCGA-BRCA.01bc5261-bf91-4f7b-a6b4-0e727c5e31d2.ascat3.allelic_specific.seg.txt (0.00 MB)... "
75968
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9207/10000] (4.04GB) Downloading: d4a85cc7-c7c1-4817-8844-30a6e1338517_noid_Grn.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9208/10000] (4.05GB) Downloading: TCGA-BH-A0DQ.D644B589-A6ED-4DCC-97D4-751E22AE3A7D.PDF (0.10 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9209/10000] (4.05GB) Downloading: TCGA-BRCA.01bc5261-bf91-4f7b-a6b4-0e727c5e31d2.ascat2.allelic_specific.seg.txt (0.01 MB)... "
75992
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9210/10000] (4.05GB) Downloading: 4fbfc232-818f-48fb-83bc-6433c9207b09.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9211/10000] (4.05GB) Downloading: 4abd29b3-0a83-41d3-a741-bcc5b6d2f98a.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
76008
+ ]
76009
+ },
76010
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9212/10000] (4.06GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_B11_698038.grch38.seg.v2.txt (0.05 MB)... "
76016
+ ]
76017
+ },
76018
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9213/10000] (4.06GB) Downloading: TCGA-B6-A0IG-01A-11D-A892-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.14 MB)... "
76024
+ ]
76025
+ },
76026
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9214/10000] (4.06GB) Downloading: TCGA-B6-A0IG-01A-01-BSA.f4b6e4d4-e56d-479f-8bd9-8be8eca6d7c7.svs (345.05 MB)... "
76032
+ ]
76033
+ },
76034
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9215/10000] (4.39GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A0DQ.xml (0.02 MB)... "
76040
+ ]
76041
+ },
76042
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9216/10000] (4.39GB) Downloading: 3d2c22a8-c817-4470-8145-c9cf79ed1368.methylation_array.sesame.level3betas.txt (0.74 MB)... "
76048
+ ]
76049
+ },
76050
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
76053
+ "text": [
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+ "OK\n",
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+ "[9217/10000] (4.39GB) Downloading: TCGA-BH-A0DQ-01Z-00-DX1.5A98747C-52D9-45AD-BC84-934A96F069EB.svs (1777.02 MB)... "
76056
+ ]
76057
+ },
76058
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
76061
+ "text": [
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+ "OK\n",
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+ "[9218/10000] (6.13GB) Downloading: df199db6-cd07-4832-a7d1-a88e5a3182f4_noid_Red.idat (7.72 MB)... "
76064
+ ]
76065
+ },
76066
+ {
76067
+ "name": "stdout",
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+ "output_type": "stream",
76069
+ "text": [
76070
+ "OK\n",
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+ "[9219/10000] (6.14GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_C03_772214.grch38.seg.v2.txt (0.06 MB)... "
76072
+ ]
76073
+ },
76074
+ {
76075
+ "name": "stdout",
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+ "output_type": "stream",
76077
+ "text": [
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+ "OK\n",
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+ "[9220/10000] (6.14GB) Downloading: TCGA-BRCA.a9914a13-282b-42c9-ae86-ad7241f462a9.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76080
+ ]
76081
+ },
76082
+ {
76083
+ "name": "stdout",
76084
+ "output_type": "stream",
76085
+ "text": [
76086
+ "OK\n",
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+ "[9221/10000] (6.14GB) Downloading: TCGA-BRCA.6275c0ff-efae-4d00-b3ae-123cbb90b4e2.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
76088
+ ]
76089
+ },
76090
+ {
76091
+ "name": "stdout",
76092
+ "output_type": "stream",
76093
+ "text": [
76094
+ "OK\n",
76095
+ "[9222/10000] (6.14GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_E03_748026.nocnv_grch38.seg.v2.txt (0.01 MB)... "
76096
+ ]
76097
+ },
76098
+ {
76099
+ "name": "stdout",
76100
+ "output_type": "stream",
76101
+ "text": [
76102
+ "OK\n",
76103
+ "[9223/10000] (6.14GB) Downloading: TCGA-BRCA.6275c0ff-efae-4d00-b3ae-123cbb90b4e2.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76104
+ ]
76105
+ },
76106
+ {
76107
+ "name": "stdout",
76108
+ "output_type": "stream",
76109
+ "text": [
76110
+ "OK\n",
76111
+ "[9224/10000] (6.15GB) Downloading: TCGA-BRCA.3830d91c-48eb-4f67-9db9-1a4ff4b28c92.ascat3.allelic_specific.seg.txt (0.01 MB)... "
76112
+ ]
76113
+ },
76114
+ {
76115
+ "name": "stdout",
76116
+ "output_type": "stream",
76117
+ "text": [
76118
+ "OK\n",
76119
+ "[9225/10000] (6.15GB) Downloading: TCGA-C8-A1HJ-01A-01-TSA.64084e7d-ec1b-43d9-8770-7635f716512f.svs (185.23 MB)... "
76120
+ ]
76121
+ },
76122
+ {
76123
+ "name": "stdout",
76124
+ "output_type": "stream",
76125
+ "text": [
76126
+ "OK\n",
76127
+ "[9226/10000] (6.33GB) Downloading: 00e0b87d-1354-4b56-91d8-84f58dfa87fe_noid_Grn.idat (7.72 MB)... "
76128
+ ]
76129
+ },
76130
+ {
76131
+ "name": "stdout",
76132
+ "output_type": "stream",
76133
+ "text": [
76134
+ "OK\n",
76135
+ "[9227/10000] (6.33GB) Downloading: 05c73d09-cd3f-49b8-9cfa-60ed07f85978_noid_Red.idat (0.69 MB)... "
76136
+ ]
76137
+ },
76138
+ {
76139
+ "name": "stdout",
76140
+ "output_type": "stream",
76141
+ "text": [
76142
+ "OK\n",
76143
+ "[9228/10000] (6.34GB) Downloading: TCGA-BRCA.a9914a13-282b-42c9-ae86-ad7241f462a9.ascat3.allelic_specific.seg.txt (0.01 MB)... "
76144
+ ]
76145
+ },
76146
+ {
76147
+ "name": "stdout",
76148
+ "output_type": "stream",
76149
+ "text": [
76150
+ "OK\n",
76151
+ "[9229/10000] (6.34GB) Downloading: TCGA-OL-A66I-01A-02-TS2.E1A6C9D3-79DB-4585-9879-1AB340415E37.svs (202.78 MB)... "
76152
+ ]
76153
+ },
76154
+ {
76155
+ "name": "stdout",
76156
+ "output_type": "stream",
76157
+ "text": [
76158
+ "OK\n",
76159
+ "[9230/10000] (6.53GB) Downloading: 2a65e10a-5fd8-4e68-ad32-7283f1887c99.mirbase21.mirnas.quantification.txt (0.05 MB)... "
76160
+ ]
76161
+ },
76162
+ {
76163
+ "name": "stdout",
76164
+ "output_type": "stream",
76165
+ "text": [
76166
+ "OK\n",
76167
+ "[9231/10000] (6.53GB) Downloading: TCGA-BRCA.6275c0ff-efae-4d00-b3ae-123cbb90b4e2.ascat2.allelic_specific.seg.txt (0.02 MB)... "
76168
+ ]
76169
+ },
76170
+ {
76171
+ "name": "stdout",
76172
+ "output_type": "stream",
76173
+ "text": [
76174
+ "OK\n",
76175
+ "[9232/10000] (6.53GB) Downloading: nationwidechildrens.org_clinical.TCGA-AQ-A54O.xml (0.08 MB)... "
76176
+ ]
76177
+ },
76178
+ {
76179
+ "name": "stdout",
76180
+ "output_type": "stream",
76181
+ "text": [
76182
+ "OK\n",
76183
+ "[9233/10000] (6.53GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_B07_1320420.nocnv_grch38.seg.v2.txt (0.01 MB)... "
76184
+ ]
76185
+ },
76186
+ {
76187
+ "name": "stdout",
76188
+ "output_type": "stream",
76189
+ "text": [
76190
+ "OK\n",
76191
+ "[9234/10000] (6.53GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_B07_1320420.grch38.seg.v2.txt (0.03 MB)... "
76192
+ ]
76193
+ },
76194
+ {
76195
+ "name": "stdout",
76196
+ "output_type": "stream",
76197
+ "text": [
76198
+ "OK\n",
76199
+ "[9235/10000] (6.53GB) Downloading: TCGA-BRCA.ccbe901d-210e-402f-92b3-875c51074ef3.ascat2.allelic_specific.seg.txt (0.02 MB)... "
76200
+ ]
76201
+ },
76202
+ {
76203
+ "name": "stdout",
76204
+ "output_type": "stream",
76205
+ "text": [
76206
+ "OK\n",
76207
+ "[9236/10000] (6.53GB) Downloading: TCGA-AQ-A54O-01A-11D-A89D-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.12 MB)... "
76208
+ ]
76209
+ },
76210
+ {
76211
+ "name": "stdout",
76212
+ "output_type": "stream",
76213
+ "text": [
76214
+ "OK\n",
76215
+ "[9237/10000] (6.53GB) Downloading: 453a933e-8b94-4eee-ad59-74975e45f6dd.mirbase21.mirnas.quantification.txt (0.05 MB)... "
76216
+ ]
76217
+ },
76218
+ {
76219
+ "name": "stdout",
76220
+ "output_type": "stream",
76221
+ "text": [
76222
+ "OK\n",
76223
+ "[9238/10000] (6.53GB) Downloading: TCGA-A8-A09D-01Z-00-DX1.66312A8A-88BA-4B58-96DF-1A7AC39F9E4A.svs (609.87 MB)... "
76224
+ ]
76225
+ },
76226
+ {
76227
+ "name": "stdout",
76228
+ "output_type": "stream",
76229
+ "text": [
76230
+ "OK\n",
76231
+ "[9239/10000] (7.13GB) Downloading: TCGA-A8-A09D-01A-01-BS1.f67237cc-27c1-4b63-8a9c-5c63791b740c.svs (136.69 MB)... "
76232
+ ]
76233
+ },
76234
+ {
76235
+ "name": "stdout",
76236
+ "output_type": "stream",
76237
+ "text": [
76238
+ "OK\n",
76239
+ "[9240/10000] (7.26GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A09D.xml (0.01 MB)... "
76240
+ ]
76241
+ },
76242
+ {
76243
+ "name": "stdout",
76244
+ "output_type": "stream",
76245
+ "text": [
76246
+ "OK\n",
76247
+ "[9241/10000] (7.26GB) Downloading: TCGA-BRCA.f9396883-7828-4aaf-b487-9deec4e199fb.gene_level_copy_number.v36.tsv (3.29 MB)... "
76248
+ ]
76249
+ },
76250
+ {
76251
+ "name": "stdout",
76252
+ "output_type": "stream",
76253
+ "text": [
76254
+ "OK\n",
76255
+ "[9242/10000] (7.27GB) Downloading: 9a0eb4bf-cc72-4155-861c-a283819f2e62_noid_Grn.idat (7.72 MB)... "
76256
+ ]
76257
+ },
76258
+ {
76259
+ "name": "stdout",
76260
+ "output_type": "stream",
76261
+ "text": [
76262
+ "OK\n",
76263
+ "[9243/10000] (7.27GB) Downloading: TCGA-BRCA.f9396883-7828-4aaf-b487-9deec4e199fb.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76264
+ ]
76265
+ },
76266
+ {
76267
+ "name": "stdout",
76268
+ "output_type": "stream",
76269
+ "text": [
76270
+ "OK\n",
76271
+ "[9244/10000] (7.28GB) Downloading: c36f7911-13d2-4230-a5f5-e9c562d763bc.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
76272
+ ]
76273
+ },
76274
+ {
76275
+ "name": "stdout",
76276
+ "output_type": "stream",
76277
+ "text": [
76278
+ "OK\n",
76279
+ "[9245/10000] (7.28GB) Downloading: TCGA-BRCA.ccbe901d-210e-402f-92b3-875c51074ef3.ascat3.allelic_specific.seg.txt (0.02 MB)... "
76280
+ ]
76281
+ },
76282
+ {
76283
+ "name": "stdout",
76284
+ "output_type": "stream",
76285
+ "text": [
76286
+ "OK\n",
76287
+ "[9246/10000] (7.28GB) Downloading: TCGA-BRCA.f9396883-7828-4aaf-b487-9deec4e199fb.ascat2.allelic_specific.seg.txt (0.01 MB)... "
76288
+ ]
76289
+ },
76290
+ {
76291
+ "name": "stdout",
76292
+ "output_type": "stream",
76293
+ "text": [
76294
+ "OK\n",
76295
+ "[9247/10000] (7.28GB) Downloading: TCGA-C8-A1HL-01A-01-TSA.81110654-fbdb-4b73-8393-1e738b63160b.svs (131.25 MB)... "
76296
+ ]
76297
+ },
76298
+ {
76299
+ "name": "stdout",
76300
+ "output_type": "stream",
76301
+ "text": [
76302
+ "OK\n",
76303
+ "[9248/10000] (7.41GB) Downloading: nationwidechildrens.org_clinical.TCGA-C8-A1HL.xml (0.05 MB)... "
76304
+ ]
76305
+ },
76306
+ {
76307
+ "name": "stdout",
76308
+ "output_type": "stream",
76309
+ "text": [
76310
+ "OK\n",
76311
+ "[9249/10000] (7.41GB) Downloading: e1582232-cd29-4d32-be86-f60b55f23744.wgs.ASCAT.gene_level.copy_number_variation.tsv (3.28 MB)... "
76312
+ ]
76313
+ },
76314
+ {
76315
+ "name": "stdout",
76316
+ "output_type": "stream",
76317
+ "text": [
76318
+ "OK\n",
76319
+ "[9250/10000] (7.41GB) Downloading: TCGA-C8-A1HL-01Z-00-DX1.CC21CAE9-DE48-4ADE-A959-5A99010AAFAC.svs (795.19 MB)... "
76320
+ ]
76321
+ },
76322
+ {
76323
+ "name": "stdout",
76324
+ "output_type": "stream",
76325
+ "text": [
76326
+ "OK\n",
76327
+ "[9251/10000] (8.19GB) Downloading: 9a0eb4bf-cc72-4155-861c-a283819f2e62.methylation_array.sesame.level3betas.txt (12.47 MB)... "
76328
+ ]
76329
+ },
76330
+ {
76331
+ "name": "stdout",
76332
+ "output_type": "stream",
76333
+ "text": [
76334
+ "OK\n",
76335
+ "[9252/10000] (8.20GB) Downloading: GAMMA_p_TCGA_b103_104_SNP_N_GenomeWideSNP_6_G06_755774.grch38.seg.v2.txt (0.03 MB)... "
76336
+ ]
76337
+ },
76338
+ {
76339
+ "name": "stdout",
76340
+ "output_type": "stream",
76341
+ "text": [
76342
+ "OK\n",
76343
+ "[9253/10000] (8.20GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_D02_697978.grch38.seg.v2.txt (0.03 MB)... "
76344
+ ]
76345
+ },
76346
+ {
76347
+ "name": "stdout",
76348
+ "output_type": "stream",
76349
+ "text": [
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+ "OK\n",
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+ "[9254/10000] (8.20GB) Downloading: GAMMA_p_TCGA_b103_104_SNP_N_GenomeWideSNP_6_B09_755826.nocnv_grch38.seg.v2.txt (0.03 MB)... "
76352
+ ]
76353
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9255/10000] (8.20GB) Downloading: TCGA-A2-A0T5-01A-11-A13D-20_RPPA_data.tsv (0.02 MB)... "
76360
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9256/10000] (8.20GB) Downloading: 58a54be6-11ed-4dfc-9a41-3405c28f5e9d_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.02 MB)... "
76368
+ ]
76369
+ },
76370
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9257/10000] (8.20GB) Downloading: nationwidechildrens.org_clinical.TCGA-A2-A0T5.xml (0.07 MB)... "
76376
+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9258/10000] (8.20GB) Downloading: a022d53e-dcf9-4172-8bd2-405c01bf6efd.mirbase21.isoforms.quantification.txt (0.31 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9259/10000] (8.20GB) Downloading: 6651d32c-cb9f-4b46-bc9b-96ceee911b80_noid_Red.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9260/10000] (8.21GB) Downloading: ef1bc266-47f5-42f6-b4c7-8f40451f5d15.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
76401
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9261/10000] (8.21GB) Downloading: TCGA-BH-A0AU-11A-01-TSA.20384e45-194c-4feb-bae0-c847ab0b6858.svs (60.87 MB)... "
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+ ]
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+ },
76410
+ {
76411
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9262/10000] (8.27GB) Downloading: ec60e081-f075-4c72-b1e7-62e1f1429fc1.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
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+ ]
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+ },
76418
+ {
76419
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9263/10000] (8.27GB) Downloading: TCGA-BRCA.368b8969-b847-4f91-8054-231f26eb565d.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76424
+ ]
76425
+ },
76426
+ {
76427
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9264/10000] (8.28GB) Downloading: 10ab1524-da3b-4b37-8884-5db813817208.mirbase21.isoforms.quantification.txt (0.27 MB)... "
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+ ]
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+ },
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+ {
76435
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9265/10000] (8.28GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A5IZ.xml (0.08 MB)... "
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+ ]
76441
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9266/10000] (8.28GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_D03_747922.nocnv_grch38.seg.v2.txt (0.02 MB)... "
76448
+ ]
76449
+ },
76450
+ {
76451
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9267/10000] (8.28GB) Downloading: TCGA-BRCA.9687f34c-0460-4fef-b5ba-d7ec23013f4d.ascat3.allelic_specific.seg.txt (0.01 MB)... "
76456
+ ]
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+ },
76458
+ {
76459
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9268/10000] (8.28GB) Downloading: TCGA-BRCA.05cc8716-27bb-48f1-8bf7-563a728a1873.ascat3.allelic_specific.seg.txt (0.00 MB)... "
76464
+ ]
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+ },
76466
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9269/10000] (8.28GB) Downloading: TCGA-BRCA.368b8969-b847-4f91-8054-231f26eb565d.gene_level_copy_number.v36.tsv (3.29 MB)... "
76472
+ ]
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+ },
76474
+ {
76475
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9270/10000] (8.28GB) Downloading: 0b1718ae-d9e5-4e15-b571-1c47c3994597_noid_Red.idat (7.72 MB)... "
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+ ]
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+ },
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+ {
76483
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9271/10000] (8.29GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_A12_747988.nocnv_grch38.seg.v2.txt (0.00 MB)... "
76488
+ ]
76489
+ },
76490
+ {
76491
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9272/10000] (8.29GB) Downloading: TCGA-BRCA.9687f34c-0460-4fef-b5ba-d7ec23013f4d.ascat2.allelic_specific.seg.txt (0.01 MB)... "
76496
+ ]
76497
+ },
76498
+ {
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+ "name": "stdout",
76500
+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9273/10000] (8.29GB) Downloading: e9e16e96-2276-4b47-a88d-bf26ec1d05b6.methylation_array.sesame.level3betas.txt (12.33 MB)... "
76504
+ ]
76505
+ },
76506
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
76509
+ "text": [
76510
+ "OK\n",
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+ "[9274/10000] (8.30GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_B02_780852.grch38.seg.v2.txt (0.06 MB)... "
76512
+ ]
76513
+ },
76514
+ {
76515
+ "name": "stdout",
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+ "output_type": "stream",
76517
+ "text": [
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+ "OK\n",
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+ "[9275/10000] (8.30GB) Downloading: TCGA-BRCA.fd2ba09e-a9f8-4cda-810c-ac29afd0e6b2.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
76520
+ ]
76521
+ },
76522
+ {
76523
+ "name": "stdout",
76524
+ "output_type": "stream",
76525
+ "text": [
76526
+ "OK\n",
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+ "[9276/10000] (8.30GB) Downloading: TCGA-LD-A66U-01A-11D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.02 MB)... "
76528
+ ]
76529
+ },
76530
+ {
76531
+ "name": "stdout",
76532
+ "output_type": "stream",
76533
+ "text": [
76534
+ "OK\n",
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+ "[9277/10000] (8.30GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_E10_780946.nocnv_grch38.seg.v2.txt (0.00 MB)... "
76536
+ ]
76537
+ },
76538
+ {
76539
+ "name": "stdout",
76540
+ "output_type": "stream",
76541
+ "text": [
76542
+ "OK\n",
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+ "[9278/10000] (8.30GB) Downloading: TCGA-BRCA.f0f7b361-1498-4cff-8929-cf600a350ce8.gene_level_copy_number.v36.tsv (3.29 MB)... "
76544
+ ]
76545
+ },
76546
+ {
76547
+ "name": "stdout",
76548
+ "output_type": "stream",
76549
+ "text": [
76550
+ "OK\n",
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+ "[9279/10000] (8.30GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_E10_780946.grch38.seg.v2.txt (0.03 MB)... "
76552
+ ]
76553
+ },
76554
+ {
76555
+ "name": "stdout",
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+ "output_type": "stream",
76557
+ "text": [
76558
+ "OK\n",
76559
+ "[9280/10000] (8.30GB) Downloading: TCGA-LD-A66U-01A-01-TS1.A7BDD6E8-BEE1-4F56-B1BF-4100706FC690.svs (236.30 MB)... "
76560
+ ]
76561
+ },
76562
+ {
76563
+ "name": "stdout",
76564
+ "output_type": "stream",
76565
+ "text": [
76566
+ "OK\n",
76567
+ "[9281/10000] (8.54GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_H01_1365118.nocnv_grch38.seg.v2.txt (0.00 MB)... "
76568
+ ]
76569
+ },
76570
+ {
76571
+ "name": "stdout",
76572
+ "output_type": "stream",
76573
+ "text": [
76574
+ "OK\n",
76575
+ "[9282/10000] (8.54GB) Downloading: TCGA-LD-A66U-01Z-00-DX1.AEC25C62-0519-47ED-A85B-2A964BA2BA87.svs (1277.26 MB)... "
76576
+ ]
76577
+ },
76578
+ {
76579
+ "name": "stdout",
76580
+ "output_type": "stream",
76581
+ "text": [
76582
+ "OK\n",
76583
+ "[9283/10000] (9.78GB) Downloading: 7d736f2b-b73e-4fc1-8d3f-9f350f88171a.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
76584
+ ]
76585
+ },
76586
+ {
76587
+ "name": "stdout",
76588
+ "output_type": "stream",
76589
+ "text": [
76590
+ "OK\n",
76591
+ "[9284/10000] (9.79GB) Downloading: TCGA-BRCA.a7e1a7ba-762d-45b0-b084-118c6ed9690b.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76592
+ ]
76593
+ },
76594
+ {
76595
+ "name": "stdout",
76596
+ "output_type": "stream",
76597
+ "text": [
76598
+ "OK\n",
76599
+ "[9285/10000] (9.79GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A09G.xml (0.03 MB)... "
76600
+ ]
76601
+ },
76602
+ {
76603
+ "name": "stdout",
76604
+ "output_type": "stream",
76605
+ "text": [
76606
+ "OK\n",
76607
+ "[9286/10000] (9.79GB) Downloading: TCGA-A8-A09G-01A-21D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.06 MB)... "
76608
+ ]
76609
+ },
76610
+ {
76611
+ "name": "stdout",
76612
+ "output_type": "stream",
76613
+ "text": [
76614
+ "OK\n",
76615
+ "[9287/10000] (9.79GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_E02_1373620.grch38.seg.v2.txt (0.02 MB)... "
76616
+ ]
76617
+ },
76618
+ {
76619
+ "name": "stdout",
76620
+ "output_type": "stream",
76621
+ "text": [
76622
+ "OK\n",
76623
+ "[9288/10000] (9.79GB) Downloading: nationwidechildrens.org_clinical.TCGA-LD-A74U.xml (0.06 MB)... "
76624
+ ]
76625
+ },
76626
+ {
76627
+ "name": "stdout",
76628
+ "output_type": "stream",
76629
+ "text": [
76630
+ "OK\n",
76631
+ "[9289/10000] (9.79GB) Downloading: TCGA-A8-A09G-01Z-00-DX1.B834728C-DAC5-4463-961D-7E3B220905C1.svs (868.25 MB)... "
76632
+ ]
76633
+ },
76634
+ {
76635
+ "name": "stdout",
76636
+ "output_type": "stream",
76637
+ "text": [
76638
+ "OK\n",
76639
+ "[9290/10000] (10.64GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_E03_1373582.grch38.seg.v2.txt (0.02 MB)... "
76640
+ ]
76641
+ },
76642
+ {
76643
+ "name": "stdout",
76644
+ "output_type": "stream",
76645
+ "text": [
76646
+ "OK\n",
76647
+ "[9291/10000] (10.64GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09G.xml (0.09 MB)... "
76648
+ ]
76649
+ },
76650
+ {
76651
+ "name": "stdout",
76652
+ "output_type": "stream",
76653
+ "text": [
76654
+ "OK\n",
76655
+ "[9292/10000] (10.64GB) Downloading: ff42fcd7-0dfc-4e77-a3d1-f192194a0730.methylation_array.sesame.level3betas.txt (0.74 MB)... "
76656
+ ]
76657
+ },
76658
+ {
76659
+ "name": "stdout",
76660
+ "output_type": "stream",
76661
+ "text": [
76662
+ "OK\n",
76663
+ "[9293/10000] (10.64GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_E03_1373582.nocnv_grch38.seg.v2.txt (0.00 MB)... "
76664
+ ]
76665
+ },
76666
+ {
76667
+ "name": "stdout",
76668
+ "output_type": "stream",
76669
+ "text": [
76670
+ "OK\n",
76671
+ "[9294/10000] (10.64GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G11_628588.grch38.seg.v2.txt (0.07 MB)... "
76672
+ ]
76673
+ },
76674
+ {
76675
+ "name": "stdout",
76676
+ "output_type": "stream",
76677
+ "text": [
76678
+ "OK\n",
76679
+ "[9295/10000] (10.64GB) Downloading: TCGA-BRCA.3cd925e9-93f6-4810-87c6-f3c7ecaf6e77.gene_level_copy_number.v36.tsv (3.29 MB)... "
76680
+ ]
76681
+ },
76682
+ {
76683
+ "name": "stdout",
76684
+ "output_type": "stream",
76685
+ "text": [
76686
+ "OK\n",
76687
+ "[9296/10000] (10.64GB) Downloading: TCGA-BRCA.a7e1a7ba-762d-45b0-b084-118c6ed9690b.gene_level_copy_number.v36.tsv (3.29 MB)... "
76688
+ ]
76689
+ },
76690
+ {
76691
+ "name": "stdout",
76692
+ "output_type": "stream",
76693
+ "text": [
76694
+ "OK\n",
76695
+ "[9297/10000] (10.65GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G11_628588.nocnv_grch38.seg.v2.txt (0.01 MB)... "
76696
+ ]
76697
+ },
76698
+ {
76699
+ "name": "stdout",
76700
+ "output_type": "stream",
76701
+ "text": [
76702
+ "OK\n",
76703
+ "[9298/10000] (10.65GB) Downloading: 09e9fbed-e4cb-4203-8645-39da98269489.wxs.aliquot_ensemble_masked.maf.gz (0.07 MB)... "
76704
+ ]
76705
+ },
76706
+ {
76707
+ "name": "stdout",
76708
+ "output_type": "stream",
76709
+ "text": [
76710
+ "OK\n",
76711
+ "[9299/10000] (10.65GB) Downloading: TCGA-BRCA.6c95b250-69e7-444d-8087-731383aaff4f.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
76712
+ ]
76713
+ },
76714
+ {
76715
+ "name": "stdout",
76716
+ "output_type": "stream",
76717
+ "text": [
76718
+ "OK\n",
76719
+ "[9300/10000] (10.65GB) Downloading: a4b75cbd-056c-4d20-aff8-b2d21f2706ef_noid_Red.idat (0.69 MB)... "
76720
+ ]
76721
+ },
76722
+ {
76723
+ "name": "stdout",
76724
+ "output_type": "stream",
76725
+ "text": [
76726
+ "OK\n",
76727
+ "[9301/10000] (10.65GB) Downloading: d276a6f0-f010-44a0-856f-cd45d8071534.mirbase21.isoforms.quantification.txt (0.25 MB)... "
76728
+ ]
76729
+ },
76730
+ {
76731
+ "name": "stdout",
76732
+ "output_type": "stream",
76733
+ "text": [
76734
+ "OK\n",
76735
+ "[9302/10000] (10.65GB) Downloading: nationwidechildrens.org_ssf.TCGA-LD-A74U.xml (0.01 MB)... "
76736
+ ]
76737
+ },
76738
+ {
76739
+ "name": "stdout",
76740
+ "output_type": "stream",
76741
+ "text": [
76742
+ "OK\n",
76743
+ "[9303/10000] (10.65GB) Downloading: e59935eb-ad2e-4644-99a3-d9508d02489c.mirbase21.isoforms.quantification.txt (0.29 MB)... "
76744
+ ]
76745
+ },
76746
+ {
76747
+ "name": "stdout",
76748
+ "output_type": "stream",
76749
+ "text": [
76750
+ "OK\n",
76751
+ "[9304/10000] (10.65GB) Downloading: TCGA-A8-A09G-01A-02-BS2.e110bb6c-7c19-4ace-9507-14ef5714a74d.svs (192.54 MB)... "
76752
+ ]
76753
+ },
76754
+ {
76755
+ "name": "stdout",
76756
+ "output_type": "stream",
76757
+ "text": [
76758
+ "OK\n",
76759
+ "[9305/10000] (10.84GB) Downloading: TCGA-BRCA.3cd925e9-93f6-4810-87c6-f3c7ecaf6e77.ascat3.allelic_specific.seg.txt (0.01 MB)... "
76760
+ ]
76761
+ },
76762
+ {
76763
+ "name": "stdout",
76764
+ "output_type": "stream",
76765
+ "text": [
76766
+ "OK\n",
76767
+ "[9306/10000] (10.84GB) Downloading: TCGA-A8-A09G.2728DB14-66D5-4E67-B9B6-63D93DBF509C.PDF (0.08 MB)... "
76768
+ ]
76769
+ },
76770
+ {
76771
+ "name": "stdout",
76772
+ "output_type": "stream",
76773
+ "text": [
76774
+ "OK\n",
76775
+ "[9307/10000] (10.84GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A1AY.xml (0.08 MB)... "
76776
+ ]
76777
+ },
76778
+ {
76779
+ "name": "stdout",
76780
+ "output_type": "stream",
76781
+ "text": [
76782
+ "OK\n",
76783
+ "[9308/10000] (10.84GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_H11_741450.grch38.seg.v2.txt (0.02 MB)... "
76784
+ ]
76785
+ },
76786
+ {
76787
+ "name": "stdout",
76788
+ "output_type": "stream",
76789
+ "text": [
76790
+ "OK\n",
76791
+ "[9309/10000] (10.84GB) Downloading: TCGA-BRCA.1d7e40a7-9af9-45db-9586-9f8a3f6a1824.ascat3.allelic_specific.seg.txt (0.01 MB)... "
76792
+ ]
76793
+ },
76794
+ {
76795
+ "name": "stdout",
76796
+ "output_type": "stream",
76797
+ "text": [
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+ "OK\n",
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+ ]
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+ {
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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76816
+ ]
76817
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
76825
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9314/10000] (10.84GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A1AH.xml (0.02 MB)... "
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+ },
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+ {
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+ "name": "stdout",
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+ "text": [
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+ ]
76841
+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9316/10000] (10.84GB) Downloading: TCGA-AR-A1AY.01D97550-C616-4001-85A5-5502D35FA38E.PDF (0.06 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9317/10000] (10.84GB) Downloading: TCGA-OL-A6VO.961547D2-F235-47E9-9A6D-D286758E332E.PDF (0.21 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9318/10000] (10.85GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_C08_747904.nocnv_grch38.seg.v2.txt (0.03 MB)... "
76864
+ ]
76865
+ },
76866
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9319/10000] (10.85GB) Downloading: TCGA-AR-A1AY-01A-21D-A896-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.21 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9320/10000] (10.85GB) Downloading: 3ca2e165-47ab-4fb1-b955-109d44f81774.mirbase21.mirnas.quantification.txt (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
76890
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9322/10000] (10.85GB) Downloading: TCGA-BRCA.dab4207f-5e33-4cbb-81af-b3f005c74c16.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
76896
+ ]
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+ },
76898
+ {
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+ "name": "stdout",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9325/10000] (10.85GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-OL-A6VO.xml (0.05 MB)... "
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+ ]
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+ },
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+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9326/10000] (10.85GB) Downloading: d5066dc8-74bb-415a-84aa-9f74b61faa20.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
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+ ]
76929
+ },
76930
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[9327/10000] (10.85GB) Downloading: EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6_C04_1244836.grch38.seg.v2.txt (0.03 MB)... "
76936
+ ]
76937
+ },
76938
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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76944
+ ]
76945
+ },
76946
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
76950
+ "OK\n",
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+ "[9329/10000] (10.85GB) Downloading: EMMER_p_8TCGA_Mx_242_238_N_GenomeWideSNP_6_C02_1244766.nocnv_grch38.seg.v2.txt (0.01 MB)... "
76952
+ ]
76953
+ },
76954
+ {
76955
+ "name": "stdout",
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+ "output_type": "stream",
76957
+ "text": [
76958
+ "OK\n",
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+ "[9330/10000] (10.85GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_F07_1373646.nocnv_grch38.seg.v2.txt (0.01 MB)... "
76960
+ ]
76961
+ },
76962
+ {
76963
+ "name": "stdout",
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+ "output_type": "stream",
76965
+ "text": [
76966
+ "OK\n",
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+ "[9331/10000] (10.85GB) Downloading: TCGA-BRCA.dab4207f-5e33-4cbb-81af-b3f005c74c16.ascat2.allelic_specific.seg.txt (0.01 MB)... "
76968
+ ]
76969
+ },
76970
+ {
76971
+ "name": "stdout",
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+ "output_type": "stream",
76973
+ "text": [
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+ "OK\n",
76975
+ "[9332/10000] (10.85GB) Downloading: TCGA-BRCA.b5370ac3-c55f-464c-bb98-6baa05d8b6b8.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
76976
+ ]
76977
+ },
76978
+ {
76979
+ "name": "stdout",
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+ "output_type": "stream",
76981
+ "text": [
76982
+ "OK\n",
76983
+ "[9333/10000] (10.86GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A3Z6.xml (0.01 MB)... "
76984
+ ]
76985
+ },
76986
+ {
76987
+ "name": "stdout",
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+ "output_type": "stream",
76989
+ "text": [
76990
+ "OK\n",
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+ "[9334/10000] (10.86GB) Downloading: 3697b6c1-cf6f-49fe-9a26-dbccdba1b836_noid_Grn.idat (0.69 MB)... "
76992
+ ]
76993
+ },
76994
+ {
76995
+ "name": "stdout",
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+ "output_type": "stream",
76997
+ "text": [
76998
+ "OK\n",
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+ "[9335/10000] (10.86GB) Downloading: TCGA-D8-A3Z6-01Z-00-DX3.66566DB7-661D-4002-90C1-B15BF3425903.svs (325.47 MB)... "
77000
+ ]
77001
+ },
77002
+ {
77003
+ "name": "stdout",
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+ "output_type": "stream",
77005
+ "text": [
77006
+ "OK\n",
77007
+ "[9336/10000] (11.17GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_B01_667198.grch38.seg.v2.txt (0.05 MB)... "
77008
+ ]
77009
+ },
77010
+ {
77011
+ "name": "stdout",
77012
+ "output_type": "stream",
77013
+ "text": [
77014
+ "OK\n",
77015
+ "[9337/10000] (11.17GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_F01_748036.nocnv_grch38.seg.v2.txt (0.01 MB)... "
77016
+ ]
77017
+ },
77018
+ {
77019
+ "name": "stdout",
77020
+ "output_type": "stream",
77021
+ "text": [
77022
+ "OK\n",
77023
+ "[9338/10000] (11.17GB) Downloading: 3ca2e165-47ab-4fb1-b955-109d44f81774.mirbase21.isoforms.quantification.txt (0.30 MB)... "
77024
+ ]
77025
+ },
77026
+ {
77027
+ "name": "stdout",
77028
+ "output_type": "stream",
77029
+ "text": [
77030
+ "OK\n",
77031
+ "[9339/10000] (11.17GB) Downloading: TCGA-BRCA.40c683dc-6337-4e19-9a9d-bad8fcfaa026.ascat3.allelic_specific.seg.txt (0.01 MB)... "
77032
+ ]
77033
+ },
77034
+ {
77035
+ "name": "stdout",
77036
+ "output_type": "stream",
77037
+ "text": [
77038
+ "OK\n",
77039
+ "[9340/10000] (11.17GB) Downloading: TCGA-AO-A0J3-01A-01-TSA.86832b75-652d-40a9-a29a-1638bcce1aef.svs (170.87 MB)... "
77040
+ ]
77041
+ },
77042
+ {
77043
+ "name": "stdout",
77044
+ "output_type": "stream",
77045
+ "text": [
77046
+ "OK\n",
77047
+ "[9341/10000] (11.34GB) Downloading: 59179476-a054-4d90-a183-30e85bc96664_noid_Red.idat (7.72 MB)... "
77048
+ ]
77049
+ },
77050
+ {
77051
+ "name": "stdout",
77052
+ "output_type": "stream",
77053
+ "text": [
77054
+ "OK\n",
77055
+ "[9342/10000] (11.35GB) Downloading: TCGA-BRCA.709852ad-ac59-48af-ba05-2d7a80326afa.ascat2.allelic_specific.seg.txt (0.00 MB)... "
77056
+ ]
77057
+ },
77058
+ {
77059
+ "name": "stdout",
77060
+ "output_type": "stream",
77061
+ "text": [
77062
+ "OK\n",
77063
+ "[9343/10000] (11.35GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_F04_787556.grch38.seg.v2.txt (0.03 MB)... "
77064
+ ]
77065
+ },
77066
+ {
77067
+ "name": "stdout",
77068
+ "output_type": "stream",
77069
+ "text": [
77070
+ "OK\n",
77071
+ "[9344/10000] (11.35GB) Downloading: TCGA-BRCA.b5370ac3-c55f-464c-bb98-6baa05d8b6b8.ascat3.allelic_specific.seg.txt (0.00 MB)... "
77072
+ ]
77073
+ },
77074
+ {
77075
+ "name": "stdout",
77076
+ "output_type": "stream",
77077
+ "text": [
77078
+ "OK\n",
77079
+ "[9345/10000] (11.35GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_D06_667126.grch38.seg.v2.txt (0.04 MB)... "
77080
+ ]
77081
+ },
77082
+ {
77083
+ "name": "stdout",
77084
+ "output_type": "stream",
77085
+ "text": [
77086
+ "OK\n",
77087
+ "[9346/10000] (11.35GB) Downloading: 7c0dd387-5c88-4b36-b856-0f92874012ea_noid_Grn.idat (0.69 MB)... "
77088
+ ]
77089
+ },
77090
+ {
77091
+ "name": "stdout",
77092
+ "output_type": "stream",
77093
+ "text": [
77094
+ "OK\n",
77095
+ "[9347/10000] (11.35GB) Downloading: 3697b6c1-cf6f-49fe-9a26-dbccdba1b836.methylation_array.sesame.level3betas.txt (0.74 MB)... "
77096
+ ]
77097
+ },
77098
+ {
77099
+ "name": "stdout",
77100
+ "output_type": "stream",
77101
+ "text": [
77102
+ "OK\n",
77103
+ "[9348/10000] (11.35GB) Downloading: 59179476-a054-4d90-a183-30e85bc96664.methylation_array.sesame.level3betas.txt (12.31 MB)... "
77104
+ ]
77105
+ },
77106
+ {
77107
+ "name": "stdout",
77108
+ "output_type": "stream",
77109
+ "text": [
77110
+ "OK\n",
77111
+ "[9349/10000] (11.36GB) Downloading: TCGA-BRCA.709852ad-ac59-48af-ba05-2d7a80326afa.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
77112
+ ]
77113
+ },
77114
+ {
77115
+ "name": "stdout",
77116
+ "output_type": "stream",
77117
+ "text": [
77118
+ "OK\n",
77119
+ "[9350/10000] (11.37GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A1RD.xml (0.08 MB)... "
77120
+ ]
77121
+ },
77122
+ {
77123
+ "name": "stdout",
77124
+ "output_type": "stream",
77125
+ "text": [
77126
+ "OK\n",
77127
+ "[9351/10000] (11.37GB) Downloading: TCGA-BRCA.298c4e12-a695-48f1-830a-ae66a78e3ee4.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
77128
+ ]
77129
+ },
77130
+ {
77131
+ "name": "stdout",
77132
+ "output_type": "stream",
77133
+ "text": [
77134
+ "OK\n",
77135
+ "[9352/10000] (11.37GB) Downloading: TCGA-BRCA.298c4e12-a695-48f1-830a-ae66a78e3ee4.gene_level_copy_number.v36.tsv (3.29 MB)... "
77136
+ ]
77137
+ },
77138
+ {
77139
+ "name": "stdout",
77140
+ "output_type": "stream",
77141
+ "text": [
77142
+ "OK\n",
77143
+ "[9353/10000] (11.37GB) Downloading: 0421c9fa-c633-4c76-be96-b476a094dbe6.mirbase21.mirnas.quantification.txt (0.05 MB)... "
77144
+ ]
77145
+ },
77146
+ {
77147
+ "name": "stdout",
77148
+ "output_type": "stream",
77149
+ "text": [
77150
+ "OK\n",
77151
+ "[9354/10000] (11.37GB) Downloading: TCGA-BH-A0DL-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
77152
+ ]
77153
+ },
77154
+ {
77155
+ "name": "stdout",
77156
+ "output_type": "stream",
77157
+ "text": [
77158
+ "OK\n",
77159
+ "[9355/10000] (11.37GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A1RD.xml (0.06 MB)... "
77160
+ ]
77161
+ },
77162
+ {
77163
+ "name": "stdout",
77164
+ "output_type": "stream",
77165
+ "text": [
77166
+ "OK\n",
77167
+ "[9356/10000] (11.37GB) Downloading: 7c0dd387-5c88-4b36-b856-0f92874012ea_noid_Red.idat (0.69 MB)... "
77168
+ ]
77169
+ },
77170
+ {
77171
+ "name": "stdout",
77172
+ "output_type": "stream",
77173
+ "text": [
77174
+ "OK\n",
77175
+ "[9357/10000] (11.37GB) Downloading: TCGA-BRCA.709852ad-ac59-48af-ba05-2d7a80326afa.ascat3.allelic_specific.seg.txt (0.00 MB)... "
77176
+ ]
77177
+ },
77178
+ {
77179
+ "name": "stdout",
77180
+ "output_type": "stream",
77181
+ "text": [
77182
+ "OK\n",
77183
+ "[9358/10000] (11.37GB) Downloading: TCGA-AO-A0J3-01A-01-BSA.b1386e94-b116-4b67-a0f8-987217b20f7c.svs (233.15 MB)... "
77184
+ ]
77185
+ },
77186
+ {
77187
+ "name": "stdout",
77188
+ "output_type": "stream",
77189
+ "text": [
77190
+ "OK\n",
77191
+ "[9359/10000] (11.60GB) Downloading: 30d5997d-396b-4345-b490-4b0879b975ef.mirbase21.isoforms.quantification.txt (0.32 MB)... "
77192
+ ]
77193
+ },
77194
+ {
77195
+ "name": "stdout",
77196
+ "output_type": "stream",
77197
+ "text": [
77198
+ "OK\n",
77199
+ "[9360/10000] (11.60GB) Downloading: nationwidechildrens.org_ssf.TCGA-AO-A0J3.xml (0.01 MB)... "
77200
+ ]
77201
+ },
77202
+ {
77203
+ "name": "stdout",
77204
+ "output_type": "stream",
77205
+ "text": [
77206
+ "OK\n",
77207
+ "[9361/10000] (11.60GB) Downloading: 5028f9f0-d9ff-4439-9084-fee423ad4ca7.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
77208
+ ]
77209
+ },
77210
+ {
77211
+ "name": "stdout",
77212
+ "output_type": "stream",
77213
+ "text": [
77214
+ "OK\n",
77215
+ "[9362/10000] (11.61GB) Downloading: 81a47ae1-b3ff-4908-af9e-c500fb1f8ecb.mirbase21.mirnas.quantification.txt (0.05 MB)... "
77216
+ ]
77217
+ },
77218
+ {
77219
+ "name": "stdout",
77220
+ "output_type": "stream",
77221
+ "text": [
77222
+ "OK\n",
77223
+ "[9363/10000] (11.61GB) Downloading: TCGA-AO-A0J3-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
77224
+ ]
77225
+ },
77226
+ {
77227
+ "name": "stdout",
77228
+ "output_type": "stream",
77229
+ "text": [
77230
+ "OK\n",
77231
+ "[9364/10000] (11.61GB) Downloading: 6596a401-07bb-46c8-9b0b-a4bfae13bafc_noid_Red.idat (7.72 MB)... "
77232
+ ]
77233
+ },
77234
+ {
77235
+ "name": "stdout",
77236
+ "output_type": "stream",
77237
+ "text": [
77238
+ "OK\n",
77239
+ "[9365/10000] (11.61GB) Downloading: 44d1ebac-5de3-4042-9b81-1c4f8c4c818c.methylation_array.sesame.level3betas.txt (0.73 MB)... "
77240
+ ]
77241
+ },
77242
+ {
77243
+ "name": "stdout",
77244
+ "output_type": "stream",
77245
+ "text": [
77246
+ "OK\n",
77247
+ "[9366/10000] (11.61GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_D10_735180.nocnv_grch38.seg.v2.txt (0.01 MB)... "
77248
+ ]
77249
+ },
77250
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+ AGID00111 913 sc-23957 Old 1433EPSILON 0.063062
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+ AGID00101 883 sc-1019 Old 1433ZETA 0.50511
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+ AGID00005 14 1768-1/ab45174 Old ACC1 0.74534
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+ AGID00408 2372 3658 Set163 AceCS1 0.591560929302002
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+ AGID00473 1182 5335 Old ACETYLATUBULINLYS40 0.16065
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+ AGID00404 2367 9189 Set163 ACSL1 0.637921398008064
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+ AGID00498 924 CA1030 Old ALPHACATENIN NA
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+ AGID00179 1170 9565 Set163 b-Catenin_pT41_S45 0.0659464425860911
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+ AGID00433 80 M0887 Old BCL2 1.2216
59
+ AGID00219 1299 PAB8528 Old BCL2A1 0.14984
60
+ AGID00012 84 1018-1 Old BCLXL 0.016511
61
+ AGID00377 87 sc-10086 Old BECLIN 0.016792
62
+ AGID00011 75 9562 Old BETACATENIN 0.088374
63
+ AGID00013 88 1008-1/ab32060 Old BID 0.051355
64
+ AGID00180 90 1036-1/ab32158 Old BIM 0.11973
65
+ AGID00221 1311 610978 Set163 BiP-GRP78 -0.115714118447162
66
+ AGID00373 2194 07-507 Set163 BMK1-Erk5_pT218_Y220 -0.197858528833049
67
+ AGID00355 92 1647/ab33899 Old BRAF 0.69427
68
+ AGID00014 94 2696 Old BRAF_pS445 0.45701
69
+ AGID00445 761 9012 Old BRCA2 0.028191
70
+ AGID00266 1567 13440 Old BRD4 0.11021
71
+ AGID00168 1146 2865 Set163 c-Abl_pY412 -0.125319294445842
72
+ AGID00278 1615 3130 Set163 c-IAP2 -0.20019367126333
73
+ AGID00345 1990 5649 Old CA9 NA
74
+ AGID00265 1565 2862 Old CABL -0.0039902
75
+ AGID00429 2407 2679 Set163 Calnexin 0.079341184033545
76
+ AGID00176 1165 9496 Set163 Caspase-8-cleaved 0.196816355665437
77
+ AGID00623 111 9665 Old CASPASE3 -0.35049
78
+ AGID00015 109 9491 Old CASPASE7CLEAVEDD198 -1.437
79
+ AGID00118 951 9746 Old CASPASE8 -0.18313
80
+ AGID00537 935 551246 Old CASPASE9 NA
81
+ AGID00016 114 3238 Old CAVEOLIN1 0.71101
82
+ AGID00358 2100 ab76000 Set163 CD134 0
83
+ AGID00303 1737 826701 Set163 CD171 -0.30560858500983
84
+ AGID00410 125 1632-1/ab78237 Old CD20 -0.094539
85
+ AGID00220 1308 ab28340 Old CD26 1.5404e-06
86
+ AGID00191 1206 610467 Set163 CD29 0.017921085260086
87
+ AGID00017 127 M0823 Old CD31 -0.025817
88
+ AGID00369 2174 ab108403 Set163 CD38 0.000291448330548437
89
+ AGID00359 2104 ab133616 Set163 CD4 -0.56467982024841
90
+ AGID00411 1398 3570 Set163 CD44 -0.407013683843951
91
+ AGID00237 1352 M070101-2 Set163 CD45 -0.308288727798143
92
+ AGID00115 937 611016 Old CD49B -0.17304
93
+ AGID02171 2482 91882 Set163 CD86 0.615231426842986
94
+ AGID00329 1873 4688 Set163 cdc25C -0.0448735506557239
95
+ AGID00227 1332 4651 Set163 Cdc42 0.0654412191761027
96
+ AGID00422 2396 3387 Set163 Cdc6 0.159381322524339
97
+ AGID00501 1007 9112 Old CDK1 -0.27795
98
+ AGID00293 1658 ab32384 Set163 CDK1_pT14 -0.316408555204502
99
+ AGID00314 1783 4539 Old CDK1_pY15 -0.34691
100
+ AGID00423 2397 8064 Set163 CDT1 -0.356344008964591
101
+ AGID02101 2348 15102 Set163 cGAS -0.184528557907776
102
+ AGID00447 2410 13460 Set163 CHD1L -0.156520391974433
103
+ AGID00189 1203 2360 Old CHK1 -0.05156
104
+ AGID00234 1348 ab79758 Old CHK1_pS296 -0.034749
105
+ AGID00107 903 2348 Old CHK1_pS345 -0.16856
106
+ AGID00018 146 3440 Old CHK2 -0.085272
107
+ AGID00019 147 2197 Old CHK2_pT68 -0.28703
108
+ AGID00527 2078 4952 Old CIAP 0.0025803
109
+ AGID00350 2018 3793 Set163 CIITA 0.00361144105250317
110
+ AGID00434 155 9164 Old CJUN_pS73 0.19359
111
+ AGID00020 157 1522-1/ab32363 Old CKIT -0.071274
112
+ AGID00400 852 NB100-91714 Old CLAUDIN7 -0.44948
113
+ AGID00466 726 3127 Old CMET 0.15195
114
+ AGID00079 727 3129 Old CMET_pY1235 -0.14948
115
+ AGID00167 161 9402 Old CMYC 0.17555
116
+ AGID00292 1656 11130-1-AP Old COG3 0.29955
117
+ AGID00021 171 sc-20649 Old COLLAGENVI 1.5145
118
+ AGID00141 1069 459230 Old COMPLEXIISUBUNIT30 NA
119
+ AGID00267 1568 3512 Set163 Connexin-43 -1.27676882823516
120
+ AGID00269 1571 6434 Set163 Coup-TFII -0.595048561234883
121
+ AGID00150 1116 4850 Set163 Cox-IV 0.325100784572911
122
+ AGID00195 1218 4842 Set163 Cox2 -0.370648555204502
123
+ AGID00188 803 05-739 Old CRAF 0.034419
124
+ AGID00022 179 9427 Old CRAF_pS338 -0.18644
125
+ AGID00023 181 9197 Set163 Creb -0.379189679766193
126
+ AGID00393 2334 9198 Set163 CREB_pS133 0.498033574760855
127
+ AGID00365 2155 4980 Set163 CSK 0.295041403206668
128
+ AGID00367 2160 9201 Set163 CtIP -0.018013897194629
129
+ AGID00536 2096 ab107198 Old CTLA4 NA
130
+ AGID00025 198 2936 Set163 Cyclin-D3 -0.329198677475661
131
+ AGID00024 192 1495-1/ab32053 Old CYCLINB1 -0.99331
132
+ AGID00382 194 sc-718 Old CYCLIND1 0.29132
133
+ AGID00437 199 sc-25303 Old CYCLINE1 -0.54302
134
+ AGID00449 202 1142-1 Old CYCLINE2 -0.31259
135
+ AGID00209 1257 ab110324 Set163 Cyclophilin-F 0.643991152841926
136
+ AGID00247 1379 ab48389 Set163 D-a-Tubulin -0.171043567395228
137
+ AGID00308 1770 GTX10524 Set163 DAPK1_pS308 0.22013138677908
138
+ AGID00304 1744 ab51601 Set163 DAPK2 -0.0743737836571362
139
+ AGID00343 1980 6998 Set163 DDB-1 -0.00633862881673112
140
+ AGID00427 2402 5583 Set163 DDR1 0.308835669588496
141
+ AGID00428 2403 SAB4504671 Set163 DDR1_pY513 -0.262808582861074
142
+ AGID00532 1273 Bast Lab Old DIRAS3 0.21965
143
+ AGID00104 891 ab76008 Old DJ1 0.53022
144
+ AGID02146 2452 4658 Set163 DM-Histone-H3 -0.115553947413134
145
+ AGID00386 1397 ab32521 Set163 DM-K9-Histone-H3 0.203466406923669
146
+ AGID00352 2030 14649 Set163 DNA-Ligase-IV 0.126736187057399
147
+ AGID00407 2371 13609 Set163 DNA_POLG 0.296731357458955
148
+ AGID00399 2344 5032 Set163 DNMT1 0.12790130519566
149
+ AGID00409 2373 5391 Set163 DRP1 0.560789869619107
150
+ AGID00253 1406 5149 Old DUSP4 -0.36504
151
+ AGID00334 1936 ab76310 Set163 DUSP6 1.83203110626244
152
+ AGID00116 940 3218 Old DVL3 0.1973
153
+ AGID00211 1261 sc-251 Old E2F1 NA
154
+ AGID00148 1099 3195 Old ECADHERIN 1.067
155
+ AGID00135 1060 2332 Old EEF2 -0.85201
156
+ AGID00136 1061 3692 Old EEF2K 0.50023
157
+ AGID00152 1120 2232 Old EGFR -0.51309
158
+ AGID00450 217 2234 Old EGFR_pY1068 0.062505
159
+ AGID00026 221 1124-1/ab32578 Old EGFR_pY1173 -0.011901
160
+ AGID00078 722 9742 Old EIF4E 0.23495
161
+ AGID00328 1871 ab76256 Set163 eIF4E_pS209 0.24931111991744
162
+ AGID00154 1124 2498 Old EIF4G 0.24997
163
+ AGID00027 228 9181 Set163 Elk1_pS383 -0.0503035574139091
164
+ AGID00235 1350 M061329-2 Set163 EMA -0.854188989253222
165
+ AGID00394 2337 3810 Set163 Enolase-1 -0.409643795163378
166
+ AGID00395 2338 8171 Set163 Enolase-2 0.523796448131269
167
+ AGID00196 1219 GTX629542 Old ENY2 -0.48444
168
+ AGID00438 1849 A302-024A Set163 EphA2 -0.314558558947497
169
+ AGID00552 2422 6347 Set163 EphA2_pS897 -0.142908555204502
170
+ AGID00553 2423 12677 Set163 EphA2_pY588 -0.146367055309003
171
+ AGID00075 693 556347 Old EPPK1 0.98055
172
+ AGID00335 238 RM-9101 Old ERALPHA 4.4045
173
+ AGID00029 241 1091-1/ab32396 Old ERALPHA_pS118 0.41028
174
+ AGID00240 247 MS-671 Old ERCC1 -0.027032
175
+ AGID00239 1355 11331-1-AP Old ERCC5 0.1181
176
+ AGID00484 249 sc-154 Old ERK2 -0.0078129
177
+ AGID00372 2193 3552 Set163 Erk5 -0.305138552570543
178
+ AGID00405 2369 13826 Set163 ERRalpha -0.0963836838439504
179
+ AGID00187 1200 A303-501A Old ETS1 -0.38614
180
+ AGID00511 2492 2593 Set163 EVI1 0.0803058363249967
181
+ AGID00485 1284 4905 Old EZH2 NA
182
+ AGID00030 252 1700-1/ab40794 Set163 FAK 1.16830143620047
183
+ AGID02151 2457 8556 Set163 FAK_pY397 -0.377985167594205
184
+ AGID00171 1156 3180 Old FASN 0.81395
185
+ AGID00356 2085 500-P18/10775-082 Set163 FGF-basic 0.181026439362957
186
+ AGID00031 262 1574-1/ab45688 Old FIBRONECTIN 0.75779
187
+ AGID00339 1959 4403 Set163 FN14 -0.197233554814607
188
+ AGID02152 2458 20459 Old FOXM1 -0.366
189
+ AGID00378 269 9467 Old FOXO3A -0.12927
190
+ AGID02197 2515 orb6051 Old FOXO3A_pS318S321 -0.036694
191
+ AGID02167 2475 PA5-64616 Set163 FRS2-alpha_pY196 -0.182588550699046
192
+ AGID02213 2575 ab124892 Set163 FTO -0.0443985560362789
193
+ AGID02141 2446 12263 Old G6PD -0.10706
194
+ AGID00117 943 3239 Old GAB2 0.9141
195
+ AGID00412 274 AM4300 Old GAPDH -1.4937
196
+ AGID00086 764 558686 Old GATA3 2.2932
197
+ AGID00383 1578 4253 Old GATA6 0.064919
198
+ AGID00289 1634 12601-1-AP Set163 GCLC -0.157293579767905
199
+ AGID00305 1745 ab124827 Set163 GCLM 0.181061439943468
200
+ AGID00212 1263 3305 Old GCN5L2 0.37812
201
+ AGID00270 1579 3538 Set163 Gli1 -0.973468958616123
202
+ AGID00263 1520 ab69838 Set163 Gli3 0.259360295072577
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor -0.680203563132373
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 0.639590307687849
205
+ AGID00262 1491 ab156876 Set163 Glutaminase -0.309538619251301
206
+ AGID00319 1807 4275 Set163 Granzyme-B 0.540486344540425
207
+ AGID00368 2169 ab183737 Set163 GRB7 -0.198189335618771
208
+ AGID00396 2339 3593 Set163 Grp75 0.508986376043963
209
+ AGID00174 1163 9315 Set163 GSK-3B 0.245210566508179
210
+ AGID00502 1082 9336 Old GSK3_pS9 0.82241
211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA -0.060295
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 0.86439
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
+ AGID01354 1342 9718 Set163 H2AX_pS139 -0.289818599357977
216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 0.222356379197783
217
+ AGID00131 1038 MS-325-P1 Old HER2 0.8852
218
+ AGID00142 299 06-229 Old HER2_pY1248 0.35788
219
+ AGID00110 911 sc-285 Old HER3 0.71931
220
+ AGID00080 728 4791 Old HER3_pY1289 -0.27493
221
+ AGID00103 890 2573 Old HEREGULIN -0.10061
222
+ AGID00271 1582 11988 Set163 HES1 -0.468188792260825
223
+ AGID00397 2340 2024 Set163 Hexokinase-I 0.65866119602499
224
+ AGID00442 1023 2867 Set163 Hexokinase-II 0.847649884383131
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
+ AGID00205 1250 ab1791 Set163 Histone-H3 1.0589812672112
227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 0.10090631182388
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 -0.433769929992181
229
+ AGID00333 1902 14832-1-AP Set163 HMHA1 -0.405989053854526
230
+ AGID00035 321 2402 Set163 HSP27 0.330866385297478
231
+ AGID00036 323 2401 Set163 HSP27_pS82 1.56422143335857
232
+ AGID00320 1808 12165 Set163 HSP60 -0.0825537780079866
233
+ AGID00037 325 4872 Old HSP70 0.35671
234
+ AGID00366 2158 86630 Set163 IDO -0.535094049686979
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.18908
236
+ AGID00038 335 3922 Old IGFBP2 1.0401
237
+ AGID00090 793 611504 Set163 IGFBP3 0.51370111991744
238
+ AGID00039 336 3027 Set163 IGFRb 1.40124144687494
239
+ AGID00336 1949 12153 Set163 IL-6 -0.541723883470317
240
+ AGID02221 2583 57145 Set163 IMP3 -0.0419786993097963
241
+ AGID02153 2459 14543 Old INPP4B 4.7087
242
+ AGID00272 1586 3025 Set163 IR-b 0.261541405701997
243
+ AGID00519 2519 4302 Set163 IRF-3 -0.203163308040175
244
+ AGID00520 2520 4947 Set163 IRF-3_pS396 -0.666659096483067
245
+ AGID00223 1316 sc-497 Old IRF1 0.036861
246
+ AGID00092 802 06-248 Old IRS1 0.67163
247
+ AGID00040 371 4502 Set163 IRS2 -0.0353090209993563
248
+ AGID00250 1394 sc-13157 Old JAB1 0.033058
249
+ AGID00256 1413 ab109536 Set163 Jagged1 -0.114893029742176
250
+ AGID00177 1166 3230 Old JAK2 -0.27456
251
+ AGID00758 377 4671 Old JNK_pT183Y185 -0.011181
252
+ AGID02136 2439 PA5-28262 Old JNK2 0.094287
253
+ AGID00307 1757 ab10484 Set163 KAP1 0.288385933538863
254
+ AGID00528 904 2180 Old KU80 -0.42329
255
+ AGID00375 2237 HPA028732 Set163 LAD1 0.123356448824416
256
+ AGID00290 1643 IHC-00439 Set163 Lasu1 0.349886420232095
257
+ AGID00279 1618 4108 Set163 LC3A-B 0.12382617485801
258
+ AGID00042 397 2752 Old LCK -0.70518
259
+ AGID00119 976 3582 Old LDHA NA
260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.17672
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 -0.458523577792436
263
+ AGID00439 2424 2796 Set163 Lyn -0.170653614702522
264
+ AGID02154 2460 4370 Old MAPK_pT202Y204 0.16214
265
+ AGID00198 1222 5453 Set163 Mcl-1 -0.605709605946056
266
+ AGID00288 1633 AB3314P Set163 MCT4 0.430961309631802
267
+ AGID00175 1164 3521 Set163 MDM2_pS166 0.291016445913198
268
+ AGID00044 417 1235-1/ab32576 Old MEK1 0.31603
269
+ AGID00143 1076 9154 Old MEK1_pS217S221 0.10656
270
+ AGID00201 1243 9125 Set163 MEK2 -0.0647190291091769
271
+ AGID00361 2118 ab51061 Set163 MelanA -0.338963577792436
272
+ AGID00362 2119 ab137078 Set163 Melanoma-gp100 0.00910134262560586
273
+ AGID00337 1951 12711 Set163 MERIT40 0.00846580835651616
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 0.21737144791466
275
+ AGID02212 2574 ab195352 Set163 METTL3 0.390001439943468
276
+ AGID00225 1323 sc-20121 Set163 MIF 0.43992144555796
277
+ AGID00137 1062 WH0054206M1 Old MIG6 0.18178
278
+ AGID00403 2117 ab20663 Set163 MITF 0.105096055652205
279
+ AGID00503 1067 ab3298 Old MITOCHONDRIA NA
280
+ AGID00321 1809 14739 Set163 Mitofusin-1 0.436392652287352
281
+ AGID00322 1810 11925 Set163 Mitofusin-2 1.01059131829614
282
+ AGID00389 2324 3515 Set163 MLH1 0.119781300690204
283
+ AGID00312 1780 14993 Set163 MLKL 0.271971291471347
284
+ AGID00402 2359 MAB3328 Set163 MMP14 -0.582298616201453
285
+ AGID00045 435 4022 Set163 MMP2 -0.156571415266503
286
+ AGID00122 1005 2195 Set163 Mnk1 0.0482502309564977
287
+ AGID00331 1899 sc-377312 Set163 MR1 -0.112903740404757
288
+ AGID00273 1589 ab103319 Set163 MRAP -0.047368550837675
289
+ AGID00530 440 4847 Old MRE11 -0.019482
290
+ AGID00390 905 2850 Old MSH2 -0.37776
291
+ AGID00138 1063 22030002 Old MSH6 -0.59386
292
+ AGID00299 1675 ab76148 Set163 MSI2 0.164046449240304
293
+ AGID00232 1344 ab14705 Set163 MTCO1 -0.108920235669871
294
+ AGID00046 444 2983 Old MTOR 0.10074
295
+ AGID00047 446 2971 Old MTOR_pS2448 0.15806
296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 -0.202693730284808
297
+ AGID00401 1139 21370002 Old MYH11 2.4083
298
+ AGID00291 1647 3403 Old MYOSINIIA -0.037369
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 -0.13066
300
+ AGID00318 1803 4282 Set163 Myt1 -0.224858809936075
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN -0.23778
303
+ AGID00156 1126 3217 Old NDRG1_pT346 0.71764
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 -0.0633085531250607
305
+ AGID00134 1046 22710002 Old NF2 -0.47294
306
+ AGID00048 457 3033 Old NFKBP65_pS536 0.019636
307
+ AGID02155 2461 3608 Old NOTCH1 -0.21284
308
+ AGID00340 1969 4147 Set163 Notch1-cleaved -0.397573801020471
309
+ AGID00087 767 sc-5593 Set163 Notch3 -0.0439485787715061
310
+ AGID00258 1420 3187 Set163 NQO1 1.28716625959524
311
+ AGID00162 1136 sc-31 Old NRAS -0.032257
312
+ AGID00257 1419 12721 Old NRF2 NA
313
+ AGID00297 1669 2750 Set163 Oct-4 -0.44563356448401
314
+ AGID00420 466 1712-1/ab40803 Old P16INK4A -0.29129
315
+ AGID00384 470 sc-6246 Old P21 -0.1443
316
+ AGID00105 897 1591-1/ab32034 Old P27 0.62911
317
+ AGID00096 842 AF1555 Old P27_pT157 0.15771
318
+ AGID00099 878 ab64949 Old P27_pT198 0.032598
319
+ AGID00181 1175 9228 Set163 p38-a 0.35104033271045
320
+ AGID00098 479 9211 Old P38_pT180Y182 0.36391
321
+ AGID00049 478 9212 Old P38MAPK 0.16985
322
+ AGID00151 1119 4695 Set163 p44-42-MAPK 0.543926434095038
323
+ AGID00050 481 9282 Old P53 -0.32528
324
+ AGID00490 1187 610833 Old P62LCKLIGAND 1.1549
325
+ AGID00545 1415 ab53039 Old P63 NA
326
+ AGID00052 494 9205 Old P70S6K_pT389 -0.081581
327
+ AGID00051 493 1494-1/ab32529 Old P70S6K1 0.2087
328
+ AGID00085 759 9347 Old P90RSK 0.024028
329
+ AGID00531 770 9344 Old P90RSK_pT359S363 0.17074
330
+ AGID00182 1178 9346 Set163 p90RSK_pT573 -0.249188677475661
331
+ AGID00053 499 612024 Old PAI1 -0.17762
332
+ AGID00224 1322 HPA035895 Set163 PAICS 0.491081447429457
333
+ AGID00323 1811 2602 Set163 PAK1 2.16588101851002
334
+ AGID02199 2517 PA5-69540 Set163 PAK4 0.0941863327915809
335
+ AGID00245 1370 4336-BPC-100 Set163 PAR 0.250940987041149
336
+ AGID00374 2209 66564 Set163 PARG -0.204108828235159
337
+ AGID00370 1372 sc-7150 Old PARP1 0.30498
338
+ AGID00468 501 9546 Old PARPCLEAVED -0.13147
339
+ AGID00274 1591 ab53715 Set163 Patched 0.123111410484713
340
+ AGID00513 2486 60433 Set163 PAX6 -0.133328657374394
341
+ AGID00441 1621 9857 Set163 PAX8 0.663845063085016
342
+ AGID00054 504 2542 Old PAXILLIN -0.15947
343
+ AGID00055 509 2130 Old PCADHERIN -0.22581
344
+ AGID00248 511 ab29 Old PCNA -0.19016
345
+ AGID00413 2095 43248 Old PDCD1 NA
346
+ AGID00094 816 600-401-965 Old PDCD4 -0.17669
347
+ AGID00385 1225 3169 Set163 PDGFRB 0.29203643551599
348
+ AGID00210 1258 ab110332 Set163 PDH -0.234514711261052
349
+ AGID00324 1817 3205 Set163 PDHA1 0.208715770094803
350
+ AGID00280 1622 3820 Set163 PDHK1 -0.105768561234883
351
+ AGID00056 515 3062 Old PDK1 0.43393
352
+ AGID00057 516 3061 Old PDK1_pS241 0.53708
353
+ AGID00300 1234 sc-19090 Old PDL1 -0.058433
354
+ AGID00124 1017 2780 Old PEA15 0.34842
355
+ AGID00125 1018 44-836G Old PEA15_pS116 -0.26255
356
+ AGID00440 2429 3192 Set163 PERK -0.304799168293095
357
+ AGID02207 2569 ab192876 Set163 PGM1 -0.121649205861661
358
+ AGID00281 1623 13428 Set163 PHGDH -0.332129177581265
359
+ AGID00425 2399 22789-1-AP Set163 PHLPP 0.277331446251107
360
+ AGID00226 1330 sc-376412 Set163 PI3K-p110-b 0.0696414348141786
361
+ AGID00093 808 4255 Old PI3KP110ALPHA 0.33457
362
+ AGID00058 523 06-195 Old PI3KP85 0.028166
363
+ AGID00296 1667 5675 Set163 PKA-a -0.257923697048404
364
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365
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367
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368
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370
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377
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380
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381
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382
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383
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384
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385
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386
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387
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388
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390
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392
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393
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395
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396
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397
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398
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399
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400
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411
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413
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424
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429
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435
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436
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440
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454
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data/gdc_data_organized/332423a7-8866-4ee3-b08f-3c8d7c16af80/TCGA-A2-A0CU.D503E73D-8B94-46A0-A24F-93069A56DC7D.PDF ADDED
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data/gdc_data_organized/332423a7-8866-4ee3-b08f-3c8d7c16af80/TCGA-BRCA.846ab0bd-1c82-48a3-a25a-8a3af1f2bfa0.ascat2.allelic_specific.seg.txt ADDED
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+ <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="175724">2005</clin_shared:year_of_initial_pathologic_diagnosis>
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+ <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="175705">NOT HISPANIC OR LATINO</clin_shared:ethnicity>
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+ <clin_shared:primary_lymph_node_presentation_assessment preferred_name="lymph_nodes_examined" display_order="47" cde="2200396" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
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+ <brca_shared:her2_neu_chromosone_17_signal_ratio_value preferred_name="her2_cent17_ratio" display_order="79" cde="2497552" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175764">1.0</brca_shared:her2_neu_chromosone_17_signal_ratio_value>
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+ <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="175733">Sentinel node biopsy alone</brca:axillary_lymph_node_stage_method_type>
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+ <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="175734"/>
56
+ <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="175727">Simple Mastectomy</brca:breast_carcinoma_surgical_procedure_name>
57
+ <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="175731" xsi:nil="true"/>
58
+ <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="175730"/>
59
+ <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="175728"/>
60
+ <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="175720">Infiltrating Ductal Carcinoma</shared:histological_type>
61
+ <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="175721" xsi:nil="true"/>
62
+ <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="175701">Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)</clin_shared:menopause_status>
63
+ <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="175750">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
64
+ <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="175735">YES</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
65
+ <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"/>
66
+ <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="175747"/>
67
+ <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="175757">2+</brca_shared:her2_immunohistochemistry_level_result>
68
+ <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="175732"/>
69
+ <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="175729">Close</clin_shared:margin_status>
70
+ <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="175725">Core needle biopsy</clin_shared:initial_pathologic_diagnosis_method>
71
+ <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="175726" xsi:nil="true"/>
72
+ <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175760">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
73
+ <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="175745">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
74
+ <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="175755">Equivocal</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
75
+ <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="175738">1</clin_shared:number_of_lymphnodes_positive_by_ihc>
76
+ <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="175737">0</clin_shared:number_of_lymphnodes_positive_by_he>
77
+ <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="175753"/>
78
+ <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="175748"/>
79
+ <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="175756"/>
80
+ <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="175758"/>
81
+ <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="175759"/>
82
+ <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="175763"/>
83
+ <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="175765"/>
84
+ <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="175766"/>
85
+ <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="175695">NO</clin_shared:tissue_prospective_collection_indicator>
86
+ <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="175696">YES</clin_shared:tissue_retrospective_collection_indicator>
87
+ <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="175762"/>
88
+ <brca:first_nonlymph_node_metastasis_anatomic_sites>
89
+ <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="175743"/>
90
+ <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="175744"/>
91
+ </brca:first_nonlymph_node_metastasis_anatomic_sites>
92
+ <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="175746">90-99%</brca_shared:er_level_cell_percentage_category>
93
+ <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="175751">&lt;10%</brca_shared:progesterone_receptor_level_cell_percent_category>
94
+ <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"/>
95
+ <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="175767"/>
96
+ <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="175768"/>
97
+ <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="175769"/>
98
+ <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="175770"/>
99
+ <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="175771"/>
100
+ <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="175772"/>
101
+ <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="175777"/>
102
+ <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="175773"/>
103
+ <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="175774"/>
104
+ <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="175775"/>
105
+ <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="175776"/>
106
+ <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="175778"/>
107
+ <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="175779"/>
108
+ <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="175780"/>
109
+ <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="175781"/>
110
+ <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="175782"/>
111
+ <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="175784"/>
112
+ <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="175785"/>
113
+ <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="175786"/>
114
+ <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="175787"/>
115
+ <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="175788"/>
116
+ <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="175783"/>
117
+ <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="175761"/>
118
+ <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"/>
119
+ <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="175752"/>
120
+ <shared_stage:stage_event system="AJCC">
121
+ <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="1079780">6th</shared_stage:system_version>
122
+ <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"/>
123
+ <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="175742">Stage IIA</shared_stage:pathologic_stage>
124
+ <shared_stage:tnm_categories>
125
+ <shared_stage:clinical_categories>
126
+ <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"/>
127
+ <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"/>
128
+ <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"/>
129
+ </shared_stage:clinical_categories>
130
+ <shared_stage:pathologic_categories>
131
+ <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="175739">T2</shared_stage:pathologic_T>
132
+ <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="175740">N0 (i+)</shared_stage:pathologic_N>
133
+ <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="175741">M0</shared_stage:pathologic_M>
134
+ </shared_stage:pathologic_categories>
135
+ </shared_stage:tnm_categories>
136
+ <shared_stage:psa>
137
+ <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"/>
138
+ <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"/>
139
+ </shared_stage:psa>
140
+ <shared_stage:gleason_grading>
141
+ <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"/>
142
+ <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"/>
143
+ <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"/>
144
+ <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"/>
145
+ </shared_stage:gleason_grading>
146
+ <shared_stage:ann_arbor>
147
+ <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"/>
148
+ <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"/>
149
+ </shared_stage:ann_arbor>
150
+ <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"/>
151
+ <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"/>
152
+ <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"/>
153
+ </shared_stage:stage_event>
154
+ <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
155
+ <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
156
+ <brca_nte:new_tumor_events>
157
+ <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
158
+ </brca_nte:new_tumor_events>
159
+ <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="175693">9</clin_shared:day_of_form_completion>
160
+ <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="175692">9</clin_shared:month_of_form_completion>
161
+ <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="175694">2010</clin_shared:year_of_form_completion>
162
+ <brca:follow_ups>
163
+ <follow_up_v2.1:follow_up version="2.1" sequence="1">
164
+ <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-A0CU-F13735</clin_shared:bcr_followup_barcode>
165
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">99B03F76-5B6B-4C3C-899F-D63D8FC39C5D</clin_shared:bcr_followup_uuid>
166
+ <clin_shared:followup_case_report_form_submission_reason preferred_name="followup_reason" display_order="999" cde="3233305" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1075061">Scheduled Follow-up Submission</clin_shared:followup_case_report_form_submission_reason>
167
+ <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="1075062">NO</clin_shared:radiation_therapy>
168
+ <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="1075063">YES</clin_shared:postoperative_rx_tx>
169
+ <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="1075064">Dead</clin_shared:vital_status>
170
+ <clin_shared:days_to_last_followup precision="day" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Not Available" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000"/>
171
+ <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Completed" preferred_name="death_days_to" display_order="25" cde_ver="1.000">158</clin_shared:days_to_death>
172
+ <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="1075071">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
173
+ <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="1075089">NO</nte:new_tumor_event_after_initial_treatment>
174
+ <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Applicable" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
175
+ <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="1075093"/>
176
+ <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="1075094"/>
177
+ <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="1075095"/>
178
+ <nte:additional_surgery_locoregional_procedure preferred_name="new_tumor_event_surgery" display_order="999" cde="3008755" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1075096"/>
179
+ <nte:days_to_additional_surgery_metastatic_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408682" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_met" display_order="9999" cde_ver="1.000"/>
180
+ <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="1075100"/>
181
+ <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="1075101"/>
182
+ <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="1075102"/>
183
+ <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="1075103"/>
184
+ <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="1075104"/>
185
+ <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="1075105"/>
186
+ <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="1075106"/>
187
+ <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="1075107"/>
188
+ <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="1075108"/>
189
+ <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="1075109"/>
190
+ <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="1075110"/>
191
+ <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="1075111"/>
192
+ <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="1075112"/>
193
+ <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="1075113"/>
194
+ <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="1075114"/>
195
+ <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="1075115"/>
196
+ <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="1075116"/>
197
+ <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="1075117"/>
198
+ <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="1075118"/>
199
+ <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="1075119"/>
200
+ <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="1075120"/>
201
+ <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="1075121"/>
202
+ <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="1075122"/>
203
+ <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="1075123"/>
204
+ <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="1075124"/>
205
+ <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="1075125"/>
206
+ <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="1075059">10</clin_shared:day_of_form_completion>
207
+ <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="1075058">6</clin_shared:month_of_form_completion>
208
+ <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="1075060">2011</clin_shared:year_of_form_completion>
209
+ </follow_up_v2.1:follow_up>
210
+ </brca:follow_ups>
211
+ <rx:drugs>
212
+ <rx:drug>
213
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
214
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175794">1</rx:regimen_number>
215
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A2-A0CU-D1971</rx:bcr_drug_barcode>
216
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">a4307c98-baf1-4f65-b40b-87bb611d8a4a</rx:bcr_drug_uuid>
217
+ <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" source_system_identifier="175803"/>
218
+ <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" source_system_identifier="175804"/>
219
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175801">10</rx:prescribed_dose>
220
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175802">mg</rx:prescribed_dose_units>
221
+ <rx:number_cycles preferred_name="pharma_adjuvant_cycles_count" display_order="999" cde="62590" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="175800"/>
222
+ <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">98</rx:days_to_drug_therapy_start>
223
+ <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"/>
224
+ <rx:therapy_types>
225
+ <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="175797">Hormone Therapy</rx:therapy_type>
226
+ <rx:therapy_type_notes preferred_name="pharma_type_other" display_order="999" cde="2001762" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="175798"/>
227
+ </rx:therapy_types>
228
+ <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="175799">Tamoxifen</rx:drug_name>
229
+ <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"/>
230
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175795">ADJUVANT</clin_shared:regimen_indication>
231
+ <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="175796"/>
232
+ <rx:route_of_administrations>
233
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="175805">PO</rx:route_of_administration>
234
+ </rx:route_of_administrations>
235
+ <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="175809">NO</rx:therapy_ongoing>
236
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
237
+ <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="175792">10</clin_shared:day_of_form_completion>
238
+ <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="175791">10</clin_shared:month_of_form_completion>
239
+ <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="175793">2010</clin_shared:year_of_form_completion>
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+ </rx:drug>
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+ </rx:drugs>
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+ <rad:radiations/>
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+ </brca:patient>
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+ </brca:tcga_bcr>
data/gdc_data_organized/332423a7-8866-4ee3-b08f-3c8d7c16af80/nationwidechildrens.org_ssf.TCGA-A2-A0CU.xml ADDED
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1
+ <?xml version="1.0" encoding="UTF-8"?>
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+ <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">
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+ <admin:admin>
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+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
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+ <admin:file_uuid xsd_ver="2.6">236BC5B7-6F00-4C6D-BECB-71AD06BFBBEC</admin:file_uuid>
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+ <admin:batch_number xsd_ver="1.17">56.91.0</admin:batch_number>
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+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
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+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
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+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
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+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
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+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
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+ <admin:patient_withdrawal>
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+ <admin:withdrawn>false</admin:withdrawn>
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+ </admin:patient_withdrawal>
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+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
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+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
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+ </admin:admin>
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+ <ssf:patient>
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+ <admin:additional_studies/>
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+ <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-A0CU</shared:bcr_patient_barcode>
21
+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">332423a7-8866-4ee3-b08f-3c8d7c16af80</shared:bcr_patient_uuid>
22
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A2</shared:tissue_source_site>
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+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0CU</shared:patient_id>
24
+ <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"/>
25
+ <ssf:tumor_samples>
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+ <ssf:tumor_sample>
27
+ <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">df545b98-f81f-4e0d-a714-90b406f2a238</ssf:bcr_sample_uuid>
28
+ <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="">48</shared:days_to_sample_procurement>
29
+ <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="123054">Other Method, specify</shared:method_of_sample_procurement>
30
+ <shared:other_method_of_sample_procurement preferred_name="cancer_procurement_method_other" display_order="12" cde="2006730" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="123055">Mastectomy</shared:other_method_of_sample_procurement>
31
+ <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="123056">Cryomold</ssf:vessel_used>
32
+ <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="123057"/>
33
+ <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"/>
34
+ <ssf:tumor_weight preferred_name="tumor_sample_weight" display_order="23" cde="3081946" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="123058">233</ssf:tumor_weight>
35
+ <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="123061">YES</ssf:sample_prescreened>
36
+ <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="123059">95</shared:tumor_nuclei_percent>
37
+ <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="123060">0</shared:tumor_necrosis_percent>
38
+ <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">1902</ssf:days_to_pathology_review>
39
+ <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="123131">YES</ssf:path_confirm_tumor_nuclei_metrics>
40
+ <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="123132">YES</ssf:path_confirm_tumor_necrosis_metrics>
41
+ <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="123134">YES</ssf:path_confirm_report_attached>
42
+ <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="123133">YES</ssf:path_confirm_diagnosis_matching>
43
+ <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"/>
44
+ <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="123062">YES</ssf:top_slide_submitted>
45
+ <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="123064">NO</ssf:digital_image_submitted>
46
+ <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>
47
+ <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"/>
48
+ <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="123136">No</shared:other_dx>
49
+ <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="123136">No</shared:history_of_neoadjuvant_treatment>
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+ <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="123137">Consented</shared:consent_or_death_status>
51
+ <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">23</shared:days_to_consent>
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+ <shared:country preferred_name="tumor_sample_procurement_country" display_order="13" cde="3203072" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="741091"/>
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+ <ssf_disease:disease_details/>
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+ <ssf:tumor_histologies>
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+ <ssf:tumor_histology>
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+ <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="123047">Infiltrating Ductal Carcinoma</shared:histological_type>
57
+ <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"/>
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+ <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"/>
59
+ <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"/>
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+ </ssf:tumor_histology>
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+ </ssf:tumor_histologies>
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+ <ssf:tumor_locations>
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+ <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"/>
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+ <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="123050">Right</ssf:laterality>
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+ <ssf:tumor_location>
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+ <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="123050">Breast</ssf:site_of_disease>
67
+ <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"/>
68
+ <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="123050"/>
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+ </ssf:tumor_location>
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+ </ssf:tumor_locations>
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+ </ssf:tumor_sample>
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+ <ssf:normal_control>
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+ <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="Completed" restricted="false" source_system_identifier="123095">Blood Draw</ssf:method_of_normal_sample_procurement>
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+ <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="123096"/>
78
+ <ssf:days_to_normal_sample_procurement precision="day" xsd_ver="2.3" tier="1" cde="3288496" owner="TSS" procurement_status="Completed" preferred_name="normal_control_procurement_days_to" display_order="55" cde_ver="1.000">48</ssf:days_to_normal_sample_procurement>
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+ <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="123097"/>
80
+ <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="123088">0.0916</ssf:ncedna_dna_conc>
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+ <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="123087">Spec (Nano drop)</ssf:ncedna_dna_qm>
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+ <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="123086">20</ssf:ncedna_dna_qty>
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+ <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="123089">218.3</ssf:ncedna_dna_vol>
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+ <ssf:normal_control_locations>
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+ <ssf:normal_control_location>
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+ <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="123090"/>
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+ </ssf:normal_control_location>
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+ </ssf:normal_control_locations>
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+ </ssf:normal_control>
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+ </ssf:normal_controls>
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+ </ssf:patient>
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+ </ssf:tcga_bcr>
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+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11</bio:bcr_portion_barcode>
61
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f0d527d2-8623-4f39-9cb2-453402c55cfe</bio:bcr_portion_uuid>
62
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
63
+ <bio:analytes>
64
+ <bio:analyte>
65
+ <admin:additional_studies/>
66
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
67
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
68
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
69
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
70
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.90</bio:a260_a280_ratio>
71
+ <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>
72
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
73
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D</bio:bcr_analyte_barcode>
74
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8f383d70-de5e-423d-a65f-3091bd00f587</bio:bcr_analyte_uuid>
75
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
76
+ <bio:aliquots>
77
+ <bio:aliquot>
78
+ <admin:additional_studies/>
79
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A00Y</bio:plate_id>
80
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81
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
82
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
83
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
84
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A00Y-05</bio:bcr_aliquot_barcode>
85
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">58c77238-7a8d-4085-96eb-10c9098dedd1</bio:bcr_aliquot_uuid>
86
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
87
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.74</bio:quantity>
88
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
89
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
90
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
91
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99026479</bio:biospecimen_barcode_bottom>
92
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
93
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
94
+ </bio:aliquot>
95
+ <bio:aliquot>
96
+ <admin:additional_studies/>
97
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A011</bio:plate_id>
98
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
99
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
100
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
101
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
102
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A011-01</bio:bcr_aliquot_barcode>
103
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">bdf230f7-71c7-4ee8-b1ed-b29015b40f57</bio:bcr_aliquot_uuid>
104
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
105
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
106
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
107
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
108
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
109
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99051561</bio:biospecimen_barcode_bottom>
110
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
111
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
112
+ </bio:aliquot>
113
+ <bio:aliquot>
114
+ <admin:additional_studies/>
115
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A015</bio:plate_id>
116
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
117
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
118
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
119
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
120
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A015-09</bio:bcr_aliquot_barcode>
121
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4b18494d-33ef-419d-b86c-fe201caa0d70</bio:bcr_aliquot_uuid>
122
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
123
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
124
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
125
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
126
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
127
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099051646</bio:biospecimen_barcode_bottom>
128
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
129
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
130
+ </bio:aliquot>
131
+ <bio:aliquot>
132
+ <admin:additional_studies/>
133
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A016</bio:plate_id>
134
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
135
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
136
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
137
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
138
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A016-08</bio:bcr_aliquot_barcode>
139
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5d3f2d6c-b2fd-4b2a-847b-b50da264b6d5</bio:bcr_aliquot_uuid>
140
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
141
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
142
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
143
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
144
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
145
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099050878</bio:biospecimen_barcode_bottom>
146
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
147
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
148
+ </bio:aliquot>
149
+ <bio:aliquot>
150
+ <admin:additional_studies/>
151
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A068</bio:plate_id>
152
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
153
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">31</bio:day_of_shipment>
154
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
155
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
156
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A068-02</bio:bcr_aliquot_barcode>
157
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">afe11155-7f91-4632-9916-2e05f7af04db</bio:bcr_aliquot_uuid>
158
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
159
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
160
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
161
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
162
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
163
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099065649</bio:biospecimen_barcode_bottom>
164
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
165
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
166
+ </bio:aliquot>
167
+ <bio:aliquot>
168
+ <admin:additional_studies/>
169
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A89F</bio:plate_id>
170
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
171
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
172
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
173
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
174
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11D-A89F-36</bio:bcr_aliquot_barcode>
175
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">98001366-9491-406E-B3DA-DA8E5012C77D</bio:bcr_aliquot_uuid>
176
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
177
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">7.00</bio:quantity>
178
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
179
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
180
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">11</bio:plate_column>
181
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112367845</bio:biospecimen_barcode_bottom>
182
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
183
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
184
+ </bio:aliquot>
185
+ </bio:aliquots>
186
+ <bio:protocols>
187
+ <bio:protocol>
188
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
189
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
190
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
191
+ </bio:protocol>
192
+ </bio:protocols>
193
+ <bio:dna>
194
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
195
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
196
+ </bio:dna>
197
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
198
+ </bio:analyte>
199
+ <bio:analyte>
200
+ <admin:additional_studies/>
201
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
202
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
203
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
204
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
205
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.78</bio:a260_a280_ratio>
206
+ <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>
207
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
208
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11R</bio:bcr_analyte_barcode>
209
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">86a8f525-590d-4c9c-b835-1c4ee47f4ca5</bio:bcr_analyte_uuid>
210
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
211
+ <bio:aliquots>
212
+ <bio:aliquot>
213
+ <admin:additional_studies/>
214
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A00Z</bio:plate_id>
215
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
216
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
217
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
218
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
219
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11R-A00Z-07</bio:bcr_aliquot_barcode>
220
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">653e3eb4-ebdb-42d2-9479-a1ea8a43bdc5</bio:bcr_aliquot_uuid>
221
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
222
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.27</bio:quantity>
223
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
224
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
225
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
226
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050287</bio:biospecimen_barcode_bottom>
227
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
228
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
229
+ </bio:aliquot>
230
+ <bio:aliquot>
231
+ <admin:additional_studies/>
232
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A010</bio:plate_id>
233
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
234
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
235
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
236
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
237
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11R-A010-13</bio:bcr_aliquot_barcode>
238
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">04a55569-6dc5-4af0-b62d-da70b09eb2c9</bio:bcr_aliquot_uuid>
239
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
240
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
241
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
242
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
243
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
244
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99051247</bio:biospecimen_barcode_bottom>
245
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
246
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
247
+ </bio:aliquot>
248
+ </bio:aliquots>
249
+ <bio:protocols>
250
+ <bio:protocol>
251
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
252
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
253
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
254
+ </bio:protocol>
255
+ </bio:protocols>
256
+ <bio:rna>
257
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.70</bio:ratio_28s_18s>
258
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.00</bio:rinvalue>
259
+ </bio:rna>
260
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
261
+ </bio:analyte>
262
+ <bio:analyte>
263
+ <admin:additional_studies/>
264
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
265
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
266
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
267
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
268
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
269
+ <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>
270
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
271
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11W</bio:bcr_analyte_barcode>
272
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">BEE683AB-A80A-43D0-BEFE-DE43C91FB76B</bio:bcr_analyte_uuid>
273
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
274
+ <bio:aliquots>
275
+ <bio:aliquot>
276
+ <admin:additional_studies/>
277
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A019</bio:plate_id>
278
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
279
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
280
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
281
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
282
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11W-A019-09</bio:bcr_aliquot_barcode>
283
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">304a2945-f134-45c7-9eaa-c6c9c2435552</bio:bcr_aliquot_uuid>
284
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
285
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
286
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
287
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
288
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
289
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034654</bio:biospecimen_barcode_bottom>
290
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
291
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
292
+ </bio:aliquot>
293
+ <bio:aliquot>
294
+ <admin:additional_studies/>
295
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A020</bio:plate_id>
296
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
297
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
298
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
299
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
300
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11W-A020-08</bio:bcr_aliquot_barcode>
301
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2f568b4c-4b40-42f2-b11f-294138df7f6b</bio:bcr_aliquot_uuid>
302
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
303
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
304
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
305
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
306
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
307
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035518</bio:biospecimen_barcode_bottom>
308
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
309
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
310
+ </bio:aliquot>
311
+ </bio:aliquots>
312
+ <bio:protocols>
313
+ <bio:protocol>
314
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
315
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
316
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
317
+ </bio:protocol>
318
+ </bio:protocols>
319
+ <bio:dna>
320
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
321
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
322
+ </bio:dna>
323
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
324
+ </bio:analyte>
325
+ <bio:analyte>
326
+ <admin:additional_studies/>
327
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
328
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
329
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
330
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
331
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
332
+ <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>
333
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
334
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11X</bio:bcr_analyte_barcode>
335
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">94B1887C-D918-4699-862E-24C766633780</bio:bcr_analyte_uuid>
336
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
337
+ <bio:aliquots>
338
+ <bio:aliquot>
339
+ <admin:additional_studies/>
340
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A023</bio:plate_id>
341
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
342
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
343
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
344
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
345
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11X-A023-09</bio:bcr_aliquot_barcode>
346
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6c202f2d-a2e6-4302-aa02-5f77323ead95</bio:bcr_aliquot_uuid>
347
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
348
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
349
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
350
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
351
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
352
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059902</bio:biospecimen_barcode_bottom>
353
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
354
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
355
+ </bio:aliquot>
356
+ <bio:aliquot>
357
+ <admin:additional_studies/>
358
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A024</bio:plate_id>
359
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
360
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
361
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
362
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
363
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-11X-A024-08</bio:bcr_aliquot_barcode>
364
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5b9c82ec-744b-47ff-92be-29551ed6f7e7</bio:bcr_aliquot_uuid>
365
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
366
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
367
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
368
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
369
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
370
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034366</bio:biospecimen_barcode_bottom>
371
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
372
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
373
+ </bio:aliquot>
374
+ </bio:aliquots>
375
+ <bio:protocols>
376
+ <bio:protocol>
377
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
378
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
379
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
380
+ </bio:protocol>
381
+ </bio:protocols>
382
+ <bio:dna>
383
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
384
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
385
+ </bio:dna>
386
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
387
+ </bio:analyte>
388
+ </bio:analytes>
389
+ <bio:slides>
390
+ <bio:slide>
391
+ <admin:additional_studies/>
392
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
393
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
394
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
395
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
396
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">3</bio:percent_normal_cells>
397
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
398
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:percent_stromal_cells>
399
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
400
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_lymphocyte_infiltration>
401
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
402
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
403
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
404
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
405
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-01-BS1</shared:bcr_slide_barcode>
406
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">48ca5ab6-429b-420a-9a89-7605aee874ab</shared:bcr_slide_uuid>
407
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-01-BS1.48ca5ab6-429b-420a-9a89-7605aee874ab.svs</shared:image_file_name>
408
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
409
+ </bio:slide>
410
+ <bio:slide>
411
+ <admin:additional_studies/>
412
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
413
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
414
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">75</bio:percent_tumor_cells>
415
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_nuclei>
416
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:percent_normal_cells>
417
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
418
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_stromal_cells>
419
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
420
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_lymphocyte_infiltration>
421
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
422
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
423
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
424
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
425
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-01-TS1</shared:bcr_slide_barcode>
426
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7e5b6b2c-52b7-4b2a-bb39-b2e8aef29605</shared:bcr_slide_uuid>
427
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09N-01A-01-TS1.7e5b6b2c-52b7-4b2a-bb39-b2e8aef29605.svs</shared:image_file_name>
428
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
429
+ </bio:slide>
430
+ </bio:slides>
431
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
432
+ </bio:portion>
433
+ </bio:portions>
434
+ <bio:tumor_pathology/>
435
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
436
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
437
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
438
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">F5A97F05-4B5C-4B10-BF10-5DDE7D412BCF</bio:pathology_report_uuid>
439
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A09N.F5A97F05-4B5C-4B10-BF10-5DDE7D412BCF.pdf</bio:pathology_report_file_name>
440
+ <bio:diagnostic_slides>
441
+ <admin:additional_studies/>
442
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A0E4EF10-5BFF-46A0-94C7-578EA3A88599</bio:ffpe_slide_uuid>
443
+ </bio:diagnostic_slides>
444
+ </bio:sample>
445
+ <bio:sample>
446
+ <admin:additional_studies/>
447
+ <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
448
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
449
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
450
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
451
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
452
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
453
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
454
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
455
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
456
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
457
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
458
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
459
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
460
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
461
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
462
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
463
+ <bio:days_to_collection precision="month" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">1276</bio:days_to_collection>
464
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
465
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
466
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A</bio:bcr_sample_barcode>
467
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">639fc0fe-863a-4b3f-9462-a22941f13167</bio:bcr_sample_uuid>
468
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
469
+ <bio:portions>
470
+ <bio:portion>
471
+ <admin:additional_studies/>
472
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
473
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
474
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_creation>
475
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
476
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
477
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
478
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01</bio:bcr_portion_barcode>
479
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">099239c3-00c8-4238-a889-dfbd96223e8f</bio:bcr_portion_uuid>
480
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
481
+ <bio:analytes>
482
+ <bio:analyte>
483
+ <admin:additional_studies/>
484
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
485
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
486
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
487
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
488
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.98</bio:a260_a280_ratio>
489
+ <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>
490
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
491
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01D</bio:bcr_analyte_barcode>
492
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c9762260-03a1-4002-82f2-95e148d35b65</bio:bcr_analyte_uuid>
493
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
494
+ <bio:aliquots>
495
+ <bio:aliquot>
496
+ <admin:additional_studies/>
497
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A012</bio:plate_id>
498
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
499
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
500
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
501
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
502
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01D-A012-01</bio:bcr_aliquot_barcode>
503
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5bc79278-10c5-4949-804e-5cb30fd548db</bio:bcr_aliquot_uuid>
504
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
505
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
506
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
507
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
508
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
509
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050191</bio:biospecimen_barcode_bottom>
510
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
511
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
512
+ </bio:aliquot>
513
+ <bio:aliquot>
514
+ <admin:additional_studies/>
515
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A017</bio:plate_id>
516
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
517
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
518
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
519
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
520
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01D-A017-09</bio:bcr_aliquot_barcode>
521
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">acb6a8aa-ce15-45e4-bebe-2099cd4ccd34</bio:bcr_aliquot_uuid>
522
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
523
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
524
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
525
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
526
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
527
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059614</bio:biospecimen_barcode_bottom>
528
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
529
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
530
+ </bio:aliquot>
531
+ <bio:aliquot>
532
+ <admin:additional_studies/>
533
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A018</bio:plate_id>
534
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
535
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
536
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
537
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
538
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01D-A018-08</bio:bcr_aliquot_barcode>
539
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7eab7d57-009f-4748-9e6c-079fbfc9fade</bio:bcr_aliquot_uuid>
540
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
541
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
542
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
543
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
544
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
545
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099051166</bio:biospecimen_barcode_bottom>
546
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
547
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
548
+ </bio:aliquot>
549
+ <bio:aliquot>
550
+ <admin:additional_studies/>
551
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A069</bio:plate_id>
552
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
553
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">31</bio:day_of_shipment>
554
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
555
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
556
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01D-A069-02</bio:bcr_aliquot_barcode>
557
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ce705088-4631-4ff8-83e2-d1894707680b</bio:bcr_aliquot_uuid>
558
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
559
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
560
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
561
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E</bio:plate_row>
562
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
563
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099036748</bio:biospecimen_barcode_bottom>
564
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
565
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
566
+ </bio:aliquot>
567
+ </bio:aliquots>
568
+ <bio:protocols>
569
+ <bio:protocol>
570
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
571
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
572
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
573
+ </bio:protocol>
574
+ </bio:protocols>
575
+ <bio:dna>
576
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
577
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
578
+ </bio:dna>
579
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
580
+ </bio:analyte>
581
+ <bio:analyte>
582
+ <admin:additional_studies/>
583
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
584
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
585
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
586
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
587
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
588
+ <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>
589
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
590
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01W</bio:bcr_analyte_barcode>
591
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">EA0734A7-34DF-45BC-A7EE-2E0CB3A72D58</bio:bcr_analyte_uuid>
592
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
593
+ <bio:aliquots>
594
+ <bio:aliquot>
595
+ <admin:additional_studies/>
596
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A021</bio:plate_id>
597
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
598
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
599
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
600
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
601
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01W-A021-09</bio:bcr_aliquot_barcode>
602
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">03c46c7b-9609-47ca-8ae5-714ce4a77860</bio:bcr_aliquot_uuid>
603
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
604
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
605
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
606
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
607
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
608
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035902</bio:biospecimen_barcode_bottom>
609
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
610
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
611
+ </bio:aliquot>
612
+ <bio:aliquot>
613
+ <admin:additional_studies/>
614
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A022</bio:plate_id>
615
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
616
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
617
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
618
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
619
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01W-A022-08</bio:bcr_aliquot_barcode>
620
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">31cefe30-7610-4ead-bf4b-236273d972b4</bio:bcr_aliquot_uuid>
621
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
622
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
623
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
624
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
625
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
626
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099037534</bio:biospecimen_barcode_bottom>
627
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
628
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
629
+ </bio:aliquot>
630
+ </bio:aliquots>
631
+ <bio:protocols>
632
+ <bio:protocol>
633
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
634
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
635
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
636
+ </bio:protocol>
637
+ </bio:protocols>
638
+ <bio:dna>
639
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
640
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
641
+ </bio:dna>
642
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
643
+ </bio:analyte>
644
+ <bio:analyte>
645
+ <admin:additional_studies/>
646
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
647
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
648
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
649
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
650
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
651
+ <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>
652
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
653
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01X</bio:bcr_analyte_barcode>
654
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">43D45BF4-8200-45DD-891E-6B3011803A07</bio:bcr_analyte_uuid>
655
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
656
+ <bio:aliquots>
657
+ <bio:aliquot>
658
+ <admin:additional_studies/>
659
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A025</bio:plate_id>
660
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
661
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
662
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
663
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
664
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01X-A025-09</bio:bcr_aliquot_barcode>
665
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">fdb7b558-4d08-473d-bd52-685c82eee52a</bio:bcr_aliquot_uuid>
666
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
667
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
668
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
669
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
670
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
671
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034846</bio:biospecimen_barcode_bottom>
672
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
673
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
674
+ </bio:aliquot>
675
+ <bio:aliquot>
676
+ <admin:additional_studies/>
677
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A026</bio:plate_id>
678
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
679
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
680
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
681
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
682
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10A-01X-A026-08</bio:bcr_aliquot_barcode>
683
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8c541a0b-ccd3-4623-9b5f-fffad79e294d</bio:bcr_aliquot_uuid>
684
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
685
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
686
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
687
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
688
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
689
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099036286</bio:biospecimen_barcode_bottom>
690
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
691
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
692
+ </bio:aliquot>
693
+ </bio:aliquots>
694
+ <bio:protocols>
695
+ <bio:protocol>
696
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
697
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
698
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
699
+ </bio:protocol>
700
+ </bio:protocols>
701
+ <bio:dna>
702
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
703
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
704
+ </bio:dna>
705
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
706
+ </bio:analyte>
707
+ </bio:analytes>
708
+ <bio:slides/>
709
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
710
+ </bio:portion>
711
+ </bio:portions>
712
+ <bio:tumor_pathology/>
713
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
714
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
715
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
716
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
717
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
718
+ <bio:diagnostic_slides>
719
+ <admin:additional_studies/>
720
+ </bio:diagnostic_slides>
721
+ </bio:sample>
722
+ <bio:sample>
723
+ <admin:additional_studies/>
724
+ <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
725
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
726
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B</bio:vial_number>
727
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
728
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
729
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
730
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
731
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
732
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
733
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
734
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
735
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
736
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
737
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
738
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
739
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
740
+ <bio:days_to_collection precision="month" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">1276</bio:days_to_collection>
741
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
742
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
743
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10B</bio:bcr_sample_barcode>
744
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">717DF59D-E7C6-4CB6-A14E-8AD3C6B8FED8</bio:bcr_sample_uuid>
745
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
746
+ <bio:portions>
747
+ <bio:portion>
748
+ <admin:additional_studies/>
749
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
750
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
751
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">28</bio:day_of_creation>
752
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_creation>
753
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2021</bio:year_of_creation>
754
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.00</bio:weight>
755
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10B-01</bio:bcr_portion_barcode>
756
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9350067C-7D72-47A2-926F-30A874D1B283</bio:bcr_portion_uuid>
757
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
758
+ <bio:analytes>
759
+ <bio:analyte>
760
+ <admin:additional_studies/>
761
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
762
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
763
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
764
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
765
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
766
+ <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>
767
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
768
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10B-01D</bio:bcr_analyte_barcode>
769
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F247741C-76BA-4FDD-AA89-4F450D898332</bio:bcr_analyte_uuid>
770
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
771
+ <bio:aliquots>
772
+ <bio:aliquot>
773
+ <admin:additional_studies/>
774
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A89F</bio:plate_id>
775
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
776
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
777
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
778
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
779
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A09N-10B-01D-A89F-36</bio:bcr_aliquot_barcode>
780
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">E17B5ED0-91B3-4405-B5E1-B3D3B6CCC8D6</bio:bcr_aliquot_uuid>
781
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
782
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">8.50</bio:quantity>
783
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
784
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
785
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">11</bio:plate_column>
786
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112367846</bio:biospecimen_barcode_bottom>
787
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
788
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
789
+ </bio:aliquot>
790
+ </bio:aliquots>
791
+ <bio:protocols>
792
+ <bio:protocol>
793
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
794
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
795
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
796
+ </bio:protocol>
797
+ </bio:protocols>
798
+ <bio:dna>
799
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
800
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
801
+ </bio:dna>
802
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">PicoGreen</bio:spectrophotometer_method>
803
+ </bio:analyte>
804
+ </bio:analytes>
805
+ <bio:slides/>
806
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
807
+ </bio:portion>
808
+ </bio:portions>
809
+ <bio:tumor_pathology/>
810
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
811
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
812
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
813
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
814
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
815
+ <bio:diagnostic_slides>
816
+ <admin:additional_studies/>
817
+ </bio:diagnostic_slides>
818
+ </bio:sample>
819
+ </bio:samples>
820
+ </bio:patient>
821
+ </bio:tcga_bcr>
data/gdc_data_organized/33919e92-4ea9-47e5-a6f4-36e51845d50f/nationwidechildrens.org_ssf.TCGA-A8-A09N.xml ADDED
@@ -0,0 +1,93 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <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">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">F654B809-8A1A-4AD8-8C75-FE4DCFC3C2DF</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">47.98.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
12
+ <admin:patient_withdrawal>
13
+ <admin:withdrawn>false</admin:withdrawn>
14
+ </admin:patient_withdrawal>
15
+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
16
+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
17
+ </admin:admin>
18
+ <ssf:patient>
19
+ <admin:additional_studies/>
20
+ <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-A09N</shared:bcr_patient_barcode>
21
+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">33919e92-4ea9-47e5-a6f4-36e51845d50f</shared:bcr_patient_uuid>
22
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A8</shared:tissue_source_site>
23
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A09N</shared:patient_id>
24
+ <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"/>
25
+ <ssf:tumor_samples>
26
+ <ssf:tumor_sample>
27
+ <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">03115606-c46f-40ef-a95f-cdc1c174797d</ssf:bcr_sample_uuid>
28
+ <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="">31</shared:days_to_sample_procurement>
29
+ <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="170888">Other Method, specify</shared:method_of_sample_procurement>
30
+ <shared:other_method_of_sample_procurement preferred_name="cancer_procurement_method_other" display_order="12" cde="2006730" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="170889">wide excision</shared:other_method_of_sample_procurement>
31
+ <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="170890">Cryovial</ssf:vessel_used>
32
+ <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="170891"/>
33
+ <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"/>
34
+ <ssf:tumor_weight preferred_name="tumor_sample_weight" display_order="23" cde="3081946" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="170892">100</ssf:tumor_weight>
35
+ <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="170895">YES</ssf:sample_prescreened>
36
+ <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="170893">70</shared:tumor_nuclei_percent>
37
+ <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="170894">20</shared:tumor_necrosis_percent>
38
+ <ssf:days_to_pathology_review precision="month" 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">17</ssf:days_to_pathology_review>
39
+ <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="171025">YES</ssf:path_confirm_tumor_nuclei_metrics>
40
+ <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="171026">YES</ssf:path_confirm_tumor_necrosis_metrics>
41
+ <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="171028">YES</ssf:path_confirm_report_attached>
42
+ <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="171027">YES</ssf:path_confirm_diagnosis_matching>
43
+ <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"/>
44
+ <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="170896">NO</ssf:top_slide_submitted>
45
+ <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="170898">NO</ssf:digital_image_submitted>
46
+ <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>
47
+ <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"/>
48
+ <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="171030">No</shared:other_dx>
49
+ <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="171030">No</shared:history_of_neoadjuvant_treatment>
50
+ <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="171031">Consented</shared:consent_or_death_status>
51
+ <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">31</shared:days_to_consent>
52
+ <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="741127">Germany</shared:country>
53
+ <ssf_disease:disease_details/>
54
+ <ssf:tumor_histologies>
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+ <ssf:tumor_histology>
56
+ <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="170881">Infiltrating Ductal Carcinoma</shared:histological_type>
57
+ <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"/>
58
+ <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"/>
59
+ <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"/>
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+ </ssf:tumor_histology>
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+ </ssf:tumor_histologies>
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+ <ssf:tumor_locations>
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+ <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"/>
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+ <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="170884">Right</ssf:laterality>
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+ <ssf:tumor_location>
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+ <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="170884">Breast</ssf:site_of_disease>
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+ <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"/>
68
+ <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="170884"/>
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+ </ssf:tumor_location>
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+ </ssf:tumor_locations>
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+ </ssf:tumor_sample>
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+ </ssf:tumor_samples>
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+ <ssf:normal_controls>
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+ <ssf:normal_control>
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+ <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">639fc0fe-863a-4b3f-9462-a22941f13167</ssf:bcr_sample_uuid>
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+ <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="Completed" restricted="false" source_system_identifier="170989">Blood Draw</ssf:method_of_normal_sample_procurement>
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+ <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="170990"/>
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+ <ssf:days_to_normal_sample_procurement precision="month" xsd_ver="2.3" tier="1" cde="3288496" owner="TSS" procurement_status="Completed" preferred_name="normal_control_procurement_days_to" display_order="55" cde_ver="1.000">31</ssf:days_to_normal_sample_procurement>
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+ <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="170991"/>
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+ <ssf:ncedna_dna_conc preferred_name="normal_control_DNA_concentration" display_order="48" cde="3288187" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="170982"/>
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+ <ssf:ncedna_dna_qm preferred_name="normal_control_DNA_quant_method" display_order="47" cde="3288186" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="170981"/>
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+ <ssf:ncedna_dna_qty preferred_name="normal_control_DNA_quantity" display_order="46" cde="3288185" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="170980"/>
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+ <ssf:ncedna_dna_vol preferred_name="normal_control_DNA_volume" display_order="49" cde="3288188" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="170983"/>
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+ <ssf:normal_control_locations>
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+ <ssf:normal_control_location>
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+ <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="170984"/>
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+ <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="170985"/>
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+ </ssf:normal_control_location>
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+ </ssf:normal_control_locations>
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+ </ssf:normal_control>
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+ </ssf:normal_controls>
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+ </ssf:patient>
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+ </ssf:tcga_bcr>
data/gdc_data_organized/33cea538-4c3f-470a-972d-257c43241ab4/4fa35f20-e26e-4bb0-811d-b307e3927904.rna_seq.augmented_star_gene_counts.tsv ADDED
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data/gdc_data_organized/33cea538-4c3f-470a-972d-257c43241ab4/GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_B02_735256.grch38.seg.v2.txt ADDED
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data/gdc_data_organized/33cea538-4c3f-470a-972d-257c43241ab4/TCGA-BRCA.dc5b229b-a3c1-4e91-a28a-809ce6035c0c.ascat3.gene_level_copy_number.v36.tsv ADDED
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1
+ AGID lab_id catalog_number set_id peptide_target protein_expression
2
+ AGID00100 882 sc-628 Old 1433BETA 0.27575
3
+ AGID00111 913 sc-23957 Old 1433EPSILON 0.15005
4
+ AGID00101 883 sc-1019 Old 1433ZETA -0.057425
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+ AGID00001 2 9452 Old 4EBP1 -0.82021
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+ AGID00002 3 9456 Old 4EBP1_pS65 0.16085
7
+ AGID00003 6 9459 Old 4EBP1_pT37T46 -0.81755
8
+ AGID00443 8 9455 Old 4EBP1_pT70 -0.14987
9
+ AGID00120 985 4937 Old 53BP1 -1.0232
10
+ AGID00004 13 3661 Old ACC_pS79 0.57461
11
+ AGID00005 14 1768-1/ab45174 Old ACC1 0.50731
12
+ AGID00408 2372 3658 Set163 AceCS1 0.5516347
13
+ AGID00473 1182 5335 Old ACETYLATUBULINLYS40 -1.0108
14
+ AGID00404 2367 9189 Set163 ACSL1 1.192505
15
+ AGID02144 2450 PA5-27081 Old ACVRL1 0.15745
16
+ AGID00186 1198 ab88574 Old ADAR1 -0.25641
17
+ AGID00146 1084 4691 Old AKT 0.23076
18
+ AGID00028 230 9271 Old AKT_pS473 0.70777
19
+ AGID00170 1154 2965 Old AKT_pT308 -0.010158
20
+ AGID00316 1800 3063 Set163 Akt2 0.1051202
21
+ AGID00347 2009 8599 Set163 Akt2_pS474 0.4979747
22
+ AGID02215 2577 ab195377 Set163 ALKBH5 0.02268003
23
+ AGID00498 924 CA1030 Old ALPHACATENIN NA
24
+ AGID00287 1630 ABC80 Set163 Ambra1_pS52 -0.0852706
25
+ AGID00236 1351 ab129081 Set163 AMPK-a2_pS345 -0.3233899
26
+ AGID00006 39 2532 Old AMPKALPHA -0.26403
27
+ AGID00007 40 2535 Old AMPKALPHA_pT172 -0.14452
28
+ AGID00193 1208 610066 Old ANNEXIN1 -0.015679
29
+ AGID00166 1142 610668 Old ANNEXINVII 0.2471
30
+ AGID00371 756 1852-1/ab52615 Old AR 3.1543
31
+ AGID00194 1217 4432 Old ARAF 0.22339
32
+ AGID02191 2507 PA5-39728 Old ARAF_pS299 0.039965
33
+ AGID00260 1053 sc-32761 Old ARID1A -0.14841
34
+ AGID00264 1560 HPA029318 Old ASNS 0.06163
35
+ AGID00276 1612 3415 Set163 Atg3 -0.005774825
36
+ AGID00309 1775 13507 Set163 Atg4B 0.05062472
37
+ AGID00310 1776 12994 Set163 Atg5 -0.5520549
38
+ AGID00277 1613 8558 Set163 Atg7 0.03729524
39
+ AGID00242 1363 2873 Old ATM -0.11697
40
+ AGID02142 2447 13050 Set163 ATM_pS1981 0.1196001
41
+ AGID00217 1289 ab14748 Set163 ATP5A 0.1822546
42
+ AGID02145 2451 PA5-43776 Set163 ATP5H 0.3510702
43
+ AGID02150 2456 13934 Set163 ATR 0.1901822
44
+ AGID00315 1795 ab178407 Set163 ATR_pS428 -0.479981
45
+ AGID00268 1569 ab97508 Set163 ATRX -0.3238074
46
+ AGID00391 2332 14475 Set163 Aurora-A -0.1286748
47
+ AGID00392 2333 2914 Set163 Aurora-ABC_pT288_pT232_pT198 0.09091525
48
+ AGID02195 2512 MA5-27890 Set163 Aurora-B -0.3647611
49
+ AGID00215 1271 8661 Old AXL 0.59086
50
+ AGID02143 2449 8457 Set163 b-Actin 0.298095
51
+ AGID00179 1170 9565 Set163 b-Catenin_pT41_S45 0.1521802
52
+ AGID00301 1725 14058 Set163 B7-H3 0.06831432
53
+ AGID00302 1726 14572 Set163 B7-H4 -0.1636901
54
+ AGID00008 63 9291 Old BAD_pS112 0.039233
55
+ AGID00009 71 1542-1/ab32371 Old BAK -0.084952
56
+ AGID00192 1207 sc-28383 Old BAP1C4 -0.30039
57
+ AGID00010 73 2772 Old BAX 0.011364
58
+ AGID00433 80 M0887 Old BCL2 0.011993
59
+ AGID00219 1299 PAB8528 Old BCL2A1 0.418
60
+ AGID00012 84 1018-1 Old BCLXL -0.30607
61
+ AGID00377 87 sc-10086 Old BECLIN 0.095639
62
+ AGID00011 75 9562 Old BETACATENIN -0.60727
63
+ AGID00013 88 1008-1/ab32060 Old BID 0.31519
64
+ AGID00180 90 1036-1/ab32158 Old BIM 0.10909
65
+ AGID00221 1311 610978 Set163 BiP-GRP78 -0.2413403
66
+ AGID00373 2194 07-507 Set163 BMK1-Erk5_pT218_Y220 -0.2313647
67
+ AGID00355 92 1647/ab33899 Old BRAF -1.0264
68
+ AGID00014 94 2696 Old BRAF_pS445 -0.44117
69
+ AGID00445 761 9012 Old BRCA2 0.11863
70
+ AGID00266 1567 13440 Old BRD4 -1.0474
71
+ AGID00168 1146 2865 Set163 c-Abl_pY412 0.2012745
72
+ AGID00278 1615 3130 Set163 c-IAP2 -0.09486987
73
+ AGID00345 1990 5649 Old CA9 NA
74
+ AGID00265 1565 2862 Old CABL 0.11518
75
+ AGID00429 2407 2679 Set163 Calnexin -0.135935
76
+ AGID00176 1165 9496 Set163 Caspase-8-cleaved 0.1723602
77
+ AGID00623 111 9665 Old CASPASE3 -0.34097
78
+ AGID00015 109 9491 Old CASPASE7CLEAVEDD198 -0.55422
79
+ AGID00118 951 9746 Old CASPASE8 0.034217
80
+ AGID00537 935 551246 Old CASPASE9 NA
81
+ AGID00016 114 3238 Old CAVEOLIN1 0.1197
82
+ AGID00358 2100 ab76000 Set163 CD134 0.1825938
83
+ AGID00303 1737 826701 Set163 CD171 -0.5302048
84
+ AGID00410 125 1632-1/ab78237 Old CD20 0.14023
85
+ AGID00220 1308 ab28340 Old CD26 0.23128
86
+ AGID00191 1206 610467 Set163 CD29 -0.3730251
87
+ AGID00017 127 M0823 Old CD31 0.21771
88
+ AGID00369 2174 ab108403 Set163 CD38 0.2375052
89
+ AGID00359 2104 ab133616 Set163 CD4 0.256054
90
+ AGID00411 1398 3570 Set163 CD44 -0.05787988
91
+ AGID00237 1352 M070101-2 Set163 CD45 0.2118851
92
+ AGID00115 937 611016 Old CD49B -0.1148
93
+ AGID02171 2482 91882 Set163 CD86 0.2055452
94
+ AGID00329 1873 4688 Set163 cdc25C -0.06204975
95
+ AGID00227 1332 4651 Set163 Cdc42 0.08188502
96
+ AGID00422 2396 3387 Set163 Cdc6 0.09447512
97
+ AGID00501 1007 9112 Old CDK1 0.05836
98
+ AGID00293 1658 ab32384 Set163 CDK1_pT14 0.1439752
99
+ AGID00314 1783 4539 Old CDK1_pY15 -0.11888
100
+ AGID00423 2397 8064 Set163 CDT1 0.6179998
101
+ AGID02101 2348 15102 Set163 cGAS -0.1887548
102
+ AGID00447 2410 13460 Set163 CHD1L -0.3869766
103
+ AGID00189 1203 2360 Old CHK1 0.21676
104
+ AGID00234 1348 ab79758 Old CHK1_pS296 0.054765
105
+ AGID00107 903 2348 Old CHK1_pS345 0.036809
106
+ AGID00018 146 3440 Old CHK2 0.051484
107
+ AGID00019 147 2197 Old CHK2_pT68 0.031994
108
+ AGID00527 2078 4952 Old CIAP -0.34992
109
+ AGID00350 2018 3793 Set163 CIITA 0.1655652
110
+ AGID00434 155 9164 Old CJUN_pS73 0.11789
111
+ AGID00020 157 1522-1/ab32363 Old CKIT 0.13452
112
+ AGID00400 852 NB100-91714 Old CLAUDIN7 -0.94278
113
+ AGID00466 726 3127 Old CMET 0.058749
114
+ AGID00079 727 3129 Old CMET_pY1235 0.081009
115
+ AGID00167 161 9402 Old CMYC 0.21465
116
+ AGID00292 1656 11130-1-AP Old COG3 -0.52026
117
+ AGID00021 171 sc-20649 Old COLLAGENVI 0.91696
118
+ AGID00141 1069 459230 Old COMPLEXIISUBUNIT30 NA
119
+ AGID00267 1568 3512 Set163 Connexin-43 -0.582375
120
+ AGID00269 1571 6434 Set163 Coup-TFII 0.06616524
121
+ AGID00150 1116 4850 Set163 Cox-IV -0.4793854
122
+ AGID00195 1218 4842 Set163 Cox2 0.1682352
123
+ AGID00188 803 05-739 Old CRAF -0.17095
124
+ AGID00022 179 9427 Old CRAF_pS338 0.0055706
125
+ AGID00023 181 9197 Set163 Creb 0.5667641
126
+ AGID00393 2334 9198 Set163 CREB_pS133 -0.2228626
127
+ AGID00365 2155 4980 Set163 CSK 0.1849752
128
+ AGID00367 2160 9201 Set163 CtIP 0.1680399
129
+ AGID00536 2096 ab107198 Old CTLA4 NA
130
+ AGID00025 198 2936 Set163 Cyclin-D3 -0.3651449
131
+ AGID00024 192 1495-1/ab32053 Old CYCLINB1 -0.24395
132
+ AGID00382 194 sc-718 Old CYCLIND1 0.23343
133
+ AGID00437 199 sc-25303 Old CYCLINE1 -0.96874
134
+ AGID00449 202 1142-1 Old CYCLINE2 0.12702
135
+ AGID00209 1257 ab110324 Set163 Cyclophilin-F -0.586915
136
+ AGID00247 1379 ab48389 Set163 D-a-Tubulin -0.1125098
137
+ AGID00308 1770 GTX10524 Set163 DAPK1_pS308 0.02399519
138
+ AGID00304 1744 ab51601 Set163 DAPK2 0.02828002
139
+ AGID00343 1980 6998 Set163 DDB-1 -0.6452048
140
+ AGID00427 2402 5583 Set163 DDR1 -0.2578405
141
+ AGID00428 2403 SAB4504671 Set163 DDR1_pY513 -0.7856748
142
+ AGID00532 1273 Bast Lab Old DIRAS3 0.30878
143
+ AGID00104 891 ab76008 Old DJ1 0.060673
144
+ AGID02146 2452 4658 Set163 DM-Histone-H3 0.3732399
145
+ AGID00386 1397 ab32521 Set163 DM-K9-Histone-H3 -0.08146979
146
+ AGID00352 2030 14649 Set163 DNA-Ligase-IV 0.08652999
147
+ AGID00407 2371 13609 Set163 DNA_POLG -0.2864848
148
+ AGID00399 2344 5032 Set163 DNMT1 -0.3658149
149
+ AGID00409 2373 5391 Set163 DRP1 -0.2906263
150
+ AGID00253 1406 5149 Old DUSP4 0.51208
151
+ AGID00334 1936 ab76310 Set163 DUSP6 0.1003149
152
+ AGID00116 940 3218 Old DVL3 -0.26001
153
+ AGID00211 1261 sc-251 Old E2F1 NA
154
+ AGID00148 1099 3195 Old ECADHERIN 0.19155
155
+ AGID00135 1060 2332 Old EEF2 -0.4821
156
+ AGID00136 1061 3692 Old EEF2K -0.18068
157
+ AGID00152 1120 2232 Old EGFR -0.15151
158
+ AGID00450 217 2234 Old EGFR_pY1068 1.3851
159
+ AGID00026 221 1124-1/ab32578 Old EGFR_pY1173 0.19716
160
+ AGID00078 722 9742 Old EIF4E 0.17828
161
+ AGID00328 1871 ab76256 Set163 eIF4E_pS209 0.3285049
162
+ AGID00154 1124 2498 Old EIF4G -0.40974
163
+ AGID00027 228 9181 Set163 Elk1_pS383 0.3130302
164
+ AGID00235 1350 M061329-2 Set163 EMA -1.918855
165
+ AGID00394 2337 3810 Set163 Enolase-1 0.06032001
166
+ AGID00395 2338 8171 Set163 Enolase-2 0.05963025
167
+ AGID00196 1219 GTX629542 Old ENY2 -0.52481
168
+ AGID00438 1849 A302-024A Set163 EphA2 -0.006414758
169
+ AGID00552 2422 6347 Set163 EphA2_pS897 -0.1446948
170
+ AGID00553 2423 12677 Set163 EphA2_pY588 0.1465667
171
+ AGID00075 693 556347 Old EPPK1 0.38509
172
+ AGID00335 238 RM-9101 Old ERALPHA -1.1951
173
+ AGID00029 241 1091-1/ab32396 Old ERALPHA_pS118 -0.56625
174
+ AGID00240 247 MS-671 Old ERCC1 -0.092417
175
+ AGID00239 1355 11331-1-AP Old ERCC5 -0.84991
176
+ AGID00484 249 sc-154 Old ERK2 -0.54243
177
+ AGID00372 2193 3552 Set163 Erk5 0.3127152
178
+ AGID00405 2369 13826 Set163 ERRalpha 0.6340801
179
+ AGID00187 1200 A303-501A Old ETS1 0.027146
180
+ AGID00511 2492 2593 Set163 EVI1 0.1569996
181
+ AGID00485 1284 4905 Old EZH2 NA
182
+ AGID00030 252 1700-1/ab40794 Set163 FAK 0.1237652
183
+ AGID02151 2457 8556 Set163 FAK_pY397 0.07964863
184
+ AGID00171 1156 3180 Old FASN 3.8213
185
+ AGID00356 2085 500-P18/10775-082 Set163 FGF-basic 0.1448502
186
+ AGID00031 262 1574-1/ab45688 Old FIBRONECTIN 1.1854
187
+ AGID00339 1959 4403 Set163 FN14 -0.1881698
188
+ AGID02152 2458 20459 Old FOXM1 -0.080098
189
+ AGID00378 269 9467 Old FOXO3A 0.3907
190
+ AGID02197 2515 orb6051 Old FOXO3A_pS318S321 -0.0035421
191
+ AGID02167 2475 PA5-64616 Set163 FRS2-alpha_pY196 0.00143525
192
+ AGID02213 2575 ab124892 Set163 FTO -0.5880248
193
+ AGID02141 2446 12263 Old G6PD 0.17176
194
+ AGID00117 943 3239 Old GAB2 -0.42223
195
+ AGID00412 274 AM4300 Old GAPDH -1.8264
196
+ AGID00086 764 558686 Old GATA3 0.20939
197
+ AGID00383 1578 4253 Old GATA6 0.43054
198
+ AGID00289 1634 12601-1-AP Set163 GCLC 0.8236402
199
+ AGID00305 1745 ab124827 Set163 GCLM 0.04973524
200
+ AGID00212 1263 3305 Old GCN5L2 -0.82742
201
+ AGID00270 1579 3538 Set163 Gli1 -1.010485
202
+ AGID00263 1520 ab69838 Set163 Gli3 -0.1519959
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor -0.01009976
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 -0.1211859
205
+ AGID00262 1491 ab156876 Set163 Glutaminase -0.1613248
206
+ AGID00319 1807 4275 Set163 Granzyme-B 0.3967201
207
+ AGID00368 2169 ab183737 Set163 GRB7 0.5099645
208
+ AGID00396 2339 3593 Set163 Grp75 0.01807018
209
+ AGID00174 1163 9315 Set163 GSK-3B -0.08396563
210
+ AGID00502 1082 9336 Old GSK3_pS9 -0.23971
211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA -0.30408
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 -0.27313
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
+ AGID01354 1342 9718 Set163 H2AX_pS139 -0.0462648
216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 -0.1541498
217
+ AGID00131 1038 MS-325-P1 Old HER2 1.4424
218
+ AGID00142 299 06-229 Old HER2_pY1248 1.3525
219
+ AGID00110 911 sc-285 Old HER3 0.18977
220
+ AGID00080 728 4791 Old HER3_pY1289 0.19738
221
+ AGID00103 890 2573 Old HEREGULIN 0.095853
222
+ AGID00271 1582 11988 Set163 HES1 -0.421645
223
+ AGID00397 2340 2024 Set163 Hexokinase-I -0.285835
224
+ AGID00442 1023 2867 Set163 Hexokinase-II -0.4120063
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
+ AGID00205 1250 ab1791 Set163 Histone-H3 0.1556351
227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 0.1840601
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 0.1044439
229
+ AGID00333 1902 14832-1-AP Set163 HMHA1 1.045735
230
+ AGID00035 321 2402 Set163 HSP27 -0.4701098
231
+ AGID00036 323 2401 Set163 HSP27_pS82 -0.4029748
232
+ AGID00320 1808 12165 Set163 HSP60 0.11983
233
+ AGID00037 325 4872 Old HSP70 1.858
234
+ AGID00366 2158 86630 Set163 IDO -0.1524202
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.39794
236
+ AGID00038 335 3922 Old IGFBP2 0.021754
237
+ AGID00090 793 611504 Set163 IGFBP3 -0.5311751
238
+ AGID00039 336 3027 Set163 IGFRb -0.6902148
239
+ AGID00336 1949 12153 Set163 IL-6 0.3703999
240
+ AGID02221 2583 57145 Set163 IMP3 -0.2430249
241
+ AGID02153 2459 14543 Old INPP4B -0.30187
242
+ AGID00272 1586 3025 Set163 IR-b -1.031535
243
+ AGID00519 2519 4302 Set163 IRF-3 -0.007499507
244
+ AGID00520 2520 4947 Set163 IRF-3_pS396 -0.5377753
245
+ AGID00223 1316 sc-497 Old IRF1 -0.011503
246
+ AGID00092 802 06-248 Old IRS1 0.14548
247
+ AGID00040 371 4502 Set163 IRS2 0.04854478
248
+ AGID00250 1394 sc-13157 Old JAB1 0.27572
249
+ AGID00256 1413 ab109536 Set163 Jagged1 0.03003077
250
+ AGID00177 1166 3230 Old JAK2 -0.1466
251
+ AGID00758 377 4671 Old JNK_pT183Y185 0.078465
252
+ AGID02136 2439 PA5-28262 Old JNK2 0.29226
253
+ AGID00307 1757 ab10484 Set163 KAP1 -0.1481703
254
+ AGID00528 904 2180 Old KU80 -0.53406
255
+ AGID00375 2237 HPA028732 Set163 LAD1 -0.2628798
256
+ AGID00290 1643 IHC-00439 Set163 Lasu1 -0.2992798
257
+ AGID00279 1618 4108 Set163 LC3A-B 0.54143
258
+ AGID00042 397 2752 Old LCK 0.46806
259
+ AGID00119 976 3582 Old LDHA NA
260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.019124
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 -0.3452898
263
+ AGID00439 2424 2796 Set163 Lyn 0.1257502
264
+ AGID02154 2460 4370 Old MAPK_pT202Y204 1.0184
265
+ AGID00198 1222 5453 Set163 Mcl-1 -0.0142558
266
+ AGID00288 1633 AB3314P Set163 MCT4 -0.4994549
267
+ AGID00175 1164 3521 Set163 MDM2_pS166 0.1087702
268
+ AGID00044 417 1235-1/ab32576 Old MEK1 0.14547
269
+ AGID00143 1076 9154 Old MEK1_pS217S221 0.098156
270
+ AGID00201 1243 9125 Set163 MEK2 -0.2179252
271
+ AGID00361 2118 ab51061 Set163 MelanA -0.1914098
272
+ AGID00362 2119 ab137078 Set163 Melanoma-gp100 0.1664651
273
+ AGID00337 1951 12711 Set163 MERIT40 -0.5845304
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 -0.1627948
275
+ AGID02212 2574 ab195352 Set163 METTL3 -0.4653348
276
+ AGID00225 1323 sc-20121 Set163 MIF 0.001385247
277
+ AGID00137 1062 WH0054206M1 Old MIG6 -0.038909
278
+ AGID00403 2117 ab20663 Set163 MITF 0.1064699
279
+ AGID00503 1067 ab3298 Old MITOCHONDRIA NA
280
+ AGID00321 1809 14739 Set163 Mitofusin-1 0.4357065
281
+ AGID00322 1810 11925 Set163 Mitofusin-2 -0.3896549
282
+ AGID00389 2324 3515 Set163 MLH1 -0.3364549
283
+ AGID00312 1780 14993 Set163 MLKL 0.5015351
284
+ AGID00402 2359 MAB3328 Set163 MMP14 -0.2934348
285
+ AGID00045 435 4022 Set163 MMP2 1.218592
286
+ AGID00122 1005 2195 Set163 Mnk1 0.06774403
287
+ AGID00331 1899 sc-377312 Set163 MR1 0.0001600606
288
+ AGID00273 1589 ab103319 Set163 MRAP -0.06205475
289
+ AGID00530 440 4847 Old MRE11 0.236
290
+ AGID00390 905 2850 Old MSH2 -0.31443
291
+ AGID00138 1063 22030002 Old MSH6 -0.80002
292
+ AGID00299 1675 ab76148 Set163 MSI2 -0.3584797
293
+ AGID00232 1344 ab14705 Set163 MTCO1 -0.9841164
294
+ AGID00046 444 2983 Old MTOR -0.53738
295
+ AGID00047 446 2971 Old MTOR_pS2448 -0.14079
296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 -0.6013699
297
+ AGID00401 1139 21370002 Old MYH11 -0.42304
298
+ AGID00291 1647 3403 Old MYOSINIIA 0.10884
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 -0.08003
300
+ AGID00318 1803 4282 Set163 Myt1 -0.237585
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN 0.35871
303
+ AGID00156 1126 3217 Old NDRG1_pT346 0.62047
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 0.8868852
305
+ AGID00134 1046 22710002 Old NF2 -0.069768
306
+ AGID00048 457 3033 Old NFKBP65_pS536 1.3991
307
+ AGID02155 2461 3608 Old NOTCH1 0.2046
308
+ AGID00340 1969 4147 Set163 Notch1-cleaved 0
309
+ AGID00087 767 sc-5593 Set163 Notch3 -0.07004478
310
+ AGID00258 1420 3187 Set163 NQO1 -0.5751899
311
+ AGID00162 1136 sc-31 Old NRAS 0.33722
312
+ AGID00257 1419 12721 Old NRF2 NA
313
+ AGID00297 1669 2750 Set163 Oct-4 0.2290902
314
+ AGID00420 466 1712-1/ab40803 Old P16INK4A 0.085317
315
+ AGID00384 470 sc-6246 Old P21 0.21288
316
+ AGID00105 897 1591-1/ab32034 Old P27 0.071399
317
+ AGID00096 842 AF1555 Old P27_pT157 0.081226
318
+ AGID00099 878 ab64949 Old P27_pT198 0.26271
319
+ AGID00181 1175 9228 Set163 p38-a -0.1486659
320
+ AGID00098 479 9211 Old P38_pT180Y182 -0.044757
321
+ AGID00049 478 9212 Old P38MAPK 0.23954
322
+ AGID00151 1119 4695 Set163 p44-42-MAPK 0.09243024
323
+ AGID00050 481 9282 Old P53 -0.27377
324
+ AGID00490 1187 610833 Old P62LCKLIGAND -0.37056
325
+ AGID00545 1415 ab53039 Old P63 NA
326
+ AGID00052 494 9205 Old P70S6K_pT389 0.461
327
+ AGID00051 493 1494-1/ab32529 Old P70S6K1 0.15147
328
+ AGID00085 759 9347 Old P90RSK -0.23979
329
+ AGID00531 770 9344 Old P90RSK_pT359S363 0.21029
330
+ AGID00182 1178 9346 Set163 p90RSK_pT573 0.1058751
331
+ AGID00053 499 612024 Old PAI1 0.26012
332
+ AGID00224 1322 HPA035895 Set163 PAICS 0.04422525
333
+ AGID00323 1811 2602 Set163 PAK1 -0.3884152
334
+ AGID02199 2517 PA5-69540 Set163 PAK4 0.01877013
335
+ AGID00245 1370 4336-BPC-100 Set163 PAR 0.7737748
336
+ AGID00374 2209 66564 Set163 PARG 0.123675
337
+ AGID00370 1372 sc-7150 Old PARP1 -0.11442
338
+ AGID00468 501 9546 Old PARPCLEAVED 0.064684
339
+ AGID00274 1591 ab53715 Set163 Patched -0.07495479
340
+ AGID00513 2486 60433 Set163 PAX6 0.01460514
341
+ AGID00441 1621 9857 Set163 PAX8 -0.1733811
342
+ AGID00054 504 2542 Old PAXILLIN -0.070825
343
+ AGID00055 509 2130 Old PCADHERIN 0.028601
344
+ AGID00248 511 ab29 Old PCNA -0.104
345
+ AGID00413 2095 43248 Old PDCD1 NA
346
+ AGID00094 816 600-401-965 Old PDCD4 -0.60259
347
+ AGID00385 1225 3169 Set163 PDGFRB 0.4475302
348
+ AGID00210 1258 ab110332 Set163 PDH -0.2423509
349
+ AGID00324 1817 3205 Set163 PDHA1 0.1459996
350
+ AGID00280 1622 3820 Set163 PDHK1 -0.00631476
351
+ AGID00056 515 3062 Old PDK1 0.11531
352
+ AGID00057 516 3061 Old PDK1_pS241 -0.28504
353
+ AGID00300 1234 sc-19090 Old PDL1 0.18159
354
+ AGID00124 1017 2780 Old PEA15 -0.0046265
355
+ AGID00125 1018 44-836G Old PEA15_pS116 0.076438
356
+ AGID00440 2429 3192 Set163 PERK -0.3660254
357
+ AGID02207 2569 ab192876 Set163 PGM1 -0.3369254
358
+ AGID00281 1623 13428 Set163 PHGDH -0.2925454
359
+ AGID00425 2399 22789-1-AP Set163 PHLPP 0.1436652
360
+ AGID00226 1330 sc-376412 Set163 PI3K-p110-b -0.1316748
361
+ AGID00093 808 4255 Old PI3KP110ALPHA -0.0082138
362
+ AGID00058 523 06-195 Old PI3KP85 -0.098805
363
+ AGID00296 1667 5675 Set163 PKA-a -0.3864099
364
+ AGID00259 1426 9375 Set163 PKC-a-b-II_pT638_T641 -0.3001748
365
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97
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98
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99
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100
+ <bio:aliquot>
101
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102
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103
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104
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105
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106
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107
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108
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109
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110
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111
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112
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113
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114
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115
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116
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
117
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118
+ <bio:aliquot>
119
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120
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121
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122
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123
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124
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125
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126
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6b47c22f-8b4e-40fd-9a12-18b539521224</bio:bcr_aliquot_uuid>
127
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128
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
129
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
130
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131
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
132
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490455</bio:biospecimen_barcode_bottom>
133
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134
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
135
+ </bio:aliquot>
136
+ <bio:aliquot>
137
+ <admin:additional_studies/>
138
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A111</bio:plate_id>
139
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140
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
141
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
142
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
143
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11D-A111-01</bio:bcr_aliquot_barcode>
144
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">dc5b229b-a3c1-4e91-a28a-809ce6035c0c</bio:bcr_aliquot_uuid>
145
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
146
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
147
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
148
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
149
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
150
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100487575</bio:biospecimen_barcode_bottom>
151
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152
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
153
+ </bio:aliquot>
154
+ <bio:aliquot>
155
+ <admin:additional_studies/>
156
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A112</bio:plate_id>
157
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
158
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
159
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
160
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
161
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11D-A112-05</bio:bcr_aliquot_barcode>
162
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">000bef24-c05c-46ee-a84c-9611a41aeb4e</bio:bcr_aliquot_uuid>
163
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
164
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.74</bio:quantity>
165
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
166
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
167
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
168
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100488823</bio:biospecimen_barcode_bottom>
169
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170
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
171
+ </bio:aliquot>
172
+ </bio:aliquots>
173
+ <bio:protocols>
174
+ <bio:protocol>
175
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
176
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
177
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
178
+ </bio:protocol>
179
+ </bio:protocols>
180
+ <bio:dna>
181
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
182
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
183
+ </bio:dna>
184
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
185
+ </bio:analyte>
186
+ <bio:analyte>
187
+ <admin:additional_studies/>
188
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
189
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
190
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
191
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
192
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.98</bio:a260_a280_ratio>
193
+ <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>
194
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
195
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11R</bio:bcr_analyte_barcode>
196
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">02829def-7ee2-4c2f-8cac-b91719a30052</bio:bcr_analyte_uuid>
197
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
198
+ <bio:aliquots>
199
+ <bio:aliquot>
200
+ <admin:additional_studies/>
201
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A114</bio:plate_id>
202
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
203
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
204
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
205
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
206
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11R-A114-13</bio:bcr_aliquot_barcode>
207
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3bac5dc1-de92-45c0-96f5-bda97299eec9</bio:bcr_aliquot_uuid>
208
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
209
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
210
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
211
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
212
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9</bio:plate_column>
213
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099014303</bio:biospecimen_barcode_bottom>
214
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215
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
216
+ </bio:aliquot>
217
+ <bio:aliquot>
218
+ <admin:additional_studies/>
219
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A115</bio:plate_id>
220
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
221
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
222
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
223
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
224
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11R-A115-07</bio:bcr_aliquot_barcode>
225
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">306818e8-2e51-4dee-b27c-53ee9cea8d03</bio:bcr_aliquot_uuid>
226
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
227
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
228
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
229
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
230
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9</bio:plate_column>
231
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099020639</bio:biospecimen_barcode_bottom>
232
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
233
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
234
+ </bio:aliquot>
235
+ </bio:aliquots>
236
+ <bio:protocols>
237
+ <bio:protocol>
238
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
239
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
240
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
241
+ </bio:protocol>
242
+ </bio:protocols>
243
+ <bio:rna>
244
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.20</bio:ratio_28s_18s>
245
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9.00</bio:rinvalue>
246
+ </bio:rna>
247
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
248
+ </bio:analyte>
249
+ <bio:analyte>
250
+ <admin:additional_studies/>
251
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
252
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253
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
254
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
255
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
256
+ <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>
257
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
258
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11W</bio:bcr_analyte_barcode>
259
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9CBF1C51-F7C1-4271-92FA-AF80BC65432B</bio:bcr_analyte_uuid>
260
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
261
+ <bio:aliquots>
262
+ <bio:aliquot>
263
+ <admin:additional_studies/>
264
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12T</bio:plate_id>
265
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
266
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
267
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
268
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
269
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-11W-A12T-09</bio:bcr_aliquot_barcode>
270
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">dbd94c07-9c13-4d24-9ad8-1340d66b31af</bio:bcr_aliquot_uuid>
271
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
272
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
273
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
274
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
275
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
276
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108432400</bio:biospecimen_barcode_bottom>
277
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
278
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
279
+ </bio:aliquot>
280
+ </bio:aliquots>
281
+ <bio:protocols>
282
+ <bio:protocol>
283
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
284
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
285
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
286
+ </bio:protocol>
287
+ </bio:protocols>
288
+ <bio:dna>
289
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
290
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
291
+ </bio:dna>
292
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
293
+ </bio:analyte>
294
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295
+ <bio:slides>
296
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297
+ <admin:additional_studies/>
298
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
299
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
300
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">70</bio:percent_tumor_cells>
301
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">70</bio:percent_tumor_nuclei>
302
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
303
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_necrosis>
304
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_stromal_cells>
305
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
306
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:percent_lymphocyte_infiltration>
307
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_monocyte_infiltration>
308
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
309
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:percent_neutrophil_infiltration>
310
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
311
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-01-BSA</shared:bcr_slide_barcode>
312
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4871792f-d00b-4541-815b-7aaa44c43f94</shared:bcr_slide_uuid>
313
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A135-01A-01-BSA.4871792f-d00b-4541-815b-7aaa44c43f94.svs</shared:image_file_name>
314
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
315
+ </bio:slide>
316
+ <bio:slide>
317
+ <admin:additional_studies/>
318
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
319
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
320
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
321
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
322
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
323
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
324
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_stromal_cells>
325
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
326
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">50</bio:percent_lymphocyte_infiltration>
327
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_monocyte_infiltration>
328
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
329
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:percent_neutrophil_infiltration>
330
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
331
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-01A-01-TSA</shared:bcr_slide_barcode>
332
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c03f75de-8d25-4f74-8ca4-498db35d5df9</shared:bcr_slide_uuid>
333
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A135-01A-01-TSA.c03f75de-8d25-4f74-8ca4-498db35d5df9.svs</shared:image_file_name>
334
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
335
+ </bio:slide>
336
+ </bio:slides>
337
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
338
+ </bio:portion>
339
+ </bio:portions>
340
+ <bio:tumor_pathology/>
341
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
342
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
343
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
344
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">7045ECC9-72B3-4AD3-A6C6-4F8C6914EAA1</bio:pathology_report_uuid>
345
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-C8-A135.7045ECC9-72B3-4AD3-A6C6-4F8C6914EAA1.pdf</bio:pathology_report_file_name>
346
+ <bio:diagnostic_slides>
347
+ <admin:additional_studies/>
348
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">B69A605E-B577-4F43-9471-2C95312B05D9</bio:ffpe_slide_uuid>
349
+ </bio:diagnostic_slides>
350
+ </bio:sample>
351
+ <bio:sample>
352
+ <admin:additional_studies/>
353
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
354
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
355
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
356
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
357
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
358
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
359
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
360
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
361
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
362
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
363
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
364
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
365
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
366
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
367
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
368
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">162</bio:days_to_collection>
369
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
370
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
371
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A</bio:bcr_sample_barcode>
372
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c1c70e7d-ccc3-4bb6-a975-1385ff0f5016</bio:bcr_sample_uuid>
373
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
374
+ <bio:portions>
375
+ <bio:portion>
376
+ <admin:additional_studies/>
377
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:portion_number>
378
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:portion_sequence>
379
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:day_of_creation>
380
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_creation>
381
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
382
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.00</bio:weight>
383
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02</bio:bcr_portion_barcode>
384
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e41bde2c-77e0-46b7-8ad2-17701401558b</bio:bcr_portion_uuid>
385
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
386
+ <bio:analytes>
387
+ <bio:analyte>
388
+ <admin:additional_studies/>
389
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
390
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
391
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
392
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
393
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.90</bio:a260_a280_ratio>
394
+ <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>
395
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
396
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02D</bio:bcr_analyte_barcode>
397
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">61293685-9d27-41a7-b16e-a84d81b7f7a5</bio:bcr_analyte_uuid>
398
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
399
+ <bio:aliquots>
400
+ <bio:aliquot>
401
+ <admin:additional_studies/>
402
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A10Z</bio:plate_id>
403
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
404
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
405
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
406
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
407
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02D-A10Z-02</bio:bcr_aliquot_barcode>
408
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0bf2367e-9b99-4676-b7f2-1546f6e8164b</bio:bcr_aliquot_uuid>
409
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
410
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.95</bio:quantity>
411
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
412
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
413
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
414
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100490743</bio:biospecimen_barcode_bottom>
415
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
416
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
417
+ </bio:aliquot>
418
+ <bio:aliquot>
419
+ <admin:additional_studies/>
420
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A110</bio:plate_id>
421
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
422
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
423
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
424
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
425
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02D-A110-09</bio:bcr_aliquot_barcode>
426
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4fef2aff-1a1d-434a-910b-ce94fff48677</bio:bcr_aliquot_uuid>
427
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
428
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
429
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</bio:volume>
430
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
431
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
432
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100489111</bio:biospecimen_barcode_bottom>
433
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
434
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
435
+ </bio:aliquot>
436
+ <bio:aliquot>
437
+ <admin:additional_studies/>
438
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A113</bio:plate_id>
439
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
440
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
441
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
442
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
443
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02D-A113-01</bio:bcr_aliquot_barcode>
444
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">540c0a51-b411-4565-ba9b-2665fd877289</bio:bcr_aliquot_uuid>
445
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
446
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.00</bio:quantity>
447
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
448
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
449
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
450
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100487863</bio:biospecimen_barcode_bottom>
451
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
452
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
453
+ </bio:aliquot>
454
+ </bio:aliquots>
455
+ <bio:protocols>
456
+ <bio:protocol>
457
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
458
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
459
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
460
+ </bio:protocol>
461
+ </bio:protocols>
462
+ <bio:dna>
463
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
464
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
465
+ </bio:dna>
466
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
467
+ </bio:analyte>
468
+ <bio:analyte>
469
+ <admin:additional_studies/>
470
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
471
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
472
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
473
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
474
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
475
+ <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>
476
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
477
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02W</bio:bcr_analyte_barcode>
478
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D5571557-BC5F-4D1C-86AE-9BEBFFAA5341</bio:bcr_analyte_uuid>
479
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
480
+ <bio:aliquots>
481
+ <bio:aliquot>
482
+ <admin:additional_studies/>
483
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12U</bio:plate_id>
484
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
485
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
486
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
487
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
488
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-C8-A135-10A-02W-A12U-09</bio:bcr_aliquot_barcode>
489
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">afa5b012-502b-4d37-9ad0-fbab263a6a48</bio:bcr_aliquot_uuid>
490
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
491
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
492
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
493
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
494
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8</bio:plate_column>
495
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108432496</bio:biospecimen_barcode_bottom>
496
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
497
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
498
+ </bio:aliquot>
499
+ </bio:aliquots>
500
+ <bio:protocols>
501
+ <bio:protocol>
502
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
503
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
504
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
505
+ </bio:protocol>
506
+ </bio:protocols>
507
+ <bio:dna>
508
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
509
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
510
+ </bio:dna>
511
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
512
+ </bio:analyte>
513
+ </bio:analytes>
514
+ <bio:slides/>
515
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
516
+ </bio:portion>
517
+ </bio:portions>
518
+ <bio:tumor_pathology/>
519
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
520
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
521
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
522
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
523
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
524
+ <bio:diagnostic_slides>
525
+ <admin:additional_studies/>
526
+ </bio:diagnostic_slides>
527
+ </bio:sample>
528
+ </bio:samples>
529
+ </bio:patient>
530
+ </bio:tcga_bcr>
data/gdc_data_organized/33cea538-4c3f-470a-972d-257c43241ab4/nationwidechildrens.org_clinical.TCGA-C8-A135.xml ADDED
@@ -0,0 +1,382 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <brca:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/brca/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/brca/2.7/TCGA_BCR.BRCA_Clinical.xsd" schemaVersion="2.7" xmlns:brca="http://tcga.nci/bcr/xml/clinical/brca/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:brca_shared="http://tcga.nci/bcr/xml/clinical/brca/shared/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:brca_nte="http://tcga.nci/bcr/xml/clinical/brca/shared/new_tumor_event/2.7/1.0" xmlns:nte="http://tcga.nci/bcr/xml/clinical/shared/new_tumor_event/2.7" xmlns:follow_up_v2.1="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/2.1" xmlns:follow_up_v4.0="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/4.0" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">6AABE76D-41B8-4D8E-B45D-F5C2BBC2A4C6</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">85.86.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
12
+ <admin:patient_withdrawal>
13
+ <admin:withdrawn>false</admin:withdrawn>
14
+ </admin:patient_withdrawal>
15
+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
16
+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
17
+ </admin:admin>
18
+ <brca:patient>
19
+ <admin:additional_studies/>
20
+ <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="748250">Breast</clin_shared:tumor_tissue_site>
21
+ <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"/>
22
+ <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="748240">No</shared:other_dx>
23
+ <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="748236">FEMALE</shared:gender>
24
+ <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="748242">Alive</clin_shared:vital_status>
25
+ <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">-23667</clin_shared:days_to_birth>
26
+ <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=""/>
27
+ <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"/>
28
+ <clin_shared:days_to_last_followup precision="month" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">13</clin_shared:days_to_last_followup>
29
+ <clin_shared:race_list>
30
+ <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="748238">ASIAN</clin_shared:race>
31
+ </clin_shared:race_list>
32
+ <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-C8-A135</shared:bcr_patient_barcode>
33
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">C8</shared:tissue_source_site>
34
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A135</shared:patient_id>
35
+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">33cea538-4c3f-470a-972d-257c43241ab4</shared:bcr_patient_uuid>
36
+ <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="748241">No</shared:history_of_neoadjuvant_treatment>
37
+ <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>
38
+ <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>
39
+ <clin_shared:icd_o_3_histology preferred_name="" display_order="9999" cde="3226275" cde_ver="" xsd_ver="2.4" tier="2" owner="TSS" procurement_status="Completed" restricted="false">8500/3</clin_shared:icd_o_3_histology>
40
+ <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>
41
+ <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>
42
+ <clin_shared:age_at_initial_pathologic_diagnosis precision="day" xsd_ver="1.12" tier="1" cde="2006657" owner="TSS" procurement_status="Completed">64</clin_shared:age_at_initial_pathologic_diagnosis>
43
+ <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="748256">2010</clin_shared:year_of_initial_pathologic_diagnosis>
44
+ <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="748239">NOT HISPANIC OR LATINO</clin_shared:ethnicity>
45
+ <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="748249">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
46
+ <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="748268">YES</clin_shared:primary_lymph_node_presentation_assessment>
47
+ <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="748269">3</clin_shared:lymph_node_examined_count>
48
+ <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="748284"/>
49
+ <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="748290"/>
50
+ <brca:anatomic_neoplasm_subdivisions>
51
+ <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="748251">Left</clin_shared:anatomic_neoplasm_subdivision>
52
+ </brca:anatomic_neoplasm_subdivisions>
53
+ <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="748300"/>
54
+ <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="748265">Axillary lymph node dissection alone</brca:axillary_lymph_node_stage_method_type>
55
+ <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="748266"/>
56
+ <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="748259">Modified Radical Mastectomy</brca:breast_carcinoma_surgical_procedure_name>
57
+ <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="748263" xsi:nil="true"/>
58
+ <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="748262"/>
59
+ <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="748260"/>
60
+ <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="748252">Infiltrating Ductal Carcinoma</shared:histological_type>
61
+ <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="748253" xsi:nil="true"/>
62
+ <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="748237">Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)</clin_shared:menopause_status>
63
+ <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="748285">Negative</brca_shared:breast_carcinoma_progesterone_receptor_status>
64
+ <brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator preferred_name="micromet_detection_by_ihc" display_order="46" cde="3086152" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="748267"/>
65
+ <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="748281"/>
66
+ <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="748282"/>
67
+ <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="748293">3+</brca_shared:her2_immunohistochemistry_level_result>
68
+ <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="748264"/>
69
+ <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="748261">Negative</clin_shared:margin_status>
70
+ <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="748257">Core needle biopsy</clin_shared:initial_pathologic_diagnosis_method>
71
+ <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="748258" xsi:nil="true"/>
72
+ <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="748296"/>
73
+ <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="748279">Negative</brca_shared:breast_carcinoma_estrogen_receptor_status>
74
+ <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="748291">Positive</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
75
+ <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="748271"/>
76
+ <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="748270">1</clin_shared:number_of_lymphnodes_positive_by_he>
77
+ <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="748289"/>
78
+ <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="748283"/>
79
+ <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="748292"/>
80
+ <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="748294"/>
81
+ <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="748295"/>
82
+ <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="748299"/>
83
+ <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="748301"/>
84
+ <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="748302"/>
85
+ <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="748231">YES</clin_shared:tissue_prospective_collection_indicator>
86
+ <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="748232">NO</clin_shared:tissue_retrospective_collection_indicator>
87
+ <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="748298"/>
88
+ <brca:first_nonlymph_node_metastasis_anatomic_sites>
89
+ <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="748277"/>
90
+ <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="748278"/>
91
+ </brca:first_nonlymph_node_metastasis_anatomic_sites>
92
+ <brca_shared:er_level_cell_percentage_category preferred_name="er_status_ihc_Percent_Positive" display_order="59" cde="3128341" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="748280"/>
93
+ <brca_shared:progesterone_receptor_level_cell_percent_category preferred_name="pr_status_ihc_percent_positive" display_order="65" cde="3128342" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="748286"/>
94
+ <brca:distant_metastasis_present_ind2 preferred_name="metastatic_tumor_indicator" display_order="999" cde="2194698" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="748303">NO</brca:distant_metastasis_present_ind2>
95
+ <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="748304"/>
96
+ <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="748305"/>
97
+ <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="748307"/>
98
+ <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="748308"/>
99
+ <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="748309"/>
100
+ <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="748310"/>
101
+ <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="748316"/>
102
+ <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="748311"/>
103
+ <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="748313"/>
104
+ <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="748314"/>
105
+ <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="748315"/>
106
+ <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="748317"/>
107
+ <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="748318"/>
108
+ <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="748319"/>
109
+ <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="748320"/>
110
+ <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="748321"/>
111
+ <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="748323"/>
112
+ <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="748324"/>
113
+ <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="748325"/>
114
+ <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="748326"/>
115
+ <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="748327"/>
116
+ <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="748322"/>
117
+ <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="748297"/>
118
+ <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="748287"/>
119
+ <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="748288"/>
120
+ <shared_stage:stage_event system="AJCC">
121
+ <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="748272">6th</shared_stage:system_version>
122
+ <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"/>
123
+ <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="748276">Stage IIB</shared_stage:pathologic_stage>
124
+ <shared_stage:tnm_categories>
125
+ <shared_stage:clinical_categories>
126
+ <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"/>
127
+ <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"/>
128
+ <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"/>
129
+ </shared_stage:clinical_categories>
130
+ <shared_stage:pathologic_categories>
131
+ <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="748273">T2</shared_stage:pathologic_T>
132
+ <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="748274">N1</shared_stage:pathologic_N>
133
+ <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="748275">M0</shared_stage:pathologic_M>
134
+ </shared_stage:pathologic_categories>
135
+ </shared_stage:tnm_categories>
136
+ <shared_stage:psa>
137
+ <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"/>
138
+ <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"/>
139
+ </shared_stage:psa>
140
+ <shared_stage:gleason_grading>
141
+ <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"/>
142
+ <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"/>
143
+ <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"/>
144
+ <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"/>
145
+ </shared_stage:gleason_grading>
146
+ <shared_stage:ann_arbor>
147
+ <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"/>
148
+ <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"/>
149
+ </shared_stage:ann_arbor>
150
+ <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"/>
151
+ <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"/>
152
+ <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"/>
153
+ </shared_stage:stage_event>
154
+ <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
155
+ <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
156
+ <brca_nte:new_tumor_events>
157
+ <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
158
+ </brca_nte:new_tumor_events>
159
+ <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="748229">15</clin_shared:day_of_form_completion>
160
+ <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="748228">4</clin_shared:month_of_form_completion>
161
+ <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="748230">2011</clin_shared:year_of_form_completion>
162
+ <brca:follow_ups>
163
+ <follow_up_v2.1:follow_up version="2.1" sequence="1">
164
+ <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-C8-A135-F19081</clin_shared:bcr_followup_barcode>
165
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">2EB99E29-CFEC-47C3-AE81-9035B00BA8BA</clin_shared:bcr_followup_uuid>
166
+ <clin_shared:followup_case_report_form_submission_reason preferred_name="followup_reason" display_order="999" cde="3233305" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1438444">Scheduled Follow-up Submission</clin_shared:followup_case_report_form_submission_reason>
167
+ <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="1438451">NO</clin_shared:radiation_therapy>
168
+ <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="1438452">NO</clin_shared:postoperative_rx_tx>
169
+ <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="1438453">Alive</clin_shared:vital_status>
170
+ <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">32</clin_shared:days_to_last_followup>
171
+ <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"/>
172
+ <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="1438460">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
173
+ <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="1438461">NO</nte:new_tumor_event_after_initial_treatment>
174
+ <nte:days_to_new_tumor_event_after_initial_treatment precision="day" xsd_ver="2.2" tier="1" cde="3392464" owner="TSS" procurement_status="Not Applicable" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
175
+ <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="1438465"/>
176
+ <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="1438466"/>
177
+ <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="1438467"/>
178
+ <nte:additional_surgery_locoregional_procedure preferred_name="new_tumor_event_surgery" display_order="999" cde="3008755" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1438468"/>
179
+ <nte:days_to_additional_surgery_metastatic_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408682" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_met" display_order="9999" cde_ver="1.000"/>
180
+ <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="1438472"/>
181
+ <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="1438473"/>
182
+ <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="1438474"/>
183
+ <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="1438475"/>
184
+ <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="1438476"/>
185
+ <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="1438477"/>
186
+ <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="1438478"/>
187
+ <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="1438479"/>
188
+ <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="1438480"/>
189
+ <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="1438481"/>
190
+ <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="1438482"/>
191
+ <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="1438483"/>
192
+ <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="1438484"/>
193
+ <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="1438485"/>
194
+ <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="1438486"/>
195
+ <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="1438487"/>
196
+ <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="1438488"/>
197
+ <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="1438489"/>
198
+ <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="1438490"/>
199
+ <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="1438491"/>
200
+ <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="1438492"/>
201
+ <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="1438493"/>
202
+ <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="1438494"/>
203
+ <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="1438495"/>
204
+ <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="1438496"/>
205
+ <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="1438497"/>
206
+ <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="1438442">2</clin_shared:day_of_form_completion>
207
+ <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="1438441">12</clin_shared:month_of_form_completion>
208
+ <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="1438443">2011</clin_shared:year_of_form_completion>
209
+ </follow_up_v2.1:follow_up>
210
+ <follow_up_v4.0:follow_up version="4.0" sequence="2">
211
+ <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-C8-A135-F70817</clin_shared:bcr_followup_barcode>
212
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">2713E11E-2440-4519-9A50-B0E7F2C3B23E</clin_shared:bcr_followup_uuid>
213
+ <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="4102609">NO</clin_shared:lost_follow_up>
214
+ <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="4102610">NO</clin_shared:radiation_therapy>
215
+ <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="4102611">YES</clin_shared:postoperative_rx_tx>
216
+ <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="4102612">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
217
+ <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="4102613">Alive</clin_shared:vital_status>
218
+ <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">393</clin_shared:days_to_last_followup>
219
+ <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"/>
220
+ <brca_nte:new_tumor_events>
221
+ <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="4102622">NO</nte:new_tumor_event_after_initial_treatment>
222
+ <brca_nte:new_tumor_event>
223
+ <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"/>
224
+ <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="4102623"/>
225
+ <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="4102624"/>
226
+ <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="4102625"/>
227
+ <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="4102630"/>
228
+ <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"/>
229
+ <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="4102635"/>
230
+ <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="4102636"/>
231
+ <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="4102637"/>
232
+ <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="4102638"/>
233
+ <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="4102639"/>
234
+ <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="4102640"/>
235
+ <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="4102641"/>
236
+ <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="4102642"/>
237
+ <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="4102643"/>
238
+ <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="4102644"/>
239
+ <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="4102645"/>
240
+ <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="4102646"/>
241
+ <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="4102647"/>
242
+ <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="4102648"/>
243
+ <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="4102649"/>
244
+ <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="4102650"/>
245
+ <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="4102651"/>
246
+ <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="4102652"/>
247
+ <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="4102653"/>
248
+ <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="4102654"/>
249
+ <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="4102655"/>
250
+ <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="4102656"/>
251
+ <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="4102657"/>
252
+ <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="4102658"/>
253
+ <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="4102659"/>
254
+ <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="4102660"/>
255
+ </brca_nte:new_tumor_event>
256
+ </brca_nte:new_tumor_events>
257
+ <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">9</clin_shared:day_of_form_completion>
258
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">3</clin_shared:month_of_form_completion>
259
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2015</clin_shared:year_of_form_completion>
260
+ </follow_up_v4.0:follow_up>
261
+ </brca:follow_ups>
262
+ <rx:drugs>
263
+ <rx:drug>
264
+ <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="4102664">NO</rx:tx_on_clinical_trial>
265
+ <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"/>
266
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-C8-A135-D70818</rx:bcr_drug_barcode>
267
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">E75ED433-A561-43B5-B3E0-5F8E12B99B40</rx:bcr_drug_uuid>
268
+ <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"/>
269
+ <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"/>
270
+ <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"/>
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+ AGID00118 951 9746 Old CASPASE8 -0.21944
80
+ AGID00537 935 551246 Old CASPASE9 NA
81
+ AGID00016 114 3238 Old CAVEOLIN1 -1.0276
82
+ AGID00358 2100 ab76000 Set163 CD134 -0.03670644
83
+ AGID00303 1737 826701 Set163 CD171 1.796845
84
+ AGID00410 125 1632-1/ab78237 Old CD20 -0.11705
85
+ AGID00220 1308 ab28340 Old CD26 0.019805
86
+ AGID00191 1206 610467 Set163 CD29 -0.1366554
87
+ AGID00017 127 M0823 Old CD31 -0.17144
88
+ AGID00369 2174 ab108403 Set163 CD38 -0.276325
89
+ AGID00359 2104 ab133616 Set163 CD4 -0.4155763
90
+ AGID00411 1398 3570 Set163 CD44 -0.4462501
91
+ AGID00237 1352 M070101-2 Set163 CD45 -0.2838452
92
+ AGID00115 937 611016 Old CD49B 0.44712
93
+ AGID02171 2482 91882 Set163 CD86 0.100645
94
+ AGID00329 1873 4688 Set163 cdc25C 0.1685
95
+ AGID00227 1332 4651 Set163 Cdc42 -0.001605223
96
+ AGID00422 2396 3387 Set163 Cdc6 -0.2638351
97
+ AGID00501 1007 9112 Old CDK1 -0.14839
98
+ AGID00293 1658 ab32384 Set163 CDK1_pT14 0.219425
99
+ AGID00314 1783 4539 Old CDK1_pY15 -0.23633
100
+ AGID00423 2397 8064 Set163 CDT1 -0.2483605
101
+ AGID02101 2348 15102 Set163 cGAS -0.140575
102
+ AGID00447 2410 13460 Set163 CHD1L -0.5785668
103
+ AGID00189 1203 2360 Old CHK1 0.071676
104
+ AGID00234 1348 ab79758 Old CHK1_pS296 0.097484
105
+ AGID00107 903 2348 Old CHK1_pS345 0.035496
106
+ AGID00018 146 3440 Old CHK2 -0.45486
107
+ AGID00019 147 2197 Old CHK2_pT68 0.024594
108
+ AGID00527 2078 4952 Old CIAP -0.039207
109
+ AGID00350 2018 3793 Set163 CIITA -0.076655
110
+ AGID00434 155 9164 Old CJUN_pS73 -0.071599
111
+ AGID00020 157 1522-1/ab32363 Old CKIT -0.4983
112
+ AGID00400 852 NB100-91714 Old CLAUDIN7 1.2901
113
+ AGID00466 726 3127 Old CMET 0.017908
114
+ AGID00079 727 3129 Old CMET_pY1235 0.019809
115
+ AGID00167 161 9402 Old CMYC -0.092531
116
+ AGID00292 1656 11130-1-AP Old COG3 0.16229
117
+ AGID00021 171 sc-20649 Old COLLAGENVI -0.55342
118
+ AGID00141 1069 459230 Old COMPLEXIISUBUNIT30 NA
119
+ AGID00267 1568 3512 Set163 Connexin-43 -0.2030953
120
+ AGID00269 1571 6434 Set163 Coup-TFII -0.433475
121
+ AGID00150 1116 4850 Set163 Cox-IV 0.4114943
122
+ AGID00195 1218 4842 Set163 Cox2 -0.003634998
123
+ AGID00188 803 05-739 Old CRAF 0.18036
124
+ AGID00022 179 9427 Old CRAF_pS338 -0.02803
125
+ AGID00023 181 9197 Set163 Creb -0.1591961
126
+ AGID00393 2334 9198 Set163 CREB_pS133 0.1170171
127
+ AGID00365 2155 4980 Set163 CSK 0.118325
128
+ AGID00367 2160 9201 Set163 CtIP 0.1390697
129
+ AGID00536 2096 ab107198 Old CTLA4 NA
130
+ AGID00025 198 2936 Set163 Cyclin-D3 0.1752249
131
+ AGID00024 192 1495-1/ab32053 Old CYCLINB1 -0.22441
132
+ AGID00382 194 sc-718 Old CYCLIND1 0.43058
133
+ AGID00437 199 sc-25303 Old CYCLINE1 -0.78527
134
+ AGID00449 202 1142-1 Old CYCLINE2 0.038957
135
+ AGID00209 1257 ab110324 Set163 Cyclophilin-F -0.6599553
136
+ AGID00247 1379 ab48389 Set163 D-a-Tubulin 0.06326999
137
+ AGID00308 1770 GTX10524 Set163 DAPK1_pS308 0.02940494
138
+ AGID00304 1744 ab51601 Set163 DAPK2 0.03435977
139
+ AGID00343 1980 6998 Set163 DDB-1 -0.02965507
140
+ AGID00427 2402 5583 Set163 DDR1 0.6288492
141
+ AGID00428 2403 SAB4504671 Set163 DDR1_pY513 0.169085
142
+ AGID00532 1273 Bast Lab Old DIRAS3 -0.10886
143
+ AGID00104 891 ab76008 Old DJ1 -0.10554
144
+ AGID02146 2452 4658 Set163 DM-Histone-H3 -0.1083804
145
+ AGID00386 1397 ab32521 Set163 DM-K9-Histone-H3 0.006519964
146
+ AGID00352 2030 14649 Set163 DNA-Ligase-IV -0.2802303
147
+ AGID00407 2371 13609 Set163 DNA_POLG 0.5446849
148
+ AGID00399 2344 5032 Set163 DNMT1 0.1382249
149
+ AGID00409 2373 5391 Set163 DRP1 -0.1402466
150
+ AGID00253 1406 5149 Old DUSP4 0.36727
151
+ AGID00334 1936 ab76310 Set163 DUSP6 0.4880947
152
+ AGID00116 940 3218 Old DVL3 0.16945
153
+ AGID00211 1261 sc-251 Old E2F1 NA
154
+ AGID00148 1099 3195 Old ECADHERIN 0.89413
155
+ AGID00135 1060 2332 Old EEF2 -0.21052
156
+ AGID00136 1061 3692 Old EEF2K -0.35091
157
+ AGID00152 1120 2232 Old EGFR -0.35559
158
+ AGID00450 217 2234 Old EGFR_pY1068 -0.15102
159
+ AGID00026 221 1124-1/ab32578 Old EGFR_pY1173 0.052083
160
+ AGID00078 722 9742 Old EIF4E -0.0079608
161
+ AGID00328 1871 ab76256 Set163 eIF4E_pS209 -0.08598532
162
+ AGID00154 1124 2498 Old EIF4G 0.12961
163
+ AGID00027 228 9181 Set163 Elk1_pS383 0
164
+ AGID00235 1350 M061329-2 Set163 EMA 2.564115
165
+ AGID00394 2337 3810 Set163 Enolase-1 -0.3848302
166
+ AGID00395 2338 8171 Set163 Enolase-2 0.09521001
167
+ AGID00196 1219 GTX629542 Old ENY2 -0.13029
168
+ AGID00438 1849 A302-024A Set163 EphA2 -0.091295
169
+ AGID00552 2422 6347 Set163 EphA2_pS897 -0.086825
170
+ AGID00553 2423 12677 Set163 EphA2_pY588 -0.1907735
171
+ AGID00075 693 556347 Old EPPK1 1.8665
172
+ AGID00335 238 RM-9101 Old ERALPHA 3.0474
173
+ AGID00029 241 1091-1/ab32396 Old ERALPHA_pS118 0.57375
174
+ AGID00240 247 MS-671 Old ERCC1 -0.020072
175
+ AGID00239 1355 11331-1-AP Old ERCC5 -0.18947
176
+ AGID00484 249 sc-154 Old ERK2 -0.55365
177
+ AGID00372 2193 3552 Set163 Erk5 -0.414785
178
+ AGID00405 2369 13826 Set163 ERRalpha -0.2771101
179
+ AGID00187 1200 A303-501A Old ETS1 -0.21746
180
+ AGID00511 2492 2593 Set163 EVI1 -0.1330406
181
+ AGID00485 1284 4905 Old EZH2 NA
182
+ AGID00030 252 1700-1/ab40794 Set163 FAK -0.182005
183
+ AGID02151 2457 8556 Set163 FAK_pY397 0.4043084
184
+ AGID00171 1156 3180 Old FASN 1.7354
185
+ AGID00356 2085 500-P18/10775-082 Set163 FGF-basic 0.35863
186
+ AGID00031 262 1574-1/ab45688 Old FIBRONECTIN 0.49087
187
+ AGID00339 1959 4403 Set163 FN14 0.2777
188
+ AGID02152 2458 20459 Old FOXM1 -0.0052233
189
+ AGID00378 269 9467 Old FOXO3A -0.27247
190
+ AGID02197 2515 orb6051 Old FOXO3A_pS318S321 0.4179
191
+ AGID02167 2475 PA5-64616 Set163 FRS2-alpha_pY196 0.04346501
192
+ AGID02213 2575 ab124892 Set163 FTO 0.142385
193
+ AGID02141 2446 12263 Old G6PD 0.063327
194
+ AGID00117 943 3239 Old GAB2 -0.0083515
195
+ AGID00412 274 AM4300 Old GAPDH -1.4494
196
+ AGID00086 764 558686 Old GATA3 2.3389
197
+ AGID00383 1578 4253 Old GATA6 -0.16103
198
+ AGID00289 1634 12601-1-AP Set163 GCLC 0.19647
199
+ AGID00305 1745 ab124827 Set163 GCLM 0.047545
200
+ AGID00212 1263 3305 Old GCN5L2 0.58862
201
+ AGID00270 1579 3538 Set163 Gli1 0.003014599
202
+ AGID00263 1520 ab69838 Set163 Gli3 0.5956339
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor -0.12113
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 0.001873865
205
+ AGID00262 1491 ab156876 Set163 Glutaminase 0.1480249
206
+ AGID00319 1807 4275 Set163 Granzyme-B -0.3083501
207
+ AGID00368 2169 ab183737 Set163 GRB7 0.4136742
208
+ AGID00396 2339 3593 Set163 Grp75 0.2094299
209
+ AGID00174 1163 9315 Set163 GSK-3B -0.09914588
210
+ AGID00502 1082 9336 Old GSK3_pS9 0.072028
211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA -0.084441
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 0.27038
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
+ AGID01354 1342 9718 Set163 H2AX_pS139 0.03023496
216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 -0.002660063
217
+ AGID00131 1038 MS-325-P1 Old HER2 0.61554
218
+ AGID00142 299 06-229 Old HER2_pY1248 0.66766
219
+ AGID00110 911 sc-285 Old HER3 0.6956
220
+ AGID00080 728 4791 Old HER3_pY1289 -0.11768
221
+ AGID00103 890 2573 Old HEREGULIN -0.045928
222
+ AGID00271 1582 11988 Set163 HES1 0.5081148
223
+ AGID00397 2340 2024 Set163 Hexokinase-I 0.1216648
224
+ AGID00442 1023 2867 Set163 Hexokinase-II -0.2122566
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
+ AGID00205 1250 ab1791 Set163 Histone-H3 0.2904248
227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 -0.1181601
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 -0.5564664
229
+ AGID00333 1902 14832-1-AP Set163 HMHA1 0.1182945
230
+ AGID00035 321 2402 Set163 HSP27 0.1497199
231
+ AGID00036 323 2401 Set163 HSP27_pS82 0.865475
232
+ AGID00320 1808 12165 Set163 HSP60 0.6790698
233
+ AGID00037 325 4872 Old HSP70 -0.14878
234
+ AGID00366 2158 86630 Set163 IDO 0.9979495
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.097337
236
+ AGID00038 335 3922 Old IGFBP2 0.3093
237
+ AGID00090 793 611504 Set163 IGFBP3 0.03741468
238
+ AGID00039 336 3027 Set163 IGFRb 0.848425
239
+ AGID00336 1949 12153 Set163 IL-6 -0.2046803
240
+ AGID02221 2583 57145 Set163 IMP3 -0.2737051
241
+ AGID02153 2459 14543 Old INPP4B 2.8586
242
+ AGID00272 1586 3025 Set163 IR-b 0.558815
243
+ AGID00519 2519 4302 Set163 IRF-3 -0.01074975
244
+ AGID00520 2520 4947 Set163 IRF-3_pS396 -0.02204554
245
+ AGID00223 1316 sc-497 Old IRF1 0.26871
246
+ AGID00092 802 06-248 Old IRS1 0.54932
247
+ AGID00040 371 4502 Set163 IRS2 -0.09161546
248
+ AGID00250 1394 sc-13157 Old JAB1 -0.17086
249
+ AGID00256 1413 ab109536 Set163 Jagged1 -0.03305947
250
+ AGID00177 1166 3230 Old JAK2 -0.052533
251
+ AGID00758 377 4671 Old JNK_pT183Y185 -0.0070449
252
+ AGID02136 2439 PA5-28262 Old JNK2 0.85594
253
+ AGID00307 1757 ab10484 Set163 KAP1 0.1735995
254
+ AGID00528 904 2180 Old KU80 0.024216
255
+ AGID00375 2237 HPA028732 Set163 LAD1 -0.33225
256
+ AGID00290 1643 IHC-00439 Set163 Lasu1 0.19198
257
+ AGID00279 1618 4108 Set163 LC3A-B -0.3002703
258
+ AGID00042 397 2752 Old LCK -0.15947
259
+ AGID00119 976 3582 Old LDHA NA
260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.0069928
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 0.15517
263
+ AGID00439 2424 2796 Set163 Lyn -0.3552401
264
+ AGID02154 2460 4370 Old MAPK_pT202Y204 -0.29666
265
+ AGID00198 1222 5453 Set163 Mcl-1 -0.197466
266
+ AGID00288 1633 AB3314P Set163 MCT4 0.3376549
267
+ AGID00175 1164 3521 Set163 MDM2_pS166 0.34741
268
+ AGID00044 417 1235-1/ab32576 Old MEK1 0.53874
269
+ AGID00143 1076 9154 Old MEK1_pS217S221 -0.3697
270
+ AGID00201 1243 9125 Set163 MEK2 0.1022845
271
+ AGID00361 2118 ab51061 Set163 MelanA 0.04690998
272
+ AGID00362 2119 ab137078 Set163 Melanoma-gp100 -0.0709451
273
+ AGID00337 1951 12711 Set163 MERIT40 0.3800894
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 -0.121705
275
+ AGID02212 2574 ab195352 Set163 METTL3 0.497585
276
+ AGID00225 1323 sc-20121 Set163 MIF -0.547805
277
+ AGID00137 1062 WH0054206M1 Old MIG6 -0.063591
278
+ AGID00403 2117 ab20663 Set163 MITF -0.1127404
279
+ AGID00503 1067 ab3298 Old MITOCHONDRIA NA
280
+ AGID00321 1809 14739 Set163 Mitofusin-1 -0.1426238
281
+ AGID00322 1810 11925 Set163 Mitofusin-2 0.6007349
282
+ AGID00389 2324 3515 Set163 MLH1 0.2520049
283
+ AGID00312 1780 14993 Set163 MLKL 0.08377485
284
+ AGID00402 2359 MAB3328 Set163 MMP14 -0.03579506
285
+ AGID00045 435 4022 Set163 MMP2 0.02736214
286
+ AGID00122 1005 2195 Set163 Mnk1 -0.03369621
287
+ AGID00331 1899 sc-377312 Set163 MR1 -0.1698302
288
+ AGID00273 1589 ab103319 Set163 MRAP 0.09649501
289
+ AGID00530 440 4847 Old MRE11 0.13178
290
+ AGID00390 905 2850 Old MSH2 -0.34386
291
+ AGID00138 1063 22030002 Old MSH6 0.067331
292
+ AGID00299 1675 ab76148 Set163 MSI2 0.49043
293
+ AGID00232 1344 ab14705 Set163 MTCO1 0.6599533
294
+ AGID00046 444 2983 Old MTOR 0.60309
295
+ AGID00047 446 2971 Old MTOR_pS2448 0.25918
296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 0.001809827
297
+ AGID00401 1139 21370002 Old MYH11 0.57879
298
+ AGID00291 1647 3403 Old MYOSINIIA 0.09737
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 0.24275
300
+ AGID00318 1803 4282 Set163 Myt1 -0.04881525
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN -0.27124
303
+ AGID00156 1126 3217 Old NDRG1_pT346 0.32974
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 -0.094315
305
+ AGID00134 1046 22710002 Old NF2 -0.24313
306
+ AGID00048 457 3033 Old NFKBP65_pS536 0.87325
307
+ AGID02155 2461 3608 Old NOTCH1 0.11403
308
+ AGID00340 1969 4147 Set163 Notch1-cleaved -0.1657802
309
+ AGID00087 767 sc-5593 Set163 Notch3 -0.07839502
310
+ AGID00258 1420 3187 Set163 NQO1 -0.6308902
311
+ AGID00162 1136 sc-31 Old NRAS -0.081559
312
+ AGID00257 1419 12721 Old NRF2 NA
313
+ AGID00297 1669 2750 Set163 Oct-4 -0.003280007
314
+ AGID00420 466 1712-1/ab40803 Old P16INK4A -0.01934
315
+ AGID00384 470 sc-6246 Old P21 -0.0078313
316
+ AGID00105 897 1591-1/ab32034 Old P27 -0.19567
317
+ AGID00096 842 AF1555 Old P27_pT157 0.10844
318
+ AGID00099 878 ab64949 Old P27_pT198 -0.096547
319
+ AGID00181 1175 9228 Set163 p38-a 0.03770389
320
+ AGID00098 479 9211 Old P38_pT180Y182 -0.31905
321
+ AGID00049 478 9212 Old P38MAPK 0.015311
322
+ AGID00151 1119 4695 Set163 p44-42-MAPK -0.01514001
323
+ AGID00050 481 9282 Old P53 -0.24348
324
+ AGID00490 1187 610833 Old P62LCKLIGAND 0.9097
325
+ AGID00545 1415 ab53039 Old P63 NA
326
+ AGID00052 494 9205 Old P70S6K_pT389 -0.25401
327
+ AGID00051 493 1494-1/ab32529 Old P70S6K1 0.81392
328
+ AGID00085 759 9347 Old P90RSK 0.023261
329
+ AGID00531 770 9344 Old P90RSK_pT359S363 -0.058927
330
+ AGID00182 1178 9346 Set163 p90RSK_pT573 -0.1214251
331
+ AGID00053 499 612024 Old PAI1 0.83916
332
+ AGID00224 1322 HPA035895 Set163 PAICS 0.150115
333
+ AGID00323 1811 2602 Set163 PAK1 -0.3685954
334
+ AGID02199 2517 PA5-69540 Set163 PAK4 0.3082299
335
+ AGID00245 1370 4336-BPC-100 Set163 PAR 0.6650845
336
+ AGID00374 2209 66564 Set163 PARG 0.03172473
337
+ AGID00370 1372 sc-7150 Old PARP1 NA
338
+ AGID00468 501 9546 Old PARPCLEAVED -0.21353
339
+ AGID00274 1591 ab53715 Set163 Patched 0.123995
340
+ AGID00513 2486 60433 Set163 PAX6 -0.2606651
341
+ AGID00441 1621 9857 Set163 PAX8 -0.2335214
342
+ AGID00054 504 2542 Old PAXILLIN 0.30003
343
+ AGID00055 509 2130 Old PCADHERIN -0.17993
344
+ AGID00248 511 ab29 Old PCNA 0.041287
345
+ AGID00413 2095 43248 Old PDCD1 NA
346
+ AGID00094 816 600-401-965 Old PDCD4 -1.1672
347
+ AGID00385 1225 3169 Set163 PDGFRB -0.19273
348
+ AGID00210 1258 ab110332 Set163 PDH -0.01997115
349
+ AGID00324 1817 3205 Set163 PDHA1 -0.08903067
350
+ AGID00280 1622 3820 Set163 PDHK1 -0.069685
351
+ AGID00056 515 3062 Old PDK1 0.23831
352
+ AGID00057 516 3061 Old PDK1_pS241 0.17168
353
+ AGID00300 1234 sc-19090 Old PDL1 0.24789
354
+ AGID00124 1017 2780 Old PEA15 -0.34356
355
+ AGID00125 1018 44-836G Old PEA15_pS116 -0.35093
356
+ AGID00440 2429 3192 Set163 PERK 0.2398944
357
+ AGID02207 2569 ab192876 Set163 PGM1 -0.09937565
358
+ AGID00281 1623 13428 Set163 PHGDH -0.1698456
359
+ AGID00425 2399 22789-1-AP Set163 PHLPP -0.068815
360
+ AGID00226 1330 sc-376412 Set163 PI3K-p110-b -0.02132501
361
+ AGID00093 808 4255 Old PI3KP110ALPHA 0.07768
362
+ AGID00058 523 06-195 Old PI3KP85 -0.3395
363
+ AGID00296 1667 5675 Set163 PKA-a 0.7184699
364
+ AGID00259 1426 9375 Set163 PKC-a-b-II_pT638_T641 -0.180135
365
+ AGID00172 529 05-154 Old PKCALPHA -0.57687
366
+ AGID00460 530 06-822 Old PKCALPHA_pS657 -0.48484
367
+ AGID00114 932 07-875 Old PKCDELTA_pS664 0.025268
368
+ AGID00163 1137 9371 Old PKCPANBETAII_pS660 -0.21972
369
+ AGID00126 1025 4053 Old PKM2 NA
370
+ AGID00512 2489 5690 Set163 PLC-gamma1 0.3251842
371
+ AGID02138 2441 GTX133463 Set163 PLC-gamma2_pY759 -0.04460016
372
+ AGID00084 754 4513 Set163 PLK1 0.03485494
373
+ AGID00203 1246 22510002 Set163 PMS2 0.367335
374
+ AGID00207 1254 ab14734 Set163 Porin 0.193485
375
+ AGID00381 549 1483-1/ab32085 Old PR 0.23737
376
+ AGID00081 738 AHO1031 Set163 PRAS40 -0.09047499
377
+ AGID00082 739 44-1100G Old PRAS40_pT246 0.035937
378
+ AGID00424 2398 OAAF05458 Set163 PRC1_pT481 -0.132205
379
+ AGID00492 1205 HPA007730 Old PRDX1 0.37095
380
+ AGID00190 1204 ab102739 Old PREX1 1.4998
381
+ AGID00061 566 9552 Old PTEN -0.038442
382
+ AGID00364 2154 ab76942 Set163 PTPN12 0.08875484
383
+ AGID00218 1290 4976 Set163 Puma 0.13466
384
+ AGID00200 1242 SAB2900066 Old PYGB NA
385
+ AGID00535 1494 ab61013 Old PYGL NA
386
+ AGID00202 1245 H00005837-M10 Old PYGM NA
387
+ AGID00275 1607 3291 Set163 Pyk2_pY402 0.08406942
388
+ AGID00145 1083 3539 Old RAB11 0.24393
389
+ AGID00169 1150 4314 Old RAB25 0.22839
390
+ AGID00342 1979 24555 Set163 Rad23A 0.6652999
391
+ AGID00261 987 05-525 Old RAD50 -0.41599
392
+ AGID00360 579 NA71 Old RAD51 0.0093311
393
+ AGID00158 1128 2280 Old RAPTOR 0.77871
394
+ AGID00059 552 9309 Old RB -0.052141
395
+ AGID00060 557 9308 Old RB_pS807S811 -0.24294
396
+ AGID00164 1138 21390002 Old RBM15 0.22642
397
+ AGID00547 735 3221 Old RET_pY905 NA
398
+ AGID00097 847 MAB3426 Set163 Rheb 0.03277491
399
+ AGID00159 1129 2114 Old RICTOR 0.2863
400
+ AGID00160 1130 3806 Old RICTOR_pT1135 0.38785
401
+ AGID00282 1624 4926 Set163 RIP 0.43982
402
+ AGID00283 1625 13526 Set163 RIP3 -0.004905747
403
+ AGID00416 1368 2208 Set163 RPA32 -0.29382
404
+ AGID00246 1375 A300-245A Set163 RPA32_pS4_S8 0.2664239
405
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data/gdc_data_organized/34a74805-300c-4773-ab59-2085fcc2e6cc/USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_G01_787490.nocnv_grch38.seg.v2.txt ADDED
@@ -0,0 +1,46 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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2
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