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Auto-upload batch data to clear storage

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  1. .gitattributes +91 -0
  2. data/__notebook__.ipynb +2897 -0
  3. data/gdc_data_organized/02f5ae33-a563-4ecb-9e33-dfa500a44931/TCGA-A8-A093-01A-11D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt +0 -0
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39852
  },
39853
  "metadata": {},
39854
  "output_type": "display_data"
39855
+ },
39856
+ {
39857
+ "name": "stdout",
39858
+ "output_type": "stream",
39859
+ "text": [
39860
+ "-> Upload thành công!\n",
39861
+ "-> Đang xóa dữ liệu local để giải phóng bộ nhớ...\n"
39862
+ ]
39863
+ },
39864
+ {
39865
+ "name": "stdout",
39866
+ "output_type": "stream",
39867
+ "text": [
39868
+ "-> Đã làm trống thư mục. Dung lượng hiện tại: 0.00 GB\n",
39869
+ "--------------------------------------------------\n",
39870
+ "[4835/10000] (15.14GB) Downloading: 82d6e956-0c30-4767-bc37-27672e58d690.mirbase21.isoforms.quantification.txt (0.33 MB)... "
39871
+ ]
39872
+ },
39873
+ {
39874
+ "name": "stdout",
39875
+ "output_type": "stream",
39876
+ "text": [
39877
+ "OK\n",
39878
+ "[4836/10000] (0.00GB) Downloading: USAGE_p_TCGA_132_133_136_SNP_N_GenomeWideSNP_6_D08_787536.nocnv_grch38.seg.v2.txt (0.01 MB)... "
39879
+ ]
39880
+ },
39881
+ {
39882
+ "name": "stdout",
39883
+ "output_type": "stream",
39884
+ "text": [
39885
+ "OK\n",
39886
+ "[4837/10000] (0.00GB) Downloading: TCGA-A8-A093-01A-11D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.10 MB)... "
39887
+ ]
39888
+ },
39889
+ {
39890
+ "name": "stdout",
39891
+ "output_type": "stream",
39892
+ "text": [
39893
+ "OK\n",
39894
+ "[4838/10000] (0.00GB) Downloading: fe2ae40f-a2d0-41a0-8847-f43858578df4.mirbase21.isoforms.quantification.txt (0.31 MB)... "
39895
+ ]
39896
+ },
39897
+ {
39898
+ "name": "stdout",
39899
+ "output_type": "stream",
39900
+ "text": [
39901
+ "OK\n",
39902
+ "[4839/10000] (0.00GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0BQ.xml (0.09 MB)... "
39903
+ ]
39904
+ },
39905
+ {
39906
+ "name": "stdout",
39907
+ "output_type": "stream",
39908
+ "text": [
39909
+ "OK\n",
39910
+ "[4840/10000] (0.00GB) Downloading: nationwidechildrens.org_clinical.TCGA-AR-A1AS.xml (0.08 MB)... "
39911
+ ]
39912
+ },
39913
+ {
39914
+ "name": "stdout",
39915
+ "output_type": "stream",
39916
+ "text": [
39917
+ "OK\n",
39918
+ "[4841/10000] (0.00GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_E03_628452.grch38.seg.v2.txt (0.02 MB)... "
39919
+ ]
39920
+ },
39921
+ {
39922
+ "name": "stdout",
39923
+ "output_type": "stream",
39924
+ "text": [
39925
+ "OK\n",
39926
+ "[4842/10000] (0.00GB) Downloading: TCGA-BRCA.cf180187-bd5a-468e-8560-da1e48441b52.ascat2.allelic_specific.seg.txt (0.01 MB)... "
39927
+ ]
39928
+ },
39929
+ {
39930
+ "name": "stdout",
39931
+ "output_type": "stream",
39932
+ "text": [
39933
+ "OK\n",
39934
+ "[4843/10000] (0.00GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A1AS.xml (0.01 MB)... "
39935
+ ]
39936
+ },
39937
+ {
39938
+ "name": "stdout",
39939
+ "output_type": "stream",
39940
+ "text": [
39941
+ "OK\n",
39942
+ "[4844/10000] (0.00GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_H08_698166.grch38.seg.v2.txt (0.05 MB)... "
39943
+ ]
39944
+ },
39945
+ {
39946
+ "name": "stdout",
39947
+ "output_type": "stream",
39948
+ "text": [
39949
+ "OK\n",
39950
+ "[4845/10000] (0.00GB) Downloading: TCGA-BRCA.75937dba-a780-42c5-91db-c7ae7a4b8c41.ascat3.allelic_specific.seg.txt (0.00 MB)... "
39951
+ ]
39952
+ },
39953
+ {
39954
+ "name": "stdout",
39955
+ "output_type": "stream",
39956
+ "text": [
39957
+ "OK\n",
39958
+ "[4846/10000] (0.00GB) Downloading: 802ef530-9a93-4e08-89ad-7b629744b080_noid_Grn.idat (7.72 MB)... "
39959
+ ]
39960
+ },
39961
+ {
39962
+ "name": "stdout",
39963
+ "output_type": "stream",
39964
+ "text": [
39965
+ "OK\n",
39966
+ "[4847/10000] (0.01GB) Downloading: TCGA-BRCA.fe041229-97be-4bac-9294-04b42df07890.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
39967
+ ]
39968
+ },
39969
+ {
39970
+ "name": "stdout",
39971
+ "output_type": "stream",
39972
+ "text": [
39973
+ "OK\n",
39974
+ "[4848/10000] (0.01GB) Downloading: TCGA-BRCA.21024980-32e1-4b97-8f04-3d2dc520b86d.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
39975
+ ]
39976
+ },
39977
+ {
39978
+ "name": "stdout",
39979
+ "output_type": "stream",
39980
+ "text": [
39981
+ "OK\n",
39982
+ "[4849/10000] (0.02GB) Downloading: 9c5a4981-efd2-4c35-b6bd-a15fbf44f7c8.mirbase21.isoforms.quantification.txt (0.36 MB)... "
39983
+ ]
39984
+ },
39985
+ {
39986
+ "name": "stdout",
39987
+ "output_type": "stream",
39988
+ "text": [
39989
+ "OK\n",
39990
+ "[4850/10000] (0.02GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_D08_802352.grch38.seg.v2.txt (0.02 MB)... "
39991
+ ]
39992
+ },
39993
+ {
39994
+ "name": "stdout",
39995
+ "output_type": "stream",
39996
+ "text": [
39997
+ "OK\n",
39998
+ "[4851/10000] (0.02GB) Downloading: TCGA-BRCA.18114439-8780-438d-a7cc-50b73533b619.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
39999
+ ]
40000
+ },
40001
+ {
40002
+ "name": "stdout",
40003
+ "output_type": "stream",
40004
+ "text": [
40005
+ "OK\n",
40006
+ "[4852/10000] (0.02GB) Downloading: TCGA-AO-A0J9-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
40007
+ ]
40008
+ },
40009
+ {
40010
+ "name": "stdout",
40011
+ "output_type": "stream",
40012
+ "text": [
40013
+ "OK\n",
40014
+ "[4853/10000] (0.02GB) Downloading: 640ecddd-7074-40ba-8dbc-40bb33965d1d.methylation_array.sesame.level3betas.txt (12.58 MB)... "
40015
+ ]
40016
+ },
40017
+ {
40018
+ "name": "stdout",
40019
+ "output_type": "stream",
40020
+ "text": [
40021
+ "OK\n",
40022
+ "[4854/10000] (0.03GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_D06_802370.grch38.seg.v2.txt (0.04 MB)... "
40023
+ ]
40024
+ },
40025
+ {
40026
+ "name": "stdout",
40027
+ "output_type": "stream",
40028
+ "text": [
40029
+ "OK\n",
40030
+ "[4855/10000] (0.03GB) Downloading: TCGA-D8-A1XC-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
40031
+ ]
40032
+ },
40033
+ {
40034
+ "name": "stdout",
40035
+ "output_type": "stream",
40036
+ "text": [
40037
+ "OK\n",
40038
+ "[4856/10000] (0.03GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A1XC.xml (0.06 MB)... "
40039
+ ]
40040
+ },
40041
+ {
40042
+ "name": "stdout",
40043
+ "output_type": "stream",
40044
+ "text": [
40045
+ "OK\n",
40046
+ "[4857/10000] (0.03GB) Downloading: TCGA-BRCA.18114439-8780-438d-a7cc-50b73533b619.ascat2.allelic_specific.seg.txt (0.01 MB)... "
40047
+ ]
40048
+ },
40049
+ {
40050
+ "name": "stdout",
40051
+ "output_type": "stream",
40052
+ "text": [
40053
+ "OK\n",
40054
+ "[4858/10000] (0.03GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AO-A0J9.xml (0.09 MB)... "
40055
+ ]
40056
+ },
40057
+ {
40058
+ "name": "stdout",
40059
+ "output_type": "stream",
40060
+ "text": [
40061
+ "OK\n",
40062
+ "[4859/10000] (0.03GB) Downloading: TCGA-E9-A1RI-01Z-00-DX1.3259644B-0888-4B18-B16F-397D55167EAD.svs (529.09 MB)... "
40063
+ ]
40064
+ },
40065
+ {
40066
+ "name": "stdout",
40067
+ "output_type": "stream",
40068
+ "text": [
40069
+ "OK\n",
40070
+ "[4860/10000] (0.55GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_H09_667226.grch38.seg.v2.txt (0.03 MB)... "
40071
+ ]
40072
+ },
40073
+ {
40074
+ "name": "stdout",
40075
+ "output_type": "stream",
40076
+ "text": [
40077
+ "OK\n",
40078
+ "[4861/10000] (0.55GB) Downloading: 68bb844b-1bd7-4828-97d0-e284a7998cbf.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
40079
+ ]
40080
+ },
40081
+ {
40082
+ "name": "stdout",
40083
+ "output_type": "stream",
40084
+ "text": [
40085
+ "OK\n",
40086
+ "[4862/10000] (0.55GB) Downloading: a0000369-4b42-4ac9-a92f-07ba03ed2826.mirbase21.isoforms.quantification.txt (0.40 MB)... "
40087
+ ]
40088
+ },
40089
+ {
40090
+ "name": "stdout",
40091
+ "output_type": "stream",
40092
+ "text": [
40093
+ "OK\n",
40094
+ "[4863/10000] (0.55GB) Downloading: fa94f266-1ed4-440a-8d10-3c72ce4100ba.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
40095
+ ]
40096
+ },
40097
+ {
40098
+ "name": "stdout",
40099
+ "output_type": "stream",
40100
+ "text": [
40101
+ "OK\n",
40102
+ "[4864/10000] (0.56GB) Downloading: TCGA-BH-A0B5-01A-01-TSA.251b1c6f-62e7-4a8d-afd4-e6dd132948fb.svs (280.02 MB)... "
40103
+ ]
40104
+ },
40105
+ {
40106
+ "name": "stdout",
40107
+ "output_type": "stream",
40108
+ "text": [
40109
+ "OK\n",
40110
+ "[4865/10000] (0.83GB) Downloading: b1467a25-e3fa-4e63-b00d-13a80b01f4fc.wxs.aliquot_ensemble_masked.maf.gz (0.04 MB)... "
40111
+ ]
40112
+ },
40113
+ {
40114
+ "name": "stdout",
40115
+ "output_type": "stream",
40116
+ "text": [
40117
+ "OK\n",
40118
+ "[4866/10000] (0.83GB) Downloading: TCGA-BH-A0B5-01A-01-BSA.6fc7f4e6-e267-4359-b472-057f1e77ae1a.svs (224.79 MB)... "
40119
+ ]
40120
+ },
40121
+ {
40122
+ "name": "stdout",
40123
+ "output_type": "stream",
40124
+ "text": [
40125
+ "OK\n",
40126
+ "[4867/10000] (1.05GB) Downloading: a0000369-4b42-4ac9-a92f-07ba03ed2826.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40127
+ ]
40128
+ },
40129
+ {
40130
+ "name": "stdout",
40131
+ "output_type": "stream",
40132
+ "text": [
40133
+ "OK\n",
40134
+ "[4868/10000] (1.05GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_H04_747986.nocnv_grch38.seg.v2.txt (0.00 MB)... "
40135
+ ]
40136
+ },
40137
+ {
40138
+ "name": "stdout",
40139
+ "output_type": "stream",
40140
+ "text": [
40141
+ "OK\n",
40142
+ "[4869/10000] (1.05GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_H04_747986.grch38.seg.v2.txt (0.01 MB)... "
40143
+ ]
40144
+ },
40145
+ {
40146
+ "name": "stdout",
40147
+ "output_type": "stream",
40148
+ "text": [
40149
+ "OK\n",
40150
+ "[4870/10000] (1.05GB) Downloading: NULLS_p_TCGA_183_185_186_SNP_N_GenomeWideSNP_6_H01_914246.grch38.seg.v2.txt (0.03 MB)... "
40151
+ ]
40152
+ },
40153
+ {
40154
+ "name": "stdout",
40155
+ "output_type": "stream",
40156
+ "text": [
40157
+ "OK\n",
40158
+ "[4871/10000] (1.05GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09B.xml (0.09 MB)... "
40159
+ ]
40160
+ },
40161
+ {
40162
+ "name": "stdout",
40163
+ "output_type": "stream",
40164
+ "text": [
40165
+ "OK\n",
40166
+ "[4872/10000] (1.05GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_C10_628454.nocnv_grch38.seg.v2.txt (0.01 MB)... "
40167
+ ]
40168
+ },
40169
+ {
40170
+ "name": "stdout",
40171
+ "output_type": "stream",
40172
+ "text": [
40173
+ "OK\n",
40174
+ "[4873/10000] (1.05GB) Downloading: 8acb1cfe-94a5-4c37-be0c-5a124129a8ba_noid_Grn.idat (7.72 MB)... "
40175
+ ]
40176
+ },
40177
+ {
40178
+ "name": "stdout",
40179
+ "output_type": "stream",
40180
+ "text": [
40181
+ "OK\n",
40182
+ "[4874/10000] (1.06GB) Downloading: TCGA-BH-A0B5-01Z-00-DX1.742DB0E8-8EB1-47C8-B698-8E2438FB6299.svs (1074.05 MB)... "
40183
+ ]
40184
+ },
40185
+ {
40186
+ "name": "stdout",
40187
+ "output_type": "stream",
40188
+ "text": [
40189
+ "OK\n",
40190
+ "[4875/10000] (2.11GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_H09_667226.nocnv_grch38.seg.v2.txt (0.01 MB)... "
40191
+ ]
40192
+ },
40193
+ {
40194
+ "name": "stdout",
40195
+ "output_type": "stream",
40196
+ "text": [
40197
+ "OK\n",
40198
+ "[4876/10000] (2.11GB) Downloading: 0754cd06-5db6-4636-9ee6-20bb60a9b9ec.mirbase21.isoforms.quantification.txt (0.33 MB)... "
40199
+ ]
40200
+ },
40201
+ {
40202
+ "name": "stdout",
40203
+ "output_type": "stream",
40204
+ "text": [
40205
+ "OK\n",
40206
+ "[4877/10000] (2.11GB) Downloading: 04321cdf-b170-4fb9-8659-11672036214f_noid_Grn.idat (0.69 MB)... "
40207
+ ]
40208
+ },
40209
+ {
40210
+ "name": "stdout",
40211
+ "output_type": "stream",
40212
+ "text": [
40213
+ "OK\n",
40214
+ "[4878/10000] (2.11GB) Downloading: d30ca62b-ad24-49dd-be75-9b510fc57bd9.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40215
+ ]
40216
+ },
40217
+ {
40218
+ "name": "stdout",
40219
+ "output_type": "stream",
40220
+ "text": [
40221
+ "OK\n",
40222
+ "[4879/10000] (2.11GB) Downloading: GHOUL_p_TCGASNP_b85and51R_N_GenomeWideSNP_6_G04_735388.grch38.seg.v2.txt (0.03 MB)... "
40223
+ ]
40224
+ },
40225
+ {
40226
+ "name": "stdout",
40227
+ "output_type": "stream",
40228
+ "text": [
40229
+ "OK\n",
40230
+ "[4880/10000] (2.11GB) Downloading: 9310b2a3-d0eb-4139-baab-b4ed7bd0c61b.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40231
+ ]
40232
+ },
40233
+ {
40234
+ "name": "stdout",
40235
+ "output_type": "stream",
40236
+ "text": [
40237
+ "OK\n",
40238
+ "[4881/10000] (2.11GB) Downloading: TCGA-C8-A1HK-01Z-00-DX1.A15F452B-1260-4106-86D1-05F00082F0CE.svs (882.99 MB)... "
40239
+ ]
40240
+ },
40241
+ {
40242
+ "name": "stdout",
40243
+ "output_type": "stream",
40244
+ "text": [
40245
+ "OK\n",
40246
+ "[4882/10000] (2.97GB) Downloading: 97eae9cb-d360-431d-a783-7c048879199f.mirbase21.isoforms.quantification.txt (0.38 MB)... "
40247
+ ]
40248
+ },
40249
+ {
40250
+ "name": "stdout",
40251
+ "output_type": "stream",
40252
+ "text": [
40253
+ "OK\n",
40254
+ "[4883/10000] (2.97GB) Downloading: aa3d8e3d-68cb-47dc-80c0-d50917cb4878.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
40255
+ ]
40256
+ },
40257
+ {
40258
+ "name": "stdout",
40259
+ "output_type": "stream",
40260
+ "text": [
40261
+ "OK\n",
40262
+ "[4884/10000] (2.97GB) Downloading: 28069268-ebac-4f83-96bd-87d80cf4ad23_noid_Red.idat (0.69 MB)... "
40263
+ ]
40264
+ },
40265
+ {
40266
+ "name": "stdout",
40267
+ "output_type": "stream",
40268
+ "text": [
40269
+ "OK\n",
40270
+ "[4885/10000] (2.98GB) Downloading: 6f47fe3d-d42a-472b-b69a-6e4c20b69893_noid_Grn.idat (7.72 MB)... "
40271
+ ]
40272
+ },
40273
+ {
40274
+ "name": "stdout",
40275
+ "output_type": "stream",
40276
+ "text": [
40277
+ "OK\n",
40278
+ "[4886/10000] (2.98GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_B07_772154.nocnv_grch38.seg.v2.txt (0.04 MB)... "
40279
+ ]
40280
+ },
40281
+ {
40282
+ "name": "stdout",
40283
+ "output_type": "stream",
40284
+ "text": [
40285
+ "OK\n",
40286
+ "[4887/10000] (2.98GB) Downloading: TCGA-BRCA.1dce5c12-1c51-4544-b148-7d313826a491.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
40287
+ ]
40288
+ },
40289
+ {
40290
+ "name": "stdout",
40291
+ "output_type": "stream",
40292
+ "text": [
40293
+ "OK\n",
40294
+ "[4888/10000] (2.99GB) Downloading: TCGA-BRCA.74864fc6-1cd0-46b0-9a71-65f73444f7ee.ascat3.allelic_specific.seg.txt (0.01 MB)... "
40295
+ ]
40296
+ },
40297
+ {
40298
+ "name": "stdout",
40299
+ "output_type": "stream",
40300
+ "text": [
40301
+ "OK\n",
40302
+ "[4889/10000] (2.99GB) Downloading: TCGA-BRCA.74864fc6-1cd0-46b0-9a71-65f73444f7ee.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
40303
+ ]
40304
+ },
40305
+ {
40306
+ "name": "stdout",
40307
+ "output_type": "stream",
40308
+ "text": [
40309
+ "OK\n",
40310
+ "[4890/10000] (2.99GB) Downloading: ETUIS_p_TCGASNP_b80_83_N_GenomeWideSNP_6_E04_734740.grch38.seg.v2.txt (0.03 MB)... "
40311
+ ]
40312
+ },
40313
+ {
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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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+ "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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+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[4894/10000] (3.14GB) Downloading: TCGA-BRCA.bce6d618-4fdf-49fe-b3fe-87709bd79d75.ascat2.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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+ "[4895/10000] (3.14GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_B08_777998.nocnv_grch38.seg.v2.txt (0.00 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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+ "[4896/10000] (3.14GB) Downloading: 95916db3-dad7-4d8f-ab68-8342284f765b.wxs.aliquot_ensemble_masked.maf.gz (0.03 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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+ "[4897/10000] (3.14GB) Downloading: c84877aa-f986-41cf-aefd-31c789004d26_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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+ ]
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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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+ "[4899/10000] (3.15GB) Downloading: nationwidechildrens.org_clinical.TCGA-EW-A1P8.xml (0.08 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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+ "[4900/10000] (3.15GB) Downloading: TCGA-BH-A0B4-01A-21-A13C-20_RPPA_data.tsv (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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+ "[4901/10000] (3.15GB) Downloading: 541eed18-2e1d-4847-b4cb-423cec947acc.wxs.aliquot_ensemble_masked.maf.gz (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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+ "[4902/10000] (3.15GB) Downloading: TCGA-BRCA.bce6d618-4fdf-49fe-b3fe-87709bd79d75.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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+ "[4903/10000] (3.15GB) Downloading: TCGA-BH-A0B4.00C75246-4343-490D-9782-E6C0068C77B2.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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+ "[4904/10000] (3.15GB) Downloading: 3fa2c954-fdae-4808-8147-c45f3daa0f92_noid_Red.idat (0.69 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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+ "[4905/10000] (3.15GB) Downloading: c84877aa-f986-41cf-aefd-31c789004d26.methylation_array.sesame.level3betas.txt (12.38 MB)... "
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+ ]
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+ },
40433
+ {
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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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+ "[4906/10000] (3.16GB) Downloading: TCGA-AO-A03M.967287FE-7751-4A90-9465-0A1AD007061D.PDF (0.34 MB)... "
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+ ]
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+ },
40441
+ {
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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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+ "[4907/10000] (3.16GB) Downloading: 97746d64-3ec5-47a7-b029-29608a77f9a4_noid_Red.idat (7.72 MB)... "
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+ ]
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+ },
40449
+ {
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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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+ "[4908/10000] (3.17GB) Downloading: nationwidechildrens.org_clinical.TCGA-AO-A03M.xml (0.09 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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+ "[4909/10000] (3.17GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G10_628528.grch38.seg.v2.txt (0.03 MB)... "
40463
+ ]
40464
+ },
40465
+ {
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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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+ "[4910/10000] (3.17GB) Downloading: ETUIS_p_TCGASNP_b80_83_N_GenomeWideSNP_6_D05_734626.grch38.seg.v2.txt (0.03 MB)... "
40471
+ ]
40472
+ },
40473
+ {
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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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+ "[4911/10000] (3.17GB) Downloading: 733ed3fd-87da-45ba-b95d-d539c784c702.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40479
+ ]
40480
+ },
40481
+ {
40482
+ "name": "stdout",
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+ "output_type": "stream",
40484
+ "text": [
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+ "OK\n",
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+ "[4912/10000] (3.17GB) Downloading: 0ee0d9df-0a66-4ea9-9535-7ef8cab950de.mirbase21.isoforms.quantification.txt (0.30 MB)... "
40487
+ ]
40488
+ },
40489
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
40492
+ "text": [
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+ "OK\n",
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+ "[4913/10000] (3.17GB) Downloading: 0ee0d9df-0a66-4ea9-9535-7ef8cab950de.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40495
+ ]
40496
+ },
40497
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
40500
+ "text": [
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+ "OK\n",
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+ "[4914/10000] (3.17GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-3C-AALK.xml (0.04 MB)... "
40503
+ ]
40504
+ },
40505
+ {
40506
+ "name": "stdout",
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+ "output_type": "stream",
40508
+ "text": [
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+ "OK\n",
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+ "[4915/10000] (3.17GB) Downloading: ae8996bd-b0b7-4f9b-91fa-606f95d49f8c.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
40511
+ ]
40512
+ },
40513
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
40516
+ "text": [
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+ "OK\n",
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+ "[4916/10000] (3.18GB) Downloading: 7b6a6685-7bf4-40ad-8164-07b38fa47a93.methylation_array.sesame.level3betas.txt (0.73 MB)... "
40519
+ ]
40520
+ },
40521
+ {
40522
+ "name": "stdout",
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+ "output_type": "stream",
40524
+ "text": [
40525
+ "OK\n",
40526
+ "[4917/10000] (3.18GB) Downloading: TCGA-AO-A12H-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
40527
+ ]
40528
+ },
40529
+ {
40530
+ "name": "stdout",
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+ "output_type": "stream",
40532
+ "text": [
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+ "OK\n",
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+ "[4918/10000] (3.18GB) Downloading: 05ebe1e0-bf0d-4622-bc45-b0eacffdebcc.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
40535
+ ]
40536
+ },
40537
+ {
40538
+ "name": "stdout",
40539
+ "output_type": "stream",
40540
+ "text": [
40541
+ "OK\n",
40542
+ "[4919/10000] (3.18GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H11_844898.nocnv_grch38.seg.v2.txt (0.00 MB)... "
40543
+ ]
40544
+ },
40545
+ {
40546
+ "name": "stdout",
40547
+ "output_type": "stream",
40548
+ "text": [
40549
+ "OK\n",
40550
+ "[4920/10000] (3.18GB) Downloading: TAKEN_p_TCGAb_379_400_FFPE_NSP_GenomeWideSNP_6_B07_1513332.grch38.seg.v2.txt (0.03 MB)... "
40551
+ ]
40552
+ },
40553
+ {
40554
+ "name": "stdout",
40555
+ "output_type": "stream",
40556
+ "text": [
40557
+ "OK\n",
40558
+ "[4921/10000] (3.18GB) Downloading: a5ac8fac-e653-4767-8629-82a8bdccc0b7_noid_Grn.idat (7.72 MB)... "
40559
+ ]
40560
+ },
40561
+ {
40562
+ "name": "stdout",
40563
+ "output_type": "stream",
40564
+ "text": [
40565
+ "OK\n",
40566
+ "[4922/10000] (3.19GB) Downloading: TCGA-AC-A2FK.1CF3FA64-EAE6-4A18-9B51-F5980A885371.PDF (0.19 MB)... "
40567
+ ]
40568
+ },
40569
+ {
40570
+ "name": "stdout",
40571
+ "output_type": "stream",
40572
+ "text": [
40573
+ "OK\n",
40574
+ "[4923/10000] (3.19GB) Downloading: nationwidechildrens.org_clinical.TCGA-3C-AALK.xml (0.09 MB)... "
40575
+ ]
40576
+ },
40577
+ {
40578
+ "name": "stdout",
40579
+ "output_type": "stream",
40580
+ "text": [
40581
+ "OK\n",
40582
+ "[4924/10000] (3.19GB) Downloading: nationwidechildrens.org_clinical.TCGA-AC-A2FK.xml (0.08 MB)... "
40583
+ ]
40584
+ },
40585
+ {
40586
+ "name": "stdout",
40587
+ "output_type": "stream",
40588
+ "text": [
40589
+ "OK\n",
40590
+ "[4925/10000] (3.19GB) Downloading: TAKEN_p_TCGAb_379_400_FFPE_NSP_GenomeWideSNP_6_B08_1513152.grch38.seg.v2.txt (0.03 MB)... "
40591
+ ]
40592
+ },
40593
+ {
40594
+ "name": "stdout",
40595
+ "output_type": "stream",
40596
+ "text": [
40597
+ "OK\n",
40598
+ "[4926/10000] (3.19GB) Downloading: 1b79fa1c-4c59-4bc8-8e77-90a700d73be8_noid_Grn.idat (7.72 MB)... "
40599
+ ]
40600
+ },
40601
+ {
40602
+ "name": "stdout",
40603
+ "output_type": "stream",
40604
+ "text": [
40605
+ "OK\n",
40606
+ "[4927/10000] (3.20GB) Downloading: 5a535c49-d42e-43c6-9d32-dc76f28d4f0f_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.03 MB)... "
40607
+ ]
40608
+ },
40609
+ {
40610
+ "name": "stdout",
40611
+ "output_type": "stream",
40612
+ "text": [
40613
+ "OK\n",
40614
+ "[4928/10000] (3.20GB) Downloading: TCGA-AC-A2FK-11A-01-TSA.5CBEF273-619D-47FD-844C-545B3253A09E.svs (37.52 MB)... "
40615
+ ]
40616
+ },
40617
+ {
40618
+ "name": "stdout",
40619
+ "output_type": "stream",
40620
+ "text": [
40621
+ "OK\n",
40622
+ "[4929/10000] (3.23GB) Downloading: TCGA-AO-A12H-01A-01-BSA.eb4b965d-5a91-4c8b-a61d-177b895d2fe5.svs (203.66 MB)... "
40623
+ ]
40624
+ },
40625
+ {
40626
+ "name": "stdout",
40627
+ "output_type": "stream",
40628
+ "text": [
40629
+ "OK\n",
40630
+ "[4930/10000] (3.43GB) Downloading: TCGA-3C-AALK-01A-11D-A89F-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.03 MB)... "
40631
+ ]
40632
+ },
40633
+ {
40634
+ "name": "stdout",
40635
+ "output_type": "stream",
40636
+ "text": [
40637
+ "OK\n",
40638
+ "[4931/10000] (3.43GB) Downloading: TCGA-AC-A2FK-11A-02-TSB.5EDF62BD-0B8E-452E-865F-FD8BFC5C0240.svs (24.30 MB)... "
40639
+ ]
40640
+ },
40641
+ {
40642
+ "name": "stdout",
40643
+ "output_type": "stream",
40644
+ "text": [
40645
+ "OK\n",
40646
+ "[4932/10000] (3.46GB) Downloading: TCGA-AC-A2FK-01A-01-TS1.807C5D36-7171-495C-B6AB-8951B77EAD21.svs (384.19 MB)... "
40647
+ ]
40648
+ },
40649
+ {
40650
+ "name": "stdout",
40651
+ "output_type": "stream",
40652
+ "text": [
40653
+ "OK\n",
40654
+ "[4933/10000] (3.83GB) Downloading: TCGA-AC-A2FK-01Z-00-DX1.033F3C27-9860-4EF3-9330-37DE5EC45724.svs (116.82 MB)... "
40655
+ ]
40656
+ },
40657
+ {
40658
+ "name": "stdout",
40659
+ "output_type": "stream",
40660
+ "text": [
40661
+ "OK\n",
40662
+ "[4934/10000] (3.95GB) Downloading: TCGA-BRCA.643d3847-9b4e-44c3-ae8e-965a14b19a55.gene_level_copy_number.v36.tsv (3.29 MB)... "
40663
+ ]
40664
+ },
40665
+ {
40666
+ "name": "stdout",
40667
+ "output_type": "stream",
40668
+ "text": [
40669
+ "OK\n",
40670
+ "[4935/10000] (3.95GB) Downloading: TCGA-BRCA.556981d5-78ea-4e3e-ad02-4d9f71729caa.gene_level_copy_number.v36.tsv (3.29 MB)... "
40671
+ ]
40672
+ },
40673
+ {
40674
+ "name": "stdout",
40675
+ "output_type": "stream",
40676
+ "text": [
40677
+ "OK\n",
40678
+ "[4936/10000] (3.95GB) Downloading: TCGA-BRCA.643d3847-9b4e-44c3-ae8e-965a14b19a55.ascat3.allelic_specific.seg.txt (0.00 MB)... "
40679
+ ]
40680
+ },
40681
+ {
40682
+ "name": "stdout",
40683
+ "output_type": "stream",
40684
+ "text": [
40685
+ "OK\n",
40686
+ "[4937/10000] (3.95GB) Downloading: TCGA-BRCA.643d3847-9b4e-44c3-ae8e-965a14b19a55.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
40687
+ ]
40688
+ },
40689
+ {
40690
+ "name": "stdout",
40691
+ "output_type": "stream",
40692
+ "text": [
40693
+ "OK\n",
40694
+ "[4938/10000] (3.95GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_C03_731064.grch38.seg.v2.txt (0.02 MB)... "
40695
+ ]
40696
+ },
40697
+ {
40698
+ "name": "stdout",
40699
+ "output_type": "stream",
40700
+ "text": [
40701
+ "OK\n",
40702
+ "[4939/10000] (3.95GB) Downloading: TCGA-GM-A2DK-01Z-00-DX1.4F81A585-9549-454C-8E15-2E4545795460.svs (1117.02 MB)... "
40703
+ ]
40704
+ },
40705
+ {
40706
+ "name": "stdout",
40707
+ "output_type": "stream",
40708
+ "text": [
40709
+ "OK\n",
40710
+ "[4940/10000] (5.05GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_F08_844760.grch38.seg.v2.txt (0.02 MB)... "
40711
+ ]
40712
+ },
40713
+ {
40714
+ "name": "stdout",
40715
+ "output_type": "stream",
40716
+ "text": [
40717
+ "OK\n",
40718
+ "[4941/10000] (5.05GB) Downloading: TCGA-GM-A2DK-01A-11-A24A-20_RPPA_data.tsv (0.02 MB)... "
40719
+ ]
40720
+ },
40721
+ {
40722
+ "name": "stdout",
40723
+ "output_type": "stream",
40724
+ "text": [
40725
+ "OK\n",
40726
+ "[4942/10000] (5.05GB) Downloading: 018e2953-7d05-4843-bb8a-bd65a209ed1c.wgs.ASCAT.gene_level.copy_number_variation.tsv (3.28 MB)... "
40727
+ ]
40728
+ },
40729
+ {
40730
+ "name": "stdout",
40731
+ "output_type": "stream",
40732
+ "text": [
40733
+ "OK\n",
40734
+ "[4943/10000] (5.05GB) Downloading: 2ae456c7-57fa-4146-9b29-2d4129f0cf7c.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
40735
+ ]
40736
+ },
40737
+ {
40738
+ "name": "stdout",
40739
+ "output_type": "stream",
40740
+ "text": [
40741
+ "OK\n",
40742
+ "[4944/10000] (5.05GB) Downloading: TCGA-BRCA.d7061bf4-68ed-452b-93d0-46005a916bd6.gene_level_copy_number.v36.tsv (3.29 MB)... "
40743
+ ]
40744
+ },
40745
+ {
40746
+ "name": "stdout",
40747
+ "output_type": "stream",
40748
+ "text": [
40749
+ "OK\n",
40750
+ "[4945/10000] (5.06GB) Downloading: TCGA-A8-A06N-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
40751
+ ]
40752
+ },
40753
+ {
40754
+ "name": "stdout",
40755
+ "output_type": "stream",
40756
+ "text": [
40757
+ "OK\n",
40758
+ "[4946/10000] (5.06GB) Downloading: 6113547a-c7be-4ea5-a17d-a6baef499c58.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40759
+ ]
40760
+ },
40761
+ {
40762
+ "name": "stdout",
40763
+ "output_type": "stream",
40764
+ "text": [
40765
+ "OK\n",
40766
+ "[4947/10000] (5.06GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_H06_844850.nocnv_grch38.seg.v2.txt (0.02 MB)... "
40767
+ ]
40768
+ },
40769
+ {
40770
+ "name": "stdout",
40771
+ "output_type": "stream",
40772
+ "text": [
40773
+ "OK\n",
40774
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40775
+ ]
40776
+ },
40777
+ {
40778
+ "name": "stdout",
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+ "output_type": "stream",
40780
+ "text": [
40781
+ "OK\n",
40782
+ "[4949/10000] (5.06GB) Downloading: nationwidechildrens.org_clinical.TCGA-GM-A2DK.xml (0.06 MB)... "
40783
+ ]
40784
+ },
40785
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
40788
+ "text": [
40789
+ "OK\n",
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+ "[4950/10000] (5.06GB) Downloading: 91492211-9a34-4a0c-bcbd-594d560a7a77.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
40791
+ ]
40792
+ },
40793
+ {
40794
+ "name": "stdout",
40795
+ "output_type": "stream",
40796
+ "text": [
40797
+ "OK\n",
40798
+ "[4951/10000] (5.06GB) Downloading: TCGA-AC-A6IV.5B978086-7443-4721-854B-877CE0FC10C0.PDF (0.36 MB)... "
40799
+ ]
40800
+ },
40801
+ {
40802
+ "name": "stdout",
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+ "output_type": "stream",
40804
+ "text": [
40805
+ "OK\n",
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+ "[4952/10000] (5.06GB) Downloading: TCGA-BRCA.d7061bf4-68ed-452b-93d0-46005a916bd6.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
40807
+ ]
40808
+ },
40809
+ {
40810
+ "name": "stdout",
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+ "output_type": "stream",
40812
+ "text": [
40813
+ "OK\n",
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+ "[4953/10000] (5.06GB) Downloading: TCGA-BRCA.d7061bf4-68ed-452b-93d0-46005a916bd6.ascat2.allelic_specific.seg.txt (0.01 MB)... "
40815
+ ]
40816
+ },
40817
+ {
40818
+ "name": "stdout",
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+ "output_type": "stream",
40820
+ "text": [
40821
+ "OK\n",
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+ "[4954/10000] (5.06GB) Downloading: 7fb3bd77-6658-4916-8c4a-a76823b41ba0.methylation_array.sesame.level3betas.txt (12.48 MB)... "
40823
+ ]
40824
+ },
40825
+ {
40826
+ "name": "stdout",
40827
+ "output_type": "stream",
40828
+ "text": [
40829
+ "OK\n",
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+ "[4955/10000] (5.07GB) Downloading: TCGA-BH-A0BL-01A-11D-A930-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.08 MB)... "
40831
+ ]
40832
+ },
40833
+ {
40834
+ "name": "stdout",
40835
+ "output_type": "stream",
40836
+ "text": [
40837
+ "OK\n",
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+ "[4956/10000] (5.07GB) Downloading: 0ce5898e-6390-4be2-81c9-a82a8bb03bb2_noid_Grn.idat (0.69 MB)... "
40839
+ ]
40840
+ },
40841
+ {
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+ "name": "stdout",
40843
+ "output_type": "stream",
40844
+ "text": [
40845
+ "OK\n",
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+ "[4957/10000] (5.07GB) Downloading: 2f79bace-d26e-4929-9ef2-722229c5de95.methylation_array.sesame.level3betas.txt (0.74 MB)... "
40847
+ ]
40848
+ },
40849
+ {
40850
+ "name": "stdout",
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+ "output_type": "stream",
40852
+ "text": [
40853
+ "OK\n",
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+ "[4958/10000] (5.07GB) Downloading: TCGA-BH-A0BL-01A-01-BSA.f8277eba-2d30-4c5f-ae15-94daba29503a.svs (257.11 MB)... "
40855
+ ]
40856
+ },
40857
+ {
40858
+ "name": "stdout",
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+ "output_type": "stream",
40860
+ "text": [
40861
+ "OK\n",
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+ "[4959/10000] (5.32GB) Downloading: TCGA-BRCA.52fad299-e76e-48e7-a770-c7737f5cd89c.ascat2.allelic_specific.seg.txt (0.01 MB)... "
40863
+ ]
40864
+ },
40865
+ {
40866
+ "name": "stdout",
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+ "output_type": "stream",
40868
+ "text": [
40869
+ "OK\n",
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+ "[4960/10000] (5.32GB) Downloading: TCGA-BRCA.833793a9-9708-4363-ac40-ce7960a5e13d.ascat2.allelic_specific.seg.txt (0.01 MB)... "
40871
+ ]
40872
+ },
40873
+ {
40874
+ "name": "stdout",
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+ "output_type": "stream",
40876
+ "text": [
40877
+ "OK\n",
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+ "[4961/10000] (5.32GB) Downloading: TCGA-BH-A0BL-01Z-00-DX1.D5A413B0-2141-4A6F-A671-6C5EA8641D25.svs (1025.03 MB)... "
40879
+ ]
40880
+ },
40881
+ {
40882
+ "name": "stdout",
40883
+ "output_type": "stream",
40884
+ "text": [
40885
+ "OK\n",
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+ "[4962/10000] (6.33GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_E04_1373728.grch38.seg.v2.txt (0.03 MB)... "
40887
+ ]
40888
+ },
40889
+ {
40890
+ "name": "stdout",
40891
+ "output_type": "stream",
40892
+ "text": [
40893
+ "OK\n",
40894
+ "[4963/10000] (6.33GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A0BL.xml (0.02 MB)... "
40895
+ ]
40896
+ },
40897
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
40900
+ "text": [
40901
+ "OK\n",
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+ "[4964/10000] (6.33GB) Downloading: TCGA-BH-A0GZ.C956B4B1-99E6-4823-886A-FA8FCD1E3E4D.PDF (0.09 MB)... "
40903
+ ]
40904
+ },
40905
+ {
40906
+ "name": "stdout",
40907
+ "output_type": "stream",
40908
+ "text": [
40909
+ "OK\n",
40910
+ "[4965/10000] (6.33GB) Downloading: TCGA-BRCA.52fad299-e76e-48e7-a770-c7737f5cd89c.gene_level_copy_number.v36.tsv (3.29 MB)... "
40911
+ ]
40912
+ },
40913
+ {
40914
+ "name": "stdout",
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+ "output_type": "stream",
40916
+ "text": [
40917
+ "OK\n",
40918
+ "[4966/10000] (6.33GB) Downloading: 0ce5898e-6390-4be2-81c9-a82a8bb03bb2_noid_Red.idat (0.69 MB)... "
40919
+ ]
40920
+ },
40921
+ {
40922
+ "name": "stdout",
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+ "output_type": "stream",
40924
+ "text": [
40925
+ "OK\n",
40926
+ "[4967/10000] (6.33GB) Downloading: nationwidechildrens.org_clinical.TCGA-AC-A6IV.xml (0.06 MB)... "
40927
+ ]
40928
+ },
40929
+ {
40930
+ "name": "stdout",
40931
+ "output_type": "stream",
40932
+ "text": [
40933
+ "OK\n",
40934
+ "[4968/10000] (6.33GB) Downloading: 333e6603-1fc8-4ce6-bae0-dba0fc46563b.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
40935
+ ]
40936
+ },
40937
+ {
40938
+ "name": "stdout",
40939
+ "output_type": "stream",
40940
+ "text": [
40941
+ "OK\n",
40942
+ "[4969/10000] (6.33GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_D03_735066.grch38.seg.v2.txt (0.02 MB)... "
40943
+ ]
40944
+ },
40945
+ {
40946
+ "name": "stdout",
40947
+ "output_type": "stream",
40948
+ "text": [
40949
+ "OK\n",
40950
+ "[4970/10000] (6.33GB) Downloading: 1d55d974-524f-4045-83ea-ffb073a57bdf.mirbase21.mirnas.quantification.txt (0.05 MB)... "
40951
+ ]
40952
+ },
40953
+ {
40954
+ "name": "stdout",
40955
+ "output_type": "stream",
40956
+ "text": [
40957
+ "OK\n",
40958
+ "[4971/10000] (6.33GB) Downloading: 03f9932a-cfee-4671-8128-0110f58168e8.mirbase21.isoforms.quantification.txt (0.42 MB)... "
40959
+ ]
40960
+ },
40961
+ {
40962
+ "name": "stdout",
40963
+ "output_type": "stream",
40964
+ "text": [
40965
+ "OK\n",
40966
+ "[4972/10000] (6.33GB) Downloading: COPAL_p_TCGAb_337_338_339_NSP_GenomeWideSNP_6_E05_1373588.nocnv_grch38.seg.v2.txt (0.00 MB)... "
40967
+ ]
40968
+ },
40969
+ {
40970
+ "name": "stdout",
40971
+ "output_type": "stream",
40972
+ "text": [
40973
+ "OK\n",
40974
+ "[4973/10000] (6.33GB) Downloading: b85209a5-128a-4aff-83d4-1ab336d82b95.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
40975
+ ]
40976
+ },
40977
+ {
40978
+ "name": "stdout",
40979
+ "output_type": "stream",
40980
+ "text": [
40981
+ "OK\n",
40982
+ "[4974/10000] (6.33GB) Downloading: TCGA-A2-A0CV.FBDDD9EE-0A5C-4CAB-9EB3-48B6431A9A84.PDF (0.22 MB)... "
40983
+ ]
40984
+ },
40985
+ {
40986
+ "name": "stdout",
40987
+ "output_type": "stream",
40988
+ "text": [
40989
+ "OK\n",
40990
+ "[4975/10000] (6.33GB) Downloading: TCGA-A2-A0CV-01A-21-A13B-20_RPPA_data.tsv (0.02 MB)... "
40991
+ ]
40992
+ },
40993
+ {
40994
+ "name": "stdout",
40995
+ "output_type": "stream",
40996
+ "text": [
40997
+ "OK\n",
40998
+ "[4976/10000] (6.33GB) Downloading: d6c112bb-b3ff-4132-a0ef-7eb32ab51655_noid_Red.idat (0.69 MB)... "
40999
+ ]
41000
+ },
41001
+ {
41002
+ "name": "stdout",
41003
+ "output_type": "stream",
41004
+ "text": [
41005
+ "OK\n",
41006
+ "[4977/10000] (6.34GB) Downloading: 03f9932a-cfee-4671-8128-0110f58168e8.mirbase21.mirnas.quantification.txt (0.05 MB)... "
41007
+ ]
41008
+ },
41009
+ {
41010
+ "name": "stdout",
41011
+ "output_type": "stream",
41012
+ "text": [
41013
+ "OK\n",
41014
+ "[4978/10000] (6.34GB) Downloading: TCGA-BRCA.833793a9-9708-4363-ac40-ce7960a5e13d.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41015
+ ]
41016
+ },
41017
+ {
41018
+ "name": "stdout",
41019
+ "output_type": "stream",
41020
+ "text": [
41021
+ "OK\n",
41022
+ "[4979/10000] (6.34GB) Downloading: TCGA-BRCA.970819ce-f25d-4f05-98d7-7b3a22b92558.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41023
+ ]
41024
+ },
41025
+ {
41026
+ "name": "stdout",
41027
+ "output_type": "stream",
41028
+ "text": [
41029
+ "OK\n",
41030
+ "[4980/10000] (6.34GB) Downloading: TCGA-A2-A0CV-01A-03-TSC.3b9baf94-f5f8-4949-a017-4cd1152f87c5.svs (204.79 MB)... "
41031
+ ]
41032
+ },
41033
+ {
41034
+ "name": "stdout",
41035
+ "output_type": "stream",
41036
+ "text": [
41037
+ "OK\n",
41038
+ "[4981/10000] (6.54GB) Downloading: 45e18fb6-931d-4d0b-845c-8fffe719eb2a_noid_Grn.idat (7.72 MB)... "
41039
+ ]
41040
+ },
41041
+ {
41042
+ "name": "stdout",
41043
+ "output_type": "stream",
41044
+ "text": [
41045
+ "OK\n",
41046
+ "[4982/10000] (6.55GB) Downloading: TCGA-BRCA.93f09df2-f3c1-43d6-9c79-4751740bfa45.gene_level_copy_number.v36.tsv (3.29 MB)... "
41047
+ ]
41048
+ },
41049
+ {
41050
+ "name": "stdout",
41051
+ "output_type": "stream",
41052
+ "text": [
41053
+ "OK\n",
41054
+ "[4983/10000] (6.55GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0GZ.xml (0.07 MB)... "
41055
+ ]
41056
+ },
41057
+ {
41058
+ "name": "stdout",
41059
+ "output_type": "stream",
41060
+ "text": [
41061
+ "OK\n",
41062
+ "[4984/10000] (6.55GB) Downloading: de320d9b-50c9-4d8c-84b9-8ad7ef5a3643_noid_Red.idat (0.69 MB)... "
41063
+ ]
41064
+ },
41065
+ {
41066
+ "name": "stdout",
41067
+ "output_type": "stream",
41068
+ "text": [
41069
+ "OK\n",
41070
+ "[4985/10000] (6.55GB) Downloading: d6c112bb-b3ff-4132-a0ef-7eb32ab51655_noid_Grn.idat (0.69 MB)... "
41071
+ ]
41072
+ },
41073
+ {
41074
+ "name": "stdout",
41075
+ "output_type": "stream",
41076
+ "text": [
41077
+ "OK\n",
41078
+ "[4986/10000] (6.55GB) Downloading: 289486b7-8213-4229-a5fe-1f2a9a25e730.mirbase21.mirnas.quantification.txt (0.05 MB)... "
41079
+ ]
41080
+ },
41081
+ {
41082
+ "name": "stdout",
41083
+ "output_type": "stream",
41084
+ "text": [
41085
+ "OK\n",
41086
+ "[4987/10000] (6.55GB) Downloading: TCGA-BRCA.8c3a83e9-071e-429b-88c7-21d4b2748ba3.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
41087
+ ]
41088
+ },
41089
+ {
41090
+ "name": "stdout",
41091
+ "output_type": "stream",
41092
+ "text": [
41093
+ "OK\n",
41094
+ "[4988/10000] (6.56GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_H08_667018.grch38.seg.v2.txt (0.06 MB)... "
41095
+ ]
41096
+ },
41097
+ {
41098
+ "name": "stdout",
41099
+ "output_type": "stream",
41100
+ "text": [
41101
+ "OK\n",
41102
+ "[4989/10000] (6.56GB) Downloading: f4a97737-76b9-4b64-adb4-c3af80c9b09a.mirbase21.isoforms.quantification.txt (0.43 MB)... "
41103
+ ]
41104
+ },
41105
+ {
41106
+ "name": "stdout",
41107
+ "output_type": "stream",
41108
+ "text": [
41109
+ "OK\n",
41110
+ "[4990/10000] (6.56GB) Downloading: nationwidechildrens.org_clinical.TCGA-C8-A12Q.xml (0.05 MB)... "
41111
+ ]
41112
+ },
41113
+ {
41114
+ "name": "stdout",
41115
+ "output_type": "stream",
41116
+ "text": [
41117
+ "OK\n",
41118
+ "[4991/10000] (6.56GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_H08_667018.nocnv_grch38.seg.v2.txt (0.03 MB)... "
41119
+ ]
41120
+ },
41121
+ {
41122
+ "name": "stdout",
41123
+ "output_type": "stream",
41124
+ "text": [
41125
+ "OK\n",
41126
+ "[4992/10000] (6.56GB) Downloading: d15a2772-6752-414d-8d5a-89fc36cc21c1.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
41127
+ ]
41128
+ },
41129
+ {
41130
+ "name": "stdout",
41131
+ "output_type": "stream",
41132
+ "text": [
41133
+ "OK\n",
41134
+ "[4993/10000] (6.56GB) Downloading: TCGA-C8-A12Q-01A-01-BSA.0ca5b171-d61d-4e6d-b365-4cd6bd288aec.svs (382.91 MB)... "
41135
+ ]
41136
+ },
41137
+ {
41138
+ "name": "stdout",
41139
+ "output_type": "stream",
41140
+ "text": [
41141
+ "OK\n",
41142
+ "[4994/10000] (6.93GB) Downloading: 0f3b932e-de72-483f-9ef6-74ae972637bd.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
41143
+ ]
41144
+ },
41145
+ {
41146
+ "name": "stdout",
41147
+ "output_type": "stream",
41148
+ "text": [
41149
+ "OK\n",
41150
+ "[4995/10000] (6.94GB) Downloading: TCGA-C8-A12Q.90AF32F0-5684-4D5B-B619-2B12DA3823C6.PDF (0.21 MB)... "
41151
+ ]
41152
+ },
41153
+ {
41154
+ "name": "stdout",
41155
+ "output_type": "stream",
41156
+ "text": [
41157
+ "OK\n",
41158
+ "[4996/10000] (6.94GB) Downloading: 289486b7-8213-4229-a5fe-1f2a9a25e730.mirbase21.isoforms.quantification.txt (0.21 MB)... "
41159
+ ]
41160
+ },
41161
+ {
41162
+ "name": "stdout",
41163
+ "output_type": "stream",
41164
+ "text": [
41165
+ "OK\n",
41166
+ "[4997/10000] (6.94GB) Downloading: TCGA-A2-A0EY-01A-21-A13C-20_RPPA_data.tsv (0.02 MB)... "
41167
+ ]
41168
+ },
41169
+ {
41170
+ "name": "stdout",
41171
+ "output_type": "stream",
41172
+ "text": [
41173
+ "OK\n",
41174
+ "[4998/10000] (6.94GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A0CV.xml (0.06 MB)... "
41175
+ ]
41176
+ },
41177
+ {
41178
+ "name": "stdout",
41179
+ "output_type": "stream",
41180
+ "text": [
41181
+ "OK\n",
41182
+ "[4999/10000] (6.94GB) Downloading: 620a34a1-f5c8-4702-ba7c-3c5e35e15945.methylation_array.sesame.level3betas.txt (0.72 MB)... "
41183
+ ]
41184
+ },
41185
+ {
41186
+ "name": "stdout",
41187
+ "output_type": "stream",
41188
+ "text": [
41189
+ "OK\n",
41190
+ "[5000/10000] (6.94GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_G12_666868.grch38.seg.v2.txt (0.03 MB)... "
41191
+ ]
41192
+ },
41193
+ {
41194
+ "name": "stdout",
41195
+ "output_type": "stream",
41196
+ "text": [
41197
+ "OK\n",
41198
+ "[5001/10000] (6.94GB) Downloading: URAEI_p_TCGASNP_b85_N_GenomeWideSNP_6_C11_735086.nocnv_grch38.seg.v2.txt (0.01 MB)... "
41199
+ ]
41200
+ },
41201
+ {
41202
+ "name": "stdout",
41203
+ "output_type": "stream",
41204
+ "text": [
41205
+ "OK\n",
41206
+ "[5002/10000] (6.94GB) Downloading: de320d9b-50c9-4d8c-84b9-8ad7ef5a3643.methylation_array.sesame.level3betas.txt (0.74 MB)... "
41207
+ ]
41208
+ },
41209
+ {
41210
+ "name": "stdout",
41211
+ "output_type": "stream",
41212
+ "text": [
41213
+ "OK\n",
41214
+ "[5003/10000] (6.94GB) Downloading: nationwidechildrens.org_ssf.TCGA-C8-A12Q.xml (0.01 MB)... "
41215
+ ]
41216
+ },
41217
+ {
41218
+ "name": "stdout",
41219
+ "output_type": "stream",
41220
+ "text": [
41221
+ "OK\n",
41222
+ "[5004/10000] (6.94GB) Downloading: TCGA-BRCA.93f09df2-f3c1-43d6-9c79-4751740bfa45.ascat2.allelic_specific.seg.txt (0.02 MB)... "
41223
+ ]
41224
+ },
41225
+ {
41226
+ "name": "stdout",
41227
+ "output_type": "stream",
41228
+ "text": [
41229
+ "OK\n",
41230
+ "[5005/10000] (6.94GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A2-A0T2.xml (0.07 MB)... "
41231
+ ]
41232
+ },
41233
+ {
41234
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[5006/10000] (6.94GB) Downloading: 620a34a1-f5c8-4702-ba7c-3c5e35e15945_noid_Grn.idat (0.69 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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+ "[5007/10000] (6.94GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AR-A1AL.xml (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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+ "[5008/10000] (6.94GB) Downloading: a93d7d12-9f06-4c31-bc6f-e131c038a82e.methylation_array.sesame.level3betas.txt (12.34 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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+ "[5009/10000] (6.95GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_C07_698036.nocnv_grch38.seg.v2.txt (0.02 MB)... "
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+ ]
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+ },
41265
+ {
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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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+ "[5010/10000] (6.95GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_G04_747978.grch38.seg.v2.txt (0.03 MB)... "
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+ ]
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+ },
41273
+ {
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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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+ "[5011/10000] (6.95GB) Downloading: e39fbb6b-c44d-4a22-81f8-d688a57e2212.mirbase21.isoforms.quantification.txt (0.33 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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+ "[5012/10000] (6.95GB) Downloading: 342bbbcb-5c42-4c9b-a779-f5925004a889.mirbase21.isoforms.quantification.txt (0.34 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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+ "[5013/10000] (6.95GB) Downloading: TCGA-A2-A0T2-01A-01-TSA.8595967b-5bf7-447f-9310-10b53a1c1dfa.svs (221.38 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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+ "[5014/10000] (7.17GB) Downloading: TCGA-A2-A0T2-01Z-00-DX1.29A5C4C8-6AE8-44EE-98C2-ACBCBFBE9D60.svs (1897.40 MB)... "
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+ ]
41304
+ },
41305
+ {
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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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+ "[5015/10000] (9.02GB) Downloading: f5b6634d-5891-4550-bde6-7a0383e5e3da.rna_seq.augmented_star_gene_counts.tsv (4.06 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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+ "[5016/10000] (9.02GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_G04_747978.nocnv_grch38.seg.v2.txt (0.00 MB)... "
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+ ]
41320
+ },
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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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+ "[5017/10000] (9.02GB) Downloading: 342bbbcb-5c42-4c9b-a779-f5925004a889.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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+ "[5018/10000] (9.02GB) Downloading: a9dc2469-5671-4c9a-8d51-c5dd72ba08dd_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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+ "[5019/10000] (9.03GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_G05_747932.nocnv_grch38.seg.v2.txt (0.00 MB)... "
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+ ]
41344
+ },
41345
+ {
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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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+ "[5020/10000] (9.03GB) Downloading: TCGA-A2-A0T2-01A-01-BSA.3613219b-687b-419f-ac8f-33b668b72446.svs (177.37 MB)... "
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+ ]
41352
+ },
41353
+ {
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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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+ "[5021/10000] (9.20GB) Downloading: TCGA-BRCA.9c918c56-fd45-443d-8137-00685de9f0c3.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
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+ },
41361
+ {
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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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+ "[5022/10000] (9.21GB) Downloading: SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_G05_697994.nocnv_grch38.seg.v2.txt (0.00 MB)... "
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+ ]
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+ },
41369
+ {
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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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+ "[5023/10000] (9.21GB) Downloading: TCGA-BRCA.9c918c56-fd45-443d-8137-00685de9f0c3.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41375
+ ]
41376
+ },
41377
+ {
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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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+ "[5024/10000] (9.21GB) Downloading: a9dc2469-5671-4c9a-8d51-c5dd72ba08dd.methylation_array.sesame.level3betas.txt (12.37 MB)... "
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+ ]
41384
+ },
41385
+ {
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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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+ "[5025/10000] (9.22GB) Downloading: JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_G05_747932.grch38.seg.v2.txt (0.02 MB)... "
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+ ]
41392
+ },
41393
+ {
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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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+ "[5026/10000] (9.22GB) Downloading: TCGA-AR-A1AL-01A-11D-A895-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.02 MB)... "
41399
+ ]
41400
+ },
41401
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
41404
+ "text": [
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+ "OK\n",
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+ "[5027/10000] (9.22GB) Downloading: TCGA-AR-A1AL-01A-02-TSB.a5a169e3-b2b7-4a89-95fb-ee01621d32ee.svs (287.54 MB)... "
41407
+ ]
41408
+ },
41409
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
41412
+ "text": [
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+ "OK\n",
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+ "[5028/10000] (9.50GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_G07_730974.nocnv_grch38.seg.v2.txt (0.00 MB)... "
41415
+ ]
41416
+ },
41417
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
41420
+ "text": [
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+ "OK\n",
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+ "[5029/10000] (9.50GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_C04_799878.nocnv_grch38.seg.v2.txt (0.01 MB)... "
41423
+ ]
41424
+ },
41425
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
41428
+ "text": [
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+ "OK\n",
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+ "[5030/10000] (9.50GB) Downloading: 8da6e66f-f014-4652-af13-c650c72c98ba_noid_Red.idat (7.72 MB)... "
41431
+ ]
41432
+ },
41433
+ {
41434
+ "name": "stdout",
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+ "output_type": "stream",
41436
+ "text": [
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+ "OK\n",
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+ "[5031/10000] (9.51GB) Downloading: TCGA-BRCA.dd464f65-b905-44a2-8e45-018d58c112c7.ascat3.allelic_specific.seg.txt (0.00 MB)... "
41439
+ ]
41440
+ },
41441
+ {
41442
+ "name": "stdout",
41443
+ "output_type": "stream",
41444
+ "text": [
41445
+ "OK\n",
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+ "[5032/10000] (9.51GB) Downloading: e9fbb4f4-c6a6-4801-a055-46fdec5c287c.mirbase21.mirnas.quantification.txt (0.05 MB)... "
41447
+ ]
41448
+ },
41449
+ {
41450
+ "name": "stdout",
41451
+ "output_type": "stream",
41452
+ "text": [
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+ "OK\n",
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+ "[5033/10000] (9.51GB) Downloading: TCGA-BRCA.764e1076-1148-442b-ade8-a9463b88e89e.ascat3.allelic_specific.seg.txt (0.00 MB)... "
41455
+ ]
41456
+ },
41457
+ {
41458
+ "name": "stdout",
41459
+ "output_type": "stream",
41460
+ "text": [
41461
+ "OK\n",
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+ "[5034/10000] (9.51GB) Downloading: nationwidechildrens.org_ssf.TCGA-D8-A27I.xml (0.01 MB)... "
41463
+ ]
41464
+ },
41465
+ {
41466
+ "name": "stdout",
41467
+ "output_type": "stream",
41468
+ "text": [
41469
+ "OK\n",
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+ "[5035/10000] (9.51GB) Downloading: TCGA-BRCA.9221bace-db00-4adc-ac61-aa064672c1ad.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41471
+ ]
41472
+ },
41473
+ {
41474
+ "name": "stdout",
41475
+ "output_type": "stream",
41476
+ "text": [
41477
+ "OK\n",
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+ "[5036/10000] (9.52GB) Downloading: 7b1a8de2-9eda-44fc-bb91-8afd83e7bf0d.mirbase21.isoforms.quantification.txt (0.26 MB)... "
41479
+ ]
41480
+ },
41481
+ {
41482
+ "name": "stdout",
41483
+ "output_type": "stream",
41484
+ "text": [
41485
+ "OK\n",
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+ "[5037/10000] (9.52GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_G07_730974.grch38.seg.v2.txt (0.02 MB)... "
41487
+ ]
41488
+ },
41489
+ {
41490
+ "name": "stdout",
41491
+ "output_type": "stream",
41492
+ "text": [
41493
+ "OK\n",
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+ "[5038/10000] (9.52GB) Downloading: TCGA-BRCA.dd464f65-b905-44a2-8e45-018d58c112c7.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
41495
+ ]
41496
+ },
41497
+ {
41498
+ "name": "stdout",
41499
+ "output_type": "stream",
41500
+ "text": [
41501
+ "OK\n",
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+ "[5039/10000] (9.52GB) Downloading: TCGA-D8-A27I-01A-01-TS1.853e903d-d155-404c-8546-19fe9464a04f.svs (149.51 MB)... "
41503
+ ]
41504
+ },
41505
+ {
41506
+ "name": "stdout",
41507
+ "output_type": "stream",
41508
+ "text": [
41509
+ "OK\n",
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+ "[5040/10000] (9.66GB) Downloading: 1261a01b-632e-41cf-a1ce-faa1798f5a9b.methylation_array.sesame.level3betas.txt (12.57 MB)... "
41511
+ ]
41512
+ },
41513
+ {
41514
+ "name": "stdout",
41515
+ "output_type": "stream",
41516
+ "text": [
41517
+ "OK\n",
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+ "[5041/10000] (9.68GB) Downloading: 2b5dcec1-681f-4bff-b60b-f3a6683121ef.methylation_array.sesame.level3betas.txt (12.01 MB)... "
41519
+ ]
41520
+ },
41521
+ {
41522
+ "name": "stdout",
41523
+ "output_type": "stream",
41524
+ "text": [
41525
+ "OK\n",
41526
+ "[5042/10000] (9.69GB) Downloading: TCGA-BH-A1F6-11B-07-TSG.e3faadcc-59ae-4ed9-9b4c-cd24dd8c93b5.svs (55.16 MB)... "
41527
+ ]
41528
+ },
41529
+ {
41530
+ "name": "stdout",
41531
+ "output_type": "stream",
41532
+ "text": [
41533
+ "OK\n",
41534
+ "[5043/10000] (9.74GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_B12_730902.grch38.seg.v2.txt (0.01 MB)... "
41535
+ ]
41536
+ },
41537
+ {
41538
+ "name": "stdout",
41539
+ "output_type": "stream",
41540
+ "text": [
41541
+ "OK\n",
41542
+ "[5044/10000] (9.74GB) Downloading: TCGA-BRCA.9221bace-db00-4adc-ac61-aa064672c1ad.ascat2.allelic_specific.seg.txt (0.02 MB)... "
41543
+ ]
41544
+ },
41545
+ {
41546
+ "name": "stdout",
41547
+ "output_type": "stream",
41548
+ "text": [
41549
+ "OK\n",
41550
+ "[5045/10000] (9.74GB) Downloading: TCGA-BRCA.dd464f65-b905-44a2-8e45-018d58c112c7.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41551
+ ]
41552
+ },
41553
+ {
41554
+ "name": "stdout",
41555
+ "output_type": "stream",
41556
+ "text": [
41557
+ "OK\n",
41558
+ "[5046/10000] (9.75GB) Downloading: TCGA-BRCA.764e1076-1148-442b-ade8-a9463b88e89e.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41559
+ ]
41560
+ },
41561
+ {
41562
+ "name": "stdout",
41563
+ "output_type": "stream",
41564
+ "text": [
41565
+ "OK\n",
41566
+ "[5047/10000] (9.75GB) Downloading: TCGA-BRCA.764e1076-1148-442b-ade8-a9463b88e89e.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
41567
+ ]
41568
+ },
41569
+ {
41570
+ "name": "stdout",
41571
+ "output_type": "stream",
41572
+ "text": [
41573
+ "OK\n",
41574
+ "[5048/10000] (9.75GB) Downloading: 34340955-ae0e-4c75-bf01-4e8f42251c04_noid_Grn.idat (7.72 MB)... "
41575
+ ]
41576
+ },
41577
+ {
41578
+ "name": "stdout",
41579
+ "output_type": "stream",
41580
+ "text": [
41581
+ "OK\n",
41582
+ "[5049/10000] (9.76GB) Downloading: TCGA-AN-A0XP-01A-21-A13D-20_RPPA_data.tsv (0.02 MB)... "
41583
+ ]
41584
+ },
41585
+ {
41586
+ "name": "stdout",
41587
+ "output_type": "stream",
41588
+ "text": [
41589
+ "OK\n",
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+ "[5050/10000] (9.76GB) Downloading: 75114e6a-dd8c-490c-99c0-a8adfb45eedf.mirbase21.mirnas.quantification.txt (0.05 MB)... "
41591
+ ]
41592
+ },
41593
+ {
41594
+ "name": "stdout",
41595
+ "output_type": "stream",
41596
+ "text": [
41597
+ "OK\n",
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+ "[5051/10000] (9.76GB) Downloading: TCGA-BRCA.764e1076-1148-442b-ade8-a9463b88e89e.ascat2.allelic_specific.seg.txt (0.00 MB)... "
41599
+ ]
41600
+ },
41601
+ {
41602
+ "name": "stdout",
41603
+ "output_type": "stream",
41604
+ "text": [
41605
+ "OK\n",
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+ "[5052/10000] (9.76GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_F06_771926.nocnv_grch38.seg.v2.txt (0.04 MB)... "
41607
+ ]
41608
+ },
41609
+ {
41610
+ "name": "stdout",
41611
+ "output_type": "stream",
41612
+ "text": [
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+ "OK\n",
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+ "[5053/10000] (9.76GB) Downloading: nationwidechildrens.org_clinical.TCGA-AN-A0XP.xml (0.05 MB)... "
41615
+ ]
41616
+ },
41617
+ {
41618
+ "name": "stdout",
41619
+ "output_type": "stream",
41620
+ "text": [
41621
+ "OK\n",
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+ "[5054/10000] (9.76GB) Downloading: 1261a01b-632e-41cf-a1ce-faa1798f5a9b_noid_Red.idat (7.72 MB)... "
41623
+ ]
41624
+ },
41625
+ {
41626
+ "name": "stdout",
41627
+ "output_type": "stream",
41628
+ "text": [
41629
+ "OK\n",
41630
+ "[5055/10000] (9.77GB) Downloading: c8e8f4e7-7aae-41f7-9d36-5938d2c2fc04.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
41631
+ ]
41632
+ },
41633
+ {
41634
+ "name": "stdout",
41635
+ "output_type": "stream",
41636
+ "text": [
41637
+ "OK\n",
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+ "[5056/10000] (9.77GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_B12_730902.nocnv_grch38.seg.v2.txt (0.01 MB)... "
41639
+ ]
41640
+ },
41641
+ {
41642
+ "name": "stdout",
41643
+ "output_type": "stream",
41644
+ "text": [
41645
+ "OK\n",
41646
+ "[5057/10000] (9.77GB) Downloading: TCGA-BH-A1F6-01A-21-A17I-20_RPPA_data.tsv (0.02 MB)... "
41647
+ ]
41648
+ },
41649
+ {
41650
+ "name": "stdout",
41651
+ "output_type": "stream",
41652
+ "text": [
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+ "OK\n",
41654
+ "[5058/10000] (9.77GB) Downloading: TCGA-AN-A0XP-01A-01-BSA.93b120d1-e962-4dcd-b4ce-c2d8e019c8e0.svs (128.23 MB)... "
41655
+ ]
41656
+ },
41657
+ {
41658
+ "name": "stdout",
41659
+ "output_type": "stream",
41660
+ "text": [
41661
+ "OK\n",
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+ "[5059/10000] (9.90GB) Downloading: 596c7aaf-4119-4b2f-8207-20531e0db945.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
41663
+ ]
41664
+ },
41665
+ {
41666
+ "name": "stdout",
41667
+ "output_type": "stream",
41668
+ "text": [
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+ "OK\n",
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+ "[5060/10000] (9.90GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_E08_772034.grch38.seg.v2.txt (0.02 MB)... "
41671
+ ]
41672
+ },
41673
+ {
41674
+ "name": "stdout",
41675
+ "output_type": "stream",
41676
+ "text": [
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+ "OK\n",
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+ "[5061/10000] (9.90GB) Downloading: TCGA-BH-A1F6-01Z-00-DX1.E83F0DC0-EA2C-4641-81B0-8702B9C5D579.svs (905.96 MB)... "
41679
+ ]
41680
+ },
41681
+ {
41682
+ "name": "stdout",
41683
+ "output_type": "stream",
41684
+ "text": [
41685
+ "OK\n",
41686
+ "[5062/10000] (10.78GB) Downloading: TCGA-BRCA.764e1076-1148-442b-ade8-a9463b88e89e.gene_level_copy_number.v36.tsv (3.29 MB)... "
41687
+ ]
41688
+ },
41689
+ {
41690
+ "name": "stdout",
41691
+ "output_type": "stream",
41692
+ "text": [
41693
+ "OK\n",
41694
+ "[5063/10000] (10.78GB) Downloading: 2b5dcec1-681f-4bff-b60b-f3a6683121ef_noid_Red.idat (7.72 MB)... "
41695
+ ]
41696
+ },
41697
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
41700
+ "text": [
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+ "OK\n",
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+ "[5064/10000] (10.79GB) Downloading: TCGA-D8-A27I.FAB622C2-3E45-4E72-AA36-9530BB830993.PDF (0.06 MB)... "
41703
+ ]
41704
+ },
41705
+ {
41706
+ "name": "stdout",
41707
+ "output_type": "stream",
41708
+ "text": [
41709
+ "OK\n",
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+ "[5065/10000] (10.79GB) Downloading: 8da6e66f-f014-4652-af13-c650c72c98ba.methylation_array.sesame.level3betas.txt (12.52 MB)... "
41711
+ ]
41712
+ },
41713
+ {
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+ "name": "stdout",
41715
+ "output_type": "stream",
41716
+ "text": [
41717
+ "OK\n",
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+ "[5066/10000] (10.80GB) Downloading: 5782ee15-ce76-43d2-ba6c-e84284f4a99f.rna_seq.augmented_star_gene_counts.tsv (4.03 MB)... "
41719
+ ]
41720
+ },
41721
+ {
41722
+ "name": "stdout",
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+ "output_type": "stream",
41724
+ "text": [
41725
+ "OK\n",
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+ "[5067/10000] (10.81GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_G03_628326.grch38.seg.v2.txt (0.04 MB)... "
41727
+ ]
41728
+ },
41729
+ {
41730
+ "name": "stdout",
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+ "output_type": "stream",
41732
+ "text": [
41733
+ "OK\n",
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+ "[5068/10000] (10.81GB) Downloading: a4cdeced-578d-45de-a38f-caa2b65b0715.methylation_array.sesame.level3betas.txt (12.24 MB)... "
41735
+ ]
41736
+ },
41737
+ {
41738
+ "name": "stdout",
41739
+ "output_type": "stream",
41740
+ "text": [
41741
+ "OK\n",
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+ "[5069/10000] (10.82GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A7-A4SF.xml (0.05 MB)... "
41743
+ ]
41744
+ },
41745
+ {
41746
+ "name": "stdout",
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+ "output_type": "stream",
41748
+ "text": [
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+ "OK\n",
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+ "[5070/10000] (10.82GB) Downloading: 462efbad-7836-4592-af9a-14be169a5a9e.methylation_array.sesame.level3betas.txt (12.51 MB)... "
41751
+ ]
41752
+ },
41753
+ {
41754
+ "name": "stdout",
41755
+ "output_type": "stream",
41756
+ "text": [
41757
+ "OK\n",
41758
+ "[5071/10000] (10.83GB) Downloading: a4cdeced-578d-45de-a38f-caa2b65b0715_noid_Red.idat (7.72 MB)... "
41759
+ ]
41760
+ },
41761
+ {
41762
+ "name": "stdout",
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+ "output_type": "stream",
41764
+ "text": [
41765
+ "OK\n",
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+ "[5072/10000] (10.84GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_A12_1320324.grch38.seg.v2.txt (0.04 MB)... "
41767
+ ]
41768
+ },
41769
+ {
41770
+ "name": "stdout",
41771
+ "output_type": "stream",
41772
+ "text": [
41773
+ "OK\n",
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+ "[5073/10000] (10.84GB) Downloading: TCGA-EW-A6S9.4FC32F17-7A4D-4FF6-A710-FFFBC610CB56.PDF (0.25 MB)... "
41775
+ ]
41776
+ },
41777
+ {
41778
+ "name": "stdout",
41779
+ "output_type": "stream",
41780
+ "text": [
41781
+ "OK\n",
41782
+ "[5074/10000] (10.84GB) Downloading: TCGA-BRCA.2080f468-6807-4c8d-a9d8-99775effd6ba.ascat2.allelic_specific.seg.txt (0.01 MB)... "
41783
+ ]
41784
+ },
41785
+ {
41786
+ "name": "stdout",
41787
+ "output_type": "stream",
41788
+ "text": [
41789
+ "OK\n",
41790
+ "[5075/10000] (10.84GB) Downloading: TCGA-BRCA.0a28c663-7cc6-466c-b64d-f9d8d6d6b4c8.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
41791
+ ]
41792
+ },
41793
+ {
41794
+ "name": "stdout",
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+ "output_type": "stream",
41796
+ "text": [
41797
+ "OK\n",
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+ "[5076/10000] (10.84GB) Downloading: TCGA-BRCA.0a28c663-7cc6-466c-b64d-f9d8d6d6b4c8.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41799
+ ]
41800
+ },
41801
+ {
41802
+ "name": "stdout",
41803
+ "output_type": "stream",
41804
+ "text": [
41805
+ "OK\n",
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+ "[5077/10000] (10.85GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-EW-A6S9.xml (0.05 MB)... "
41807
+ ]
41808
+ },
41809
+ {
41810
+ "name": "stdout",
41811
+ "output_type": "stream",
41812
+ "text": [
41813
+ "OK\n",
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+ "[5078/10000] (10.85GB) Downloading: a4cdeced-578d-45de-a38f-caa2b65b0715_noid_Grn.idat (7.72 MB)... "
41815
+ ]
41816
+ },
41817
+ {
41818
+ "name": "stdout",
41819
+ "output_type": "stream",
41820
+ "text": [
41821
+ "OK\n",
41822
+ "[5079/10000] (10.85GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_F01_777970.grch38.seg.v2.txt (0.02 MB)... "
41823
+ ]
41824
+ },
41825
+ {
41826
+ "name": "stdout",
41827
+ "output_type": "stream",
41828
+ "text": [
41829
+ "OK\n",
41830
+ "[5080/10000] (10.85GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_B12_772088.grch38.seg.v2.txt (0.04 MB)... "
41831
+ ]
41832
+ },
41833
+ {
41834
+ "name": "stdout",
41835
+ "output_type": "stream",
41836
+ "text": [
41837
+ "OK\n",
41838
+ "[5081/10000] (10.85GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_E11_778136.grch38.seg.v2.txt (0.03 MB)... "
41839
+ ]
41840
+ },
41841
+ {
41842
+ "name": "stdout",
41843
+ "output_type": "stream",
41844
+ "text": [
41845
+ "OK\n",
41846
+ "[5082/10000] (10.85GB) Downloading: nationwidechildrens.org_ssf.TCGA-EW-A1IX.xml (0.02 MB)... "
41847
+ ]
41848
+ },
41849
+ {
41850
+ "name": "stdout",
41851
+ "output_type": "stream",
41852
+ "text": [
41853
+ "OK\n",
41854
+ "[5083/10000] (10.85GB) Downloading: f1600b0c-f3ac-4c19-8c43-6af450abb6a3.rna_seq.augmented_star_gene_counts.tsv (4.07 MB)... "
41855
+ ]
41856
+ },
41857
+ {
41858
+ "name": "stdout",
41859
+ "output_type": "stream",
41860
+ "text": [
41861
+ "OK\n",
41862
+ "[5084/10000] (10.86GB) Downloading: TCGA-BRCA.e52f1f1f-dfed-49b5-a7f2-f81e0af3c810.ascat2.allelic_specific.seg.txt (0.04 MB)... "
41863
+ ]
41864
+ },
41865
+ {
41866
+ "name": "stdout",
41867
+ "output_type": "stream",
41868
+ "text": [
41869
+ "OK\n",
41870
+ "[5085/10000] (10.86GB) Downloading: TCGA-E9-A1N6-11A-03-TSC.7fc99944-9421-4376-b64c-c5f3536a02ff.svs (30.62 MB)... "
41871
+ ]
41872
+ },
41873
+ {
41874
+ "name": "stdout",
41875
+ "output_type": "stream",
41876
+ "text": [
41877
+ "OK\n",
41878
+ "[5086/10000] (10.89GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A1N6.xml (0.08 MB)... "
41879
+ ]
41880
+ },
41881
+ {
41882
+ "name": "stdout",
41883
+ "output_type": "stream",
41884
+ "text": [
41885
+ "OK\n",
41886
+ "[5087/10000] (10.89GB) Downloading: TCGA-E9-A1N6-01A-21-A17K-20_RPPA_data.tsv (0.02 MB)... "
41887
+ ]
41888
+ },
41889
+ {
41890
+ "name": "stdout",
41891
+ "output_type": "stream",
41892
+ "text": [
41893
+ "OK\n",
41894
+ "[5088/10000] (10.89GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_F01_772040.nocnv_grch38.seg.v2.txt (0.00 MB)... "
41895
+ ]
41896
+ },
41897
+ {
41898
+ "name": "stdout",
41899
+ "output_type": "stream",
41900
+ "text": [
41901
+ "OK\n",
41902
+ "[5089/10000] (10.89GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-EW-A1J5.xml (0.06 MB)... "
41903
+ ]
41904
+ },
41905
+ {
41906
+ "name": "stdout",
41907
+ "output_type": "stream",
41908
+ "text": [
41909
+ "OK\n",
41910
+ "[5090/10000] (10.89GB) Downloading: TCGA-E9-A1N6-11A-02-TSB.51757c9b-a6ff-40e3-878f-5baa1ca92941.svs (91.04 MB)... "
41911
+ ]
41912
+ },
41913
+ {
41914
+ "name": "stdout",
41915
+ "output_type": "stream",
41916
+ "text": [
41917
+ "OK\n",
41918
+ "[5091/10000] (10.98GB) Downloading: 0b0e74c7-04dd-48d7-be8c-ea2069f1f99c.methylation_array.sesame.level3betas.txt (12.58 MB)... "
41919
+ ]
41920
+ },
41921
+ {
41922
+ "name": "stdout",
41923
+ "output_type": "stream",
41924
+ "text": [
41925
+ "OK\n",
41926
+ "[5092/10000] (10.99GB) Downloading: TCGA-BRCA.e52f1f1f-dfed-49b5-a7f2-f81e0af3c810.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41927
+ ]
41928
+ },
41929
+ {
41930
+ "name": "stdout",
41931
+ "output_type": "stream",
41932
+ "text": [
41933
+ "OK\n",
41934
+ "[5093/10000] (10.99GB) Downloading: c186a5f0-883d-425a-8b78-f2ef5bb570b6.methylation_array.sesame.level3betas.txt (12.54 MB)... "
41935
+ ]
41936
+ },
41937
+ {
41938
+ "name": "stdout",
41939
+ "output_type": "stream",
41940
+ "text": [
41941
+ "OK\n",
41942
+ "[5094/10000] (11.01GB) Downloading: TCGA-BRCA.8069f916-9d52-4a2c-b30d-3f10e520e1e1.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
41943
+ ]
41944
+ },
41945
+ {
41946
+ "name": "stdout",
41947
+ "output_type": "stream",
41948
+ "text": [
41949
+ "OK\n",
41950
+ "[5095/10000] (11.01GB) Downloading: c186a5f0-883d-425a-8b78-f2ef5bb570b6_noid_Grn.idat (7.72 MB)... "
41951
+ ]
41952
+ },
41953
+ {
41954
+ "name": "stdout",
41955
+ "output_type": "stream",
41956
+ "text": [
41957
+ "OK\n",
41958
+ "[5096/10000] (11.02GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A1N6.xml (0.02 MB)... "
41959
+ ]
41960
+ },
41961
+ {
41962
+ "name": "stdout",
41963
+ "output_type": "stream",
41964
+ "text": [
41965
+ "OK\n",
41966
+ "[5097/10000] (11.02GB) Downloading: TCGA-BRCA.8069f916-9d52-4a2c-b30d-3f10e520e1e1.ascat3.allelic_specific.seg.txt (0.01 MB)... "
41967
+ ]
41968
+ },
41969
+ {
41970
+ "name": "stdout",
41971
+ "output_type": "stream",
41972
+ "text": [
41973
+ "OK\n",
41974
+ "[5098/10000] (11.02GB) Downloading: 19475873-d8f4-4954-8339-d0f9f1ab2bdc.mirbase21.isoforms.quantification.txt (0.45 MB)... "
41975
+ ]
41976
+ },
41977
+ {
41978
+ "name": "stdout",
41979
+ "output_type": "stream",
41980
+ "text": [
41981
+ "OK\n",
41982
+ "[5099/10000] (11.02GB) Downloading: TCGA-B6-A0RO-01A-02-TSB.af00bb62-e1ef-4042-a8fe-80173e42c9f8.svs (137.39 MB)... "
41983
+ ]
41984
+ },
41985
+ {
41986
+ "name": "stdout",
41987
+ "output_type": "stream",
41988
+ "text": [
41989
+ "OK\n",
41990
+ "[5100/10000] (11.15GB) Downloading: TCGA-EW-A1J5-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
41991
+ ]
41992
+ },
41993
+ {
41994
+ "name": "stdout",
41995
+ "output_type": "stream",
41996
+ "text": [
41997
+ "OK\n",
41998
+ "[5101/10000] (11.15GB) Downloading: TCGA-BRCA.8069f916-9d52-4a2c-b30d-3f10e520e1e1.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
41999
+ ]
42000
+ },
42001
+ {
42002
+ "name": "stdout",
42003
+ "output_type": "stream",
42004
+ "text": [
42005
+ "OK\n",
42006
+ "[5102/10000] (11.15GB) Downloading: nationwidechildrens.org_omf.TCGA-EW-A1J5.xml (0.01 MB)... "
42007
+ ]
42008
+ },
42009
+ {
42010
+ "name": "stdout",
42011
+ "output_type": "stream",
42012
+ "text": [
42013
+ "OK\n",
42014
+ "[5103/10000] (11.15GB) Downloading: 0c29517c-8763-4cc0-8acc-32d24d209f26.methylation_array.sesame.level3betas.txt (0.74 MB)... "
42015
+ ]
42016
+ },
42017
+ {
42018
+ "name": "stdout",
42019
+ "output_type": "stream",
42020
+ "text": [
42021
+ "OK\n",
42022
+ "[5104/10000] (11.15GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_F01_667056.grch38.seg.v2.txt (0.06 MB)... "
42023
+ ]
42024
+ },
42025
+ {
42026
+ "name": "stdout",
42027
+ "output_type": "stream",
42028
+ "text": [
42029
+ "OK\n",
42030
+ "[5105/10000] (11.15GB) Downloading: 0c29517c-8763-4cc0-8acc-32d24d209f26_noid_Grn.idat (0.69 MB)... "
42031
+ ]
42032
+ },
42033
+ {
42034
+ "name": "stdout",
42035
+ "output_type": "stream",
42036
+ "text": [
42037
+ "OK\n",
42038
+ "[5106/10000] (11.16GB) Downloading: 26df43a5-3f2c-42c5-96fe-53543a24f282.methylation_array.sesame.level3betas.txt (12.46 MB)... "
42039
+ ]
42040
+ },
42041
+ {
42042
+ "name": "stdout",
42043
+ "output_type": "stream",
42044
+ "text": [
42045
+ "OK\n",
42046
+ "[5107/10000] (11.17GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A046.xml (0.08 MB)... "
42047
+ ]
42048
+ },
42049
+ {
42050
+ "name": "stdout",
42051
+ "output_type": "stream",
42052
+ "text": [
42053
+ "OK\n",
42054
+ "[5108/10000] (11.17GB) Downloading: TCGA-BRCA.bed7e88d-b9ca-480b-b4c5-43c3403c7990.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
42055
+ ]
42056
+ },
42057
+ {
42058
+ "name": "stdout",
42059
+ "output_type": "stream",
42060
+ "text": [
42061
+ "OK\n",
42062
+ "[5109/10000] (11.17GB) Downloading: TCGA-E2-A1L6-01Z-00-DX1.AFE87067-2BFD-42C2-9334-9DDE8AB61B49.svs (1208.89 MB)... "
42063
+ ]
42064
+ },
42065
+ {
42066
+ "name": "stdout",
42067
+ "output_type": "stream",
42068
+ "text": [
42069
+ "OK\n",
42070
+ "[5110/10000] (12.35GB) Downloading: 90e83adc-6d01-4959-b6bd-08d156f45b0f.mirbase21.mirnas.quantification.txt (0.05 MB)... "
42071
+ ]
42072
+ },
42073
+ {
42074
+ "name": "stdout",
42075
+ "output_type": "stream",
42076
+ "text": [
42077
+ "OK\n",
42078
+ "[5111/10000] (12.35GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A07R.xml (0.10 MB)... "
42079
+ ]
42080
+ },
42081
+ {
42082
+ "name": "stdout",
42083
+ "output_type": "stream",
42084
+ "text": [
42085
+ "OK\n",
42086
+ "[5112/10000] (12.35GB) Downloading: TCGA-E2-A1L6-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
42087
+ ]
42088
+ },
42089
+ {
42090
+ "name": "stdout",
42091
+ "output_type": "stream",
42092
+ "text": [
42093
+ "OK\n",
42094
+ "[5113/10000] (12.35GB) Downloading: fe15bb7d-6469-4778-9dc8-9e4c5877942c.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
42095
+ ]
42096
+ },
42097
+ {
42098
+ "name": "stdout",
42099
+ "output_type": "stream",
42100
+ "text": [
42101
+ "OK\n",
42102
+ "[5114/10000] (12.36GB) Downloading: 05ea028e-6b8a-4352-88aa-057494cf5e80.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
42103
+ ]
42104
+ },
42105
+ {
42106
+ "name": "stdout",
42107
+ "output_type": "stream",
42108
+ "text": [
42109
+ "OK\n",
42110
+ "[5115/10000] (12.36GB) Downloading: TCGA-AN-A046.1304FB17-A20A-4EBC-9CC8-1554808AC1F6.PDF (0.04 MB)... "
42111
+ ]
42112
+ },
42113
+ {
42114
+ "name": "stdout",
42115
+ "output_type": "stream",
42116
+ "text": [
42117
+ "OK\n",
42118
+ "[5116/10000] (12.36GB) Downloading: BEAUX_p_TCGA_b109_SNP_2N_GenomeWideSNP_6_E11_772108.nocnv_grch38.seg.v2.txt (0.00 MB)... "
42119
+ ]
42120
+ },
42121
+ {
42122
+ "name": "stdout",
42123
+ "output_type": "stream",
42124
+ "text": [
42125
+ "OK\n",
42126
+ "[5117/10000] (12.36GB) Downloading: TCGA-A8-A07R-01A-21D-A89H-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.39 MB)... "
42127
+ ]
42128
+ },
42129
+ {
42130
+ "name": "stdout",
42131
+ "output_type": "stream",
42132
+ "text": [
42133
+ "OK\n",
42134
+ "[5118/10000] (12.36GB) Downloading: TCGA-A8-A07R-01A-01-BS1.12d7cbf6-6c9e-43b0-b386-4ba1a0a29e04.svs (664.43 MB)... "
42135
+ ]
42136
+ },
42137
+ {
42138
+ "name": "stdout",
42139
+ "output_type": "stream",
42140
+ "text": [
42141
+ "OK\n",
42142
+ "[5119/10000] (13.01GB) Downloading: TCGA-BRCA.bed7e88d-b9ca-480b-b4c5-43c3403c7990.ascat3.allelic_specific.seg.txt (0.00 MB)... "
42143
+ ]
42144
+ },
42145
+ {
42146
+ "name": "stdout",
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+ "output_type": "stream",
42148
+ "text": [
42149
+ "OK\n",
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+ "[5120/10000] (13.01GB) Downloading: TCGA-AN-A046-01Z-00-DX1.C529B94F-AFE3-4701-BC98-5D6EDF7B82C0.svs (402.77 MB)... "
42151
+ ]
42152
+ },
42153
+ {
42154
+ "name": "stdout",
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+ "output_type": "stream",
42156
+ "text": [
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+ "OK\n",
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+ "[5121/10000] (13.40GB) Downloading: 209ef313-d8e8-4527-a9ba-231701c08a7c_noid_Red.idat (0.69 MB)... "
42159
+ ]
42160
+ },
42161
+ {
42162
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[5122/10000] (13.40GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A07R.xml (0.01 MB)... "
42167
+ ]
42168
+ },
42169
+ {
42170
+ "name": "stdout",
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+ "output_type": "stream",
42172
+ "text": [
42173
+ "OK\n",
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+ "[5123/10000] (13.40GB) Downloading: 911df7f3-c231-4174-b941-9cc054a81e77.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
42175
+ ]
42176
+ },
42177
+ {
42178
+ "name": "stdout",
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+ "output_type": "stream",
42180
+ "text": [
42181
+ "OK\n",
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+ "[5124/10000] (13.40GB) Downloading: TCGA-BRCA.bed7e88d-b9ca-480b-b4c5-43c3403c7990.ascat2.allelic_specific.seg.txt (0.02 MB)... "
42183
+ ]
42184
+ },
42185
+ {
42186
+ "name": "stdout",
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+ "output_type": "stream",
42188
+ "text": [
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+ "OK\n",
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+ "[5125/10000] (13.40GB) Downloading: 636c9329-44fb-4dd4-b0d6-2bf0bc9531de.mirbase21.mirnas.quantification.txt (0.05 MB)... "
42191
+ ]
42192
+ },
42193
+ {
42194
+ "name": "stdout",
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+ "output_type": "stream",
42196
+ "text": [
42197
+ "OK\n",
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+ "[5126/10000] (13.40GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B03_667046.nocnv_grch38.seg.v2.txt (0.01 MB)... "
42199
+ ]
42200
+ },
42201
+ {
42202
+ "name": "stdout",
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+ "output_type": "stream",
42204
+ "text": [
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+ "OK\n",
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+ "[5127/10000] (13.40GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_E12_741548.nocnv_grch38.seg.v2.txt (0.00 MB)... "
42207
+ ]
42208
+ },
42209
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
42212
+ "text": [
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+ "OK\n",
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+ "[5128/10000] (13.40GB) Downloading: nationwidechildrens.org_clinical.TCGA-AN-A046.xml (0.05 MB)... "
42215
+ ]
42216
+ },
42217
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
42220
+ "text": [
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+ "OK\n",
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+ "[5129/10000] (13.40GB) Downloading: 927ab78f-09af-4367-ab60-427185570a19.wxs.aliquot_ensemble_masked.maf.gz (0.08 MB)... "
42223
+ ]
42224
+ },
42225
+ {
42226
+ "name": "stdout",
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+ "output_type": "stream",
42228
+ "text": [
42229
+ "OK\n",
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+ "[5130/10000] (13.40GB) Downloading: 901b2b17-0430-4a15-88e8-224a00c0946c_noid_Red.idat (0.69 MB)... "
42231
+ ]
42232
+ },
42233
+ {
42234
+ "name": "stdout",
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+ "output_type": "stream",
42236
+ "text": [
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+ "OK\n",
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+ "[5131/10000] (13.40GB) Downloading: TCGA-BRCA.b5e9e344-a813-442e-8bd4-504111e98c0b.ascat2.allelic_specific.seg.txt (0.02 MB)... "
42239
+ ]
42240
+ },
42241
+ {
42242
+ "name": "stdout",
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+ "output_type": "stream",
42244
+ "text": [
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+ "OK\n",
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+ "[5132/10000] (13.40GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A5UO.xml (0.07 MB)... "
42247
+ ]
42248
+ },
42249
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
42252
+ "text": [
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+ "OK\n",
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+ "[5133/10000] (13.40GB) Downloading: HITCH_p_TCGASNP_b93_N_GenomeWideSNP_6_C09_741444.grch38.seg.v2.txt (0.02 MB)... "
42255
+ ]
42256
+ },
42257
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
42260
+ "text": [
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+ "OK\n",
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+ "[5134/10000] (13.40GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A5UO.xml (0.01 MB)... "
42263
+ ]
42264
+ },
42265
+ {
42266
+ "name": "stdout",
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+ "output_type": "stream",
42268
+ "text": [
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+ "OK\n",
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+ "[5135/10000] (13.40GB) Downloading: 0c29517c-8763-4cc0-8acc-32d24d209f26_noid_Red.idat (0.69 MB)... "
42271
+ ]
42272
+ },
42273
+ {
42274
+ "name": "stdout",
42275
+ "output_type": "stream",
42276
+ "text": [
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+ "OK\n",
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+ "[5136/10000] (13.40GB) Downloading: TCGA-BRCA.b5e9e344-a813-442e-8bd4-504111e98c0b.gene_level_copy_number.v36.tsv (3.29 MB)... "
42279
+ ]
42280
+ },
42281
+ {
42282
+ "name": "stdout",
42283
+ "output_type": "stream",
42284
+ "text": [
42285
+ "OK\n",
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+ "[5137/10000] (13.41GB) Downloading: b2f29fc2-4e0c-42ab-99af-05dd050ea004.methylation_array.sesame.level3betas.txt (12.28 MB)... "
42287
+ ]
42288
+ },
42289
+ {
42290
+ "name": "stdout",
42291
+ "output_type": "stream",
42292
+ "text": [
42293
+ "OK\n",
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+ "[5138/10000] (13.42GB) Downloading: TCGA-BRCA.fc728459-51da-4bed-8f19-89c724e2139f.ascat2.allelic_specific.seg.txt (0.02 MB)... "
42295
+ ]
42296
+ },
42297
+ {
42298
+ "name": "stdout",
42299
+ "output_type": "stream",
42300
+ "text": [
42301
+ "OK\n",
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+ "[5139/10000] (13.42GB) Downloading: cf72c0cf-6136-4a13-8855-1cadcdf6ecc1.mirbase21.mirnas.quantification.txt (0.05 MB)... "
42303
+ ]
42304
+ },
42305
+ {
42306
+ "name": "stdout",
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+ "output_type": "stream",
42308
+ "text": [
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+ "OK\n",
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+ "[5140/10000] (13.42GB) Downloading: TCGA-BRCA.c70418fa-6b66-401e-b1c4-330100fe60a0.ascat3.allelic_specific.seg.txt (0.01 MB)... "
42311
+ ]
42312
+ },
42313
+ {
42314
+ "name": "stdout",
42315
+ "output_type": "stream",
42316
+ "text": [
42317
+ "OK\n",
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+ "[5141/10000] (13.42GB) Downloading: TCGA-BRCA.fc728459-51da-4bed-8f19-89c724e2139f.gene_level_copy_number.v36.tsv (3.30 MB)... "
42319
+ ]
42320
+ },
42321
+ {
42322
+ "name": "stdout",
42323
+ "output_type": "stream",
42324
+ "text": [
42325
+ "OK\n",
42326
+ "[5142/10000] (13.42GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A18G.xml (0.06 MB)... "
42327
+ ]
42328
+ },
42329
+ {
42330
+ "name": "stdout",
42331
+ "output_type": "stream",
42332
+ "text": [
42333
+ "OK\n",
42334
+ "[5143/10000] (13.42GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A54Y.xml (0.01 MB)... "
42335
+ ]
42336
+ },
42337
+ {
42338
+ "name": "stdout",
42339
+ "output_type": "stream",
42340
+ "text": [
42341
+ "OK\n",
42342
+ "[5144/10000] (13.42GB) Downloading: 512f4412-c3e0-42b2-8f8c-aebfaabf5192.wxs.aliquot_ensemble_masked.maf.gz (0.49 MB)... "
42343
+ ]
42344
+ },
42345
+ {
42346
+ "name": "stdout",
42347
+ "output_type": "stream",
42348
+ "text": [
42349
+ "OK\n",
42350
+ "[5145/10000] (13.42GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A54Y.xml (0.05 MB)... "
42351
+ ]
42352
+ },
42353
+ {
42354
+ "name": "stdout",
42355
+ "output_type": "stream",
42356
+ "text": [
42357
+ "OK\n",
42358
+ "[5146/10000] (13.42GB) Downloading: TCGA-BRCA.c70418fa-6b66-401e-b1c4-330100fe60a0.gene_level_copy_number.v36.tsv (3.29 MB)... "
42359
+ ]
42360
+ },
42361
+ {
42362
+ "name": "stdout",
42363
+ "output_type": "stream",
42364
+ "text": [
42365
+ "OK\n",
42366
+ "[5147/10000] (13.43GB) Downloading: cf72c0cf-6136-4a13-8855-1cadcdf6ecc1.mirbase21.isoforms.quantification.txt (0.34 MB)... "
42367
+ ]
42368
+ },
42369
+ {
42370
+ "name": "stdout",
42371
+ "output_type": "stream",
42372
+ "text": [
42373
+ "OK\n",
42374
+ "[5148/10000] (13.43GB) Downloading: TCGA-BRCA.ee9101bf-b45d-41d3-bc63-16d9ca91e714.ascat3.allelic_specific.seg.txt (0.00 MB)... "
42375
+ ]
42376
+ },
42377
+ {
42378
+ "name": "stdout",
42379
+ "output_type": "stream",
42380
+ "text": [
42381
+ "OK\n",
42382
+ "[5149/10000] (13.43GB) Downloading: 52ced3b3-f4a7-41a2-bdf8-16fee8595bfd.mirbase21.mirnas.quantification.txt (0.05 MB)... "
42383
+ ]
42384
+ },
42385
+ {
42386
+ "name": "stdout",
42387
+ "output_type": "stream",
42388
+ "text": [
42389
+ "OK\n",
42390
+ "[5150/10000] (13.43GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_E09_1343764.grch38.seg.v2.txt (0.06 MB)... "
42391
+ ]
42392
+ },
42393
+ {
42394
+ "name": "stdout",
42395
+ "output_type": "stream",
42396
+ "text": [
42397
+ "OK\n",
42398
+ "[5151/10000] (13.43GB) Downloading: DRIPS_p_TCGA_295_296_297_N_GenomeWideSNP_6_E09_1343764.nocnv_grch38.seg.v2.txt (0.04 MB)... "
42399
+ ]
42400
+ },
42401
+ {
42402
+ "name": "stdout",
42403
+ "output_type": "stream",
42404
+ "text": [
42405
+ "OK\n",
42406
+ "[5152/10000] (13.43GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_A08_1320308.nocnv_grch38.seg.v2.txt (0.02 MB)... "
42407
+ ]
42408
+ },
42409
+ {
42410
+ "name": "stdout",
42411
+ "output_type": "stream",
42412
+ "text": [
42413
+ "OK\n",
42414
+ "[5153/10000] (13.43GB) Downloading: e13a1beb-e1d2-4f0d-a24d-018e131e3c93.mirbase21.mirnas.quantification.txt (0.05 MB)... "
42415
+ ]
42416
+ },
42417
+ {
42418
+ "name": "stdout",
42419
+ "output_type": "stream",
42420
+ "text": [
42421
+ "OK\n",
42422
+ "[5154/10000] (13.43GB) Downloading: TCGA-LL-A740-01A-11-A43F-20_RPPA_data.tsv (0.02 MB)... "
42423
+ ]
42424
+ },
42425
+ {
42426
+ "name": "stdout",
42427
+ "output_type": "stream",
42428
+ "text": [
42429
+ "OK\n",
42430
+ "[5155/10000] (13.43GB) Downloading: TCGA-E9-A54Y-01A-21-A321-20_RPPA_data.tsv (0.02 MB)... "
42431
+ ]
42432
+ },
42433
+ {
42434
+ "name": "stdout",
42435
+ "output_type": "stream",
42436
+ "text": [
42437
+ "OK\n",
42438
+ "[5156/10000] (13.43GB) Downloading: TCGA-E2-A1LB-11A-01-TSA.099aaa2f-dc57-4d07-b4ac-c53fdf724aa1.svs (64.88 MB)... "
42439
+ ]
42440
+ },
42441
+ {
42442
+ "name": "stdout",
42443
+ "output_type": "stream",
42444
+ "text": [
42445
+ "OK\n",
42446
+ "[5157/10000] (13.49GB) Downloading: b2f29fc2-4e0c-42ab-99af-05dd050ea004_noid_Red.idat (7.72 MB)... "
42447
+ ]
42448
+ },
42449
+ {
42450
+ "name": "stdout",
42451
+ "output_type": "stream",
42452
+ "text": [
42453
+ "OK\n",
42454
+ "[5158/10000] (13.50GB) Downloading: GOOFS_p_TCGA_b117_118_SNP_N_GenomeWideSNP_6_C01_778114.grch38.seg.v2.txt (0.03 MB)... "
42455
+ ]
42456
+ },
42457
+ {
42458
+ "name": "stdout",
42459
+ "output_type": "stream",
42460
+ "text": [
42461
+ "OK\n",
42462
+ "[5159/10000] (13.50GB) Downloading: TCGA-LL-A740-01Z-00-DX1.757D94A5-EF0F-4A0E-99A9-8809B66438DA.svs (1207.41 MB)... "
42463
+ ]
42464
+ },
42465
+ {
42466
+ "name": "stdout",
42467
+ "output_type": "stream",
42468
+ "text": [
42469
+ "OK\n",
42470
+ "[5160/10000] (14.68GB) Downloading: b2f29fc2-4e0c-42ab-99af-05dd050ea004_noid_Grn.idat (7.72 MB)... "
42471
+ ]
42472
+ },
42473
+ {
42474
+ "name": "stdout",
42475
+ "output_type": "stream",
42476
+ "text": [
42477
+ "OK\n",
42478
+ "[5161/10000] (14.68GB) Downloading: TCGA-BRCA.b690db1d-6560-4c02-a3b9-3abc43d39c03.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
42479
+ ]
42480
+ },
42481
+ {
42482
+ "name": "stdout",
42483
+ "output_type": "stream",
42484
+ "text": [
42485
+ "OK\n",
42486
+ "[5162/10000] (14.69GB) Downloading: 37d359b3-d8f5-44cf-8f30-57dfdbbab8c1.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
42487
+ ]
42488
+ },
42489
+ {
42490
+ "name": "stdout",
42491
+ "output_type": "stream",
42492
+ "text": [
42493
+ "OK\n",
42494
+ "[5163/10000] (14.69GB) Downloading: TCGA-BRCA.02600c52-6742-4d06-b417-16694f0c026b.ascat3.allelic_specific.seg.txt (0.01 MB)... "
42495
+ ]
42496
+ },
42497
+ {
42498
+ "name": "stdout",
42499
+ "output_type": "stream",
42500
+ "text": [
42501
+ "OK\n",
42502
+ "[5164/10000] (14.69GB) Downloading: GAMMA_p_TCGA_b103_104_SNP_N_GenomeWideSNP_6_B10_755918.nocnv_grch38.seg.v2.txt (0.00 MB)... "
42503
+ ]
42504
+ },
42505
+ {
42506
+ "name": "stdout",
42507
+ "output_type": "stream",
42508
+ "text": [
42509
+ "OK\n",
42510
+ "[5165/10000] (14.69GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E2-A15I.xml (0.09 MB)... "
42511
+ ]
42512
+ },
42513
+ {
42514
+ "name": "stdout",
42515
+ "output_type": "stream",
42516
+ "text": [
42517
+ "OK\n",
42518
+ "[5166/10000] (14.69GB) Downloading: TCGA-E2-A15I-01A-11-A17I-20_RPPA_data.tsv (0.02 MB)... "
42519
+ ]
42520
+ },
42521
+ {
42522
+ "name": "stdout",
42523
+ "output_type": "stream",
42524
+ "text": [
42525
+ "OK\n",
42526
+ "[5167/10000] (14.69GB) Downloading: 839aaefe-1755-4131-9b89-2610481a13c4.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
42527
+ ]
42528
+ },
42529
+ {
42530
+ "name": "stdout",
42531
+ "output_type": "stream",
42532
+ "text": [
42533
+ "OK\n",
42534
+ "[5168/10000] (14.70GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-LL-A740.xml (0.05 MB)... "
42535
+ ]
42536
+ },
42537
+ {
42538
+ "name": "stdout",
42539
+ "output_type": "stream",
42540
+ "text": [
42541
+ "OK\n",
42542
+ "[5169/10000] (14.70GB) Downloading: 0247ae5b-2c4b-4190-aa02-ccec21933db3_noid_Grn.idat (7.72 MB)... "
42543
+ ]
42544
+ },
42545
+ {
42546
+ "name": "stdout",
42547
+ "output_type": "stream",
42548
+ "text": [
42549
+ "OK\n",
42550
+ "[5170/10000] (14.70GB) Downloading: TCGA-E2-A1LB-01A-01-TSA.421ba6bf-0e55-4fa7-81f3-3cf0fde480ed.svs (181.34 MB)... "
42551
+ ]
42552
+ },
42553
+ {
42554
+ "name": "stdout",
42555
+ "output_type": "stream",
42556
+ "text": [
42557
+ "OK\n",
42558
+ "[5171/10000] (14.88GB) Downloading: TCGA-LL-A740-01A-21D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.03 MB)... "
42559
+ ]
42560
+ },
42561
+ {
42562
+ "name": "stdout",
42563
+ "output_type": "stream",
42564
+ "text": [
42565
+ "OK\n",
42566
+ "[5172/10000] (14.88GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A15I.xml (0.07 MB)... "
42567
+ ]
42568
+ },
42569
+ {
42570
+ "name": "stdout",
42571
+ "output_type": "stream",
42572
+ "text": [
42573
+ "OK\n",
42574
+ "[5173/10000] (14.88GB) Downloading: ebc5fba5-4d76-4c73-8e6a-a2543f2dd210_noid_Red.idat (7.72 MB)... "
42575
+ ]
42576
+ },
42577
+ {
42578
+ "name": "stdout",
42579
+ "output_type": "stream",
42580
+ "text": [
42581
+ "OK\n",
42582
+ "[5174/10000] (14.89GB) Downloading: nationwidechildrens.org_clinical.TCGA-E2-A1LB.xml (0.09 MB)... "
42583
+ ]
42584
+ },
42585
+ {
42586
+ "name": "stdout",
42587
+ "output_type": "stream",
42588
+ "text": [
42589
+ "OK\n",
42590
+ "[5175/10000] (14.89GB) Downloading: TCGA-BRCA.d9b9b065-fec4-4abf-b818-6f832d64ead4.ascat3.allelic_specific.seg.txt (0.01 MB)... "
42591
+ ]
42592
+ },
42593
+ {
42594
+ "name": "stdout",
42595
+ "output_type": "stream",
42596
+ "text": [
42597
+ "OK\n",
42598
+ "[5176/10000] (14.89GB) Downloading: nationwidechildrens.org_ssf.TCGA-LL-A740.xml (0.01 MB)... "
42599
+ ]
42600
+ },
42601
+ {
42602
+ "name": "stdout",
42603
+ "output_type": "stream",
42604
+ "text": [
42605
+ "OK\n",
42606
+ "[5177/10000] (14.89GB) Downloading: TCGA-BRCA.db6a187b-083a-4f71-9d8b-f08b5f208d7e.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
42607
+ ]
42608
+ },
42609
+ {
42610
+ "name": "stdout",
42611
+ "output_type": "stream",
42612
+ "text": [
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134
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191
+ AGID02167 2475 PA5-64616 Set163 FRS2-alpha_pY196 0.2023903
192
+ AGID02213 2575 ab124892 Set163 FTO -0.2977397
193
+ AGID02141 2446 12263 Old G6PD 0.8537
194
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195
+ AGID00412 274 AM4300 Old GAPDH 0.20565
196
+ AGID00086 764 558686 Old GATA3 2.0604
197
+ AGID00383 1578 4253 Old GATA6 0.169815
198
+ AGID00289 1634 12601-1-AP Set163 GCLC -0.3057848
199
+ AGID00305 1745 ab124827 Set163 GCLM 0.0006002499
200
+ AGID00212 1263 3305 Old GCN5L2 -0.117714
201
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202
+ AGID00263 1520 ab69838 Set163 Gli3 0.2770391
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor -0.2498348
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 -0.8945709
205
+ AGID00262 1491 ab156876 Set163 Glutaminase -0.03212981
206
+ AGID00319 1807 4275 Set163 Granzyme-B -0.4274848
207
+ AGID00368 2169 ab183737 Set163 GRB7 0.2120695
208
+ AGID00396 2339 3593 Set163 Grp75 -0.5717748
209
+ AGID00174 1163 9315 Set163 GSK-3B 0.2437794
210
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211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA -0.062695
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 0.897895
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
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216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 -0.01654481
217
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218
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219
+ AGID00110 911 sc-285 Old HER3 -0.197065
220
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221
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222
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223
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224
+ AGID00442 1023 2867 Set163 Hexokinase-II -0.1661813
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
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227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 0.5024351
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 0.1184389
229
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230
+ AGID00035 321 2402 Set163 HSP27 0.2948052
231
+ AGID00036 323 2401 Set163 HSP27_pS82 1.47898
232
+ AGID00320 1808 12165 Set163 HSP60 -0.237975
233
+ AGID00037 325 4872 Old HSP70 1.7222
234
+ AGID00366 2158 86630 Set163 IDO 1.017675
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.308965
236
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237
+ AGID00090 793 611504 Set163 IGFBP3 0.07196993
238
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239
+ AGID00336 1949 12153 Set163 IL-6 0.4430549
240
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241
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242
+ AGID00272 1586 3025 Set163 IR-b -0.6058198
243
+ AGID00519 2519 4302 Set163 IRF-3 0.4753355
244
+ AGID00520 2520 4947 Set163 IRF-3_pS396 0.02552971
245
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246
+ AGID00092 802 06-248 Old IRS1 0.25558
247
+ AGID00040 371 4502 Set163 IRS2 -0.3132302
248
+ AGID00250 1394 sc-13157 Old JAB1 0.0241075
249
+ AGID00256 1413 ab109536 Set163 Jagged1 -0.05888422
250
+ AGID00177 1166 3230 Old JAK2 0.187935
251
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252
+ AGID02136 2439 PA5-28262 Old JNK2 0.0823835
253
+ AGID00307 1757 ab10484 Set163 KAP1 0.6400047
254
+ AGID00528 904 2180 Old KU80 -0.2147905
255
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256
+ AGID00290 1643 IHC-00439 Set163 Lasu1 0.1613952
257
+ AGID00279 1618 4108 Set163 LC3A-B 0.05918498
258
+ AGID00042 397 2752 Old LCK 0.297075
259
+ AGID00119 976 3582 Old LDHA NA
260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.024214
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 0.2099952
263
+ AGID00439 2424 2796 Set163 Lyn -0.1024848
264
+ AGID02154 2460 4370 Old MAPK_pT202Y204 -0.73635
265
+ AGID00198 1222 5453 Set163 Mcl-1 -0.2744708
266
+ AGID00288 1633 AB3314P Set163 MCT4 0.05975012
267
+ AGID00175 1164 3521 Set163 MDM2_pS166 -0.06435474
268
+ AGID00044 417 1235-1/ab32576 Old MEK1 -0.17376
269
+ AGID00143 1076 9154 Old MEK1_pS217S221 -0.162315
270
+ AGID00201 1243 9125 Set163 MEK2 0.08511978
271
+ AGID00361 2118 ab51061 Set163 MelanA 0.006835232
272
+ AGID00362 2119 ab137078 Set163 Melanoma-gp100 -0.03656985
273
+ AGID00337 1951 12711 Set163 MERIT40 -0.4382954
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 0.05258026
275
+ AGID02212 2574 ab195352 Set163 METTL3 0.1052102
276
+ AGID00225 1323 sc-20121 Set163 MIF -0.2662897
277
+ AGID00137 1062 WH0054206M1 Old MIG6 -0.028728
278
+ AGID00403 2117 ab20663 Set163 MITF -0.09793513
279
+ AGID00503 1067 ab3298 Old MITOCHONDRIA NA
280
+ AGID00321 1809 14739 Set163 Mitofusin-1 -0.2854585
281
+ AGID00322 1810 11925 Set163 Mitofusin-2 -0.2144399
282
+ AGID00389 2324 3515 Set163 MLH1 -0.1225599
283
+ AGID00312 1780 14993 Set163 MLKL -0.0989599
284
+ AGID00402 2359 MAB3328 Set163 MMP14 0.4496302
285
+ AGID00045 435 4022 Set163 MMP2 0.002907395
286
+ AGID00122 1005 2195 Set163 Mnk1 0.530289
287
+ AGID00331 1899 sc-377312 Set163 MR1 0.3994651
288
+ AGID00273 1589 ab103319 Set163 MRAP -0.04616974
289
+ AGID00530 440 4847 Old MRE11 0.23928
290
+ AGID00390 905 2850 Old MSH2 -0.3525645
291
+ AGID00138 1063 22030002 Old MSH6 -0.53061
292
+ AGID00299 1675 ab76148 Set163 MSI2 0.1369553
293
+ AGID00232 1344 ab14705 Set163 MTCO1 -0.5611314
294
+ AGID00046 444 2983 Old MTOR -0.367755
295
+ AGID00047 446 2971 Old MTOR_pS2448 0.12312
296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 0.05518508
297
+ AGID00401 1139 21370002 Old MYH11 -0.371595
298
+ AGID00291 1647 3403 Old MYOSINIIA 0.2788
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 0.0221275
300
+ AGID00318 1803 4282 Set163 Myt1 0.07034
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN 0.2807945
303
+ AGID00156 1126 3217 Old NDRG1_pT346 0.778665
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 0.03122026
305
+ AGID00134 1046 22710002 Old NF2 -0.253726
306
+ AGID00048 457 3033 Old NFKBP65_pS536 0.545145
307
+ AGID02155 2461 3608 Old NOTCH1 -0.066861
308
+ AGID00340 1969 4147 Set163 Notch1-cleaved 0.189195
309
+ AGID00087 767 sc-5593 Set163 Notch3 0.1687902
310
+ AGID00258 1420 3187 Set163 NQO1 0.4200451
311
+ AGID00162 1136 sc-31 Old NRAS -0.105615
312
+ AGID00257 1419 12721 Old NRF2 NA
313
+ AGID00297 1669 2750 Set163 Oct-4 0.1880952
314
+ AGID00420 466 1712-1/ab40803 Old P16INK4A -0.134599
315
+ AGID00384 470 sc-6246 Old P21 0.20935
316
+ AGID00105 897 1591-1/ab32034 Old P27 0.038506
317
+ AGID00096 842 AF1555 Old P27_pT157 0.15456
318
+ AGID00099 878 ab64949 Old P27_pT198 0.20466
319
+ AGID00181 1175 9228 Set163 p38-a 0.1399791
320
+ AGID00098 479 9211 Old P38_pT180Y182 -0.275185
321
+ AGID00049 478 9212 Old P38MAPK 0.28694
322
+ AGID00151 1119 4695 Set163 p44-42-MAPK -0.1330648
323
+ AGID00050 481 9282 Old P53 -0.17937
324
+ AGID00490 1187 610833 Old P62LCKLIGAND -0.1370195
325
+ AGID00545 1415 ab53039 Old P63 NA
326
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327
+ AGID00051 493 1494-1/ab32529 Old P70S6K1 -0.1938
328
+ AGID00085 759 9347 Old P90RSK -0.218985
329
+ AGID00531 770 9344 Old P90RSK_pT359S363 -0.060685
330
+ AGID00182 1178 9346 Set163 p90RSK_pT573 0.02446013
331
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332
+ AGID00224 1322 HPA035895 Set163 PAICS -0.2956397
333
+ AGID00323 1811 2602 Set163 PAK1 -0.3115602
334
+ AGID02199 2517 PA5-69540 Set163 PAK4 0.07068514
335
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336
+ AGID00374 2209 66564 Set163 PARG 0.16583
337
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338
+ AGID00468 501 9546 Old PARPCLEAVED -0.0241385
339
+ AGID00274 1591 ab53715 Set163 Patched -0.06469978
340
+ AGID00513 2486 60433 Set163 PAX6 -0.03166985
341
+ AGID00441 1621 9857 Set163 PAX8 0.6636739
342
+ AGID00054 504 2542 Old PAXILLIN 0.303655
343
+ AGID00055 509 2130 Old PCADHERIN -0.0896045
344
+ AGID00248 511 ab29 Old PCNA -0.0619666
345
+ AGID00413 2095 43248 Old PDCD1 NA
346
+ AGID00094 816 600-401-965 Old PDCD4 -0.574895
347
+ AGID00385 1225 3169 Set163 PDGFRB 0.1809852
348
+ AGID00210 1258 ab110332 Set163 PDH 0.1356841
349
+ AGID00324 1817 3205 Set163 PDHA1 -0.1796854
350
+ AGID00280 1622 3820 Set163 PDHK1 0.1573502
351
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352
+ AGID00057 516 3061 Old PDK1_pS241 0.0840242
353
+ AGID00300 1234 sc-19090 Old PDL1 0.2942
354
+ AGID00124 1017 2780 Old PEA15 -0.36538
355
+ AGID00125 1018 44-836G Old PEA15_pS116 0.17453
356
+ AGID00440 2429 3192 Set163 PERK -0.2251904
357
+ AGID02207 2569 ab192876 Set163 PGM1 -0.1481804
358
+ AGID00281 1623 13428 Set163 PHGDH -0.01804037
359
+ AGID00425 2399 22789-1-AP Set163 PHLPP -0.09213974
360
+ AGID00226 1330 sc-376412 Set163 PI3K-p110-b -0.06861976
361
+ AGID00093 808 4255 Old PI3KP110ALPHA -0.0928875
362
+ AGID00058 523 06-195 Old PI3KP85 -0.0898595
363
+ AGID00296 1667 5675 Set163 PKA-a -0.05106489
364
+ AGID00259 1426 9375 Set163 PKC-a-b-II_pT638_T641 -0.03882975
365
+ AGID00172 529 05-154 Old PKCALPHA -0.912005
366
+ AGID00460 530 06-822 Old PKCALPHA_pS657 -0.71439
367
+ AGID00114 932 07-875 Old PKCDELTA_pS664 0.125097
368
+ AGID00163 1137 9371 Old PKCPANBETAII_pS660 -0.261785
369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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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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389
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390
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391
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392
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393
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394
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395
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396
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397
+ AGID00547 735 3221 Old RET_pY905 NA
398
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399
+ AGID00159 1129 2114 Old RICTOR -0.716995
400
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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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412
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413
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414
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415
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416
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417
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418
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419
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420
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421
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422
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423
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424
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425
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426
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427
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428
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429
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430
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431
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432
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433
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434
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435
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436
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437
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438
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439
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440
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441
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442
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443
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444
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445
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446
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447
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448
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449
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450
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451
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452
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453
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454
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455
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456
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457
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458
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459
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460
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461
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462
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463
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464
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465
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466
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467
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468
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469
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470
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471
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472
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473
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474
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475
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476
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477
+ AGID00076 699 2042 Set163 XIAP -0.2484203
478
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479
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480
+ AGID02137 2440 PA5-29359 Old XRCC1 -0.101623
481
+ AGID00088 780 sc-15407 Old YAP -0.19417
482
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483
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484
+ AGID00095 835 2900 Old YB1_pS102 -0.235464
485
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486
+ AGID02210 2572 ab220161 Set163 YTHDF3 0.006450208
487
+ AGID00326 1828 2705 Set163 ZAP-70 0.7596431
488
+ AGID00432 2244 sc-25388 Set163 ZEB1 0.09314853
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data/gdc_data_organized/095c7985-3842-494f-b591-706ad1cd2133/nationwidechildrens.org_clinical.TCGA-AO-A03M.xml ADDED
@@ -0,0 +1,397 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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_v1.5="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/1.5" xmlns:follow_up_v2.1="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/2.1" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">0EFB790C-A9C7-4CA2-991F-7478EC9D324A</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">80.84.0</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="465082">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" source_system_identifier="465083" 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="465071">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="465062">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="465067">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">-10616</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="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">1455</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="465069">WHITE</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-AO-A03M</shared:bcr_patient_barcode>
33
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">AO</shared:tissue_source_site>
34
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A03M</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">095c7985-3842-494f-b591-706ad1cd2133</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="465072">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">29</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="465089">2006</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="465070">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="465068">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="Not Available" restricted="false"/>
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="465101">2</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="465114"/>
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="465119"/>
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="465084">Left Upper Outer Quadrant</clin_shared:anatomic_neoplasm_subdivision>
52
+ <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="465084">Left</clin_shared:anatomic_neoplasm_subdivision>
53
+ </brca:anatomic_neoplasm_subdivisions>
54
+ <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="465129">1.3</brca_shared:her2_neu_chromosone_17_signal_ratio_value>
55
+ <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="465098">Sentinel node biopsy alone</brca:axillary_lymph_node_stage_method_type>
56
+ <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="465099"/>
57
+ <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="465092">Simple Mastectomy</brca:breast_carcinoma_surgical_procedure_name>
58
+ <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="465096" xsi:nil="true"/>
59
+ <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="465095"/>
60
+ <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="465093"/>
61
+ <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="465085">Infiltrating Ductal Carcinoma</shared:histological_type>
62
+ <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="465086" xsi:nil="true"/>
63
+ <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="465066">Pre (&lt;6 months since LMP AND no prior bilateral ovariectomy AND not on estrogen replacement)</clin_shared:menopause_status>
64
+ <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="465115">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
65
+ <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="465100">YES</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
66
+ <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"/>
67
+ <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="465112">2+</brca_shared:immunohistochemistry_positive_cell_score>
68
+ <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="465122">2+</brca_shared:her2_immunohistochemistry_level_result>
69
+ <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="465097"/>
70
+ <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="465094">Negative</clin_shared:margin_status>
71
+ <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="465090">Core needle biopsy</clin_shared:initial_pathologic_diagnosis_method>
72
+ <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="465091" xsi:nil="true"/>
73
+ <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="465125">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
74
+ <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="465110">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
75
+ <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="465120">Negative</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
76
+ <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="465103">0</clin_shared:number_of_lymphnodes_positive_by_ihc>
77
+ <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="465102">0</clin_shared:number_of_lymphnodes_positive_by_he>
78
+ <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="465118"/>
79
+ <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="465113"/>
80
+ <brca_shared:her2_erbb_pos_finding_cell_percent_category preferred_name="her2_ihc_percent_positive" display_order="71" cde="3086980" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="465121">30-39%</brca_shared:her2_erbb_pos_finding_cell_percent_category>
81
+ <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="465123"/>
82
+ <brca_shared:her2_erbb_method_calculation_method_text preferred_name="her2_positivity_method_text" display_order="74" cde="3087487" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="465124">3+ Positive</brca_shared:her2_erbb_method_calculation_method_text>
83
+ <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="465128"/>
84
+ <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="465130"/>
85
+ <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="Completed" restricted="false" source_system_identifier="465131">>= 2.0 Positive</brca_shared:her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text>
86
+ <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="465060">NO</clin_shared:tissue_prospective_collection_indicator>
87
+ <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="465061">YES</clin_shared:tissue_retrospective_collection_indicator>
88
+ <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="465127"/>
89
+ <brca:first_nonlymph_node_metastasis_anatomic_sites>
90
+ <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="465108"/>
91
+ <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="465109"/>
92
+ </brca:first_nonlymph_node_metastasis_anatomic_sites>
93
+ <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="465111">70-79%</brca_shared:er_level_cell_percentage_category>
94
+ <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="465116">60-69%</brca_shared:progesterone_receptor_level_cell_percent_category>
95
+ <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"/>
96
+ <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="465132"/>
97
+ <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="465133"/>
98
+ <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="465134"/>
99
+ <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="465135"/>
100
+ <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="465136"/>
101
+ <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="465137"/>
102
+ <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="465142"/>
103
+ <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="465138"/>
104
+ <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="465139"/>
105
+ <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="465140"/>
106
+ <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="465141"/>
107
+ <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="465143"/>
108
+ <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="465144"/>
109
+ <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="465145"/>
110
+ <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="465146"/>
111
+ <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="465147"/>
112
+ <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="465149"/>
113
+ <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="465150"/>
114
+ <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="465151"/>
115
+ <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="465152"/>
116
+ <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="465153"/>
117
+ <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="465148"/>
118
+ <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="465126"/>
119
+ <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"/>
120
+ <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="465117">3+</brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score>
121
+ <shared_stage:stage_event system="AJCC">
122
+ <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="1080136">6th</shared_stage:system_version>
123
+ <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"/>
124
+ <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="465107">Stage I</shared_stage:pathologic_stage>
125
+ <shared_stage:tnm_categories>
126
+ <shared_stage:clinical_categories>
127
+ <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"/>
128
+ <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"/>
129
+ <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"/>
130
+ </shared_stage:clinical_categories>
131
+ <shared_stage:pathologic_categories>
132
+ <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="465104">T1c</shared_stage:pathologic_T>
133
+ <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="465105">N0 (i-)</shared_stage:pathologic_N>
134
+ <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="465106">M0</shared_stage:pathologic_M>
135
+ </shared_stage:pathologic_categories>
136
+ </shared_stage:tnm_categories>
137
+ <shared_stage:psa>
138
+ <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"/>
139
+ <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"/>
140
+ </shared_stage:psa>
141
+ <shared_stage:gleason_grading>
142
+ <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"/>
143
+ <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"/>
144
+ <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"/>
145
+ <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"/>
146
+ </shared_stage:gleason_grading>
147
+ <shared_stage:ann_arbor>
148
+ <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"/>
149
+ <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"/>
150
+ </shared_stage:ann_arbor>
151
+ <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"/>
152
+ <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"/>
153
+ <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"/>
154
+ </shared_stage:stage_event>
155
+ <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"/>
156
+ <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"/>
157
+ <brca_nte:new_tumor_events>
158
+ <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"/>
159
+ </brca_nte:new_tumor_events>
160
+ <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="465058">9</clin_shared:day_of_form_completion>
161
+ <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="465057">1</clin_shared:month_of_form_completion>
162
+ <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="465059">2011</clin_shared:year_of_form_completion>
163
+ <brca:follow_ups>
164
+ <follow_up_v1.5:follow_up version="1.5" sequence="1">
165
+ <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-AO-A03M-F5861</clin_shared:bcr_followup_barcode>
166
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">1F587B26-56C6-43CE-B5E9-1666DA4EAB4D</clin_shared:bcr_followup_uuid>
167
+ <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">1455</clin_shared:days_to_last_followup>
168
+ <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="465162">Alive</clin_shared:vital_status>
169
+ <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="465163">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
170
+ <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=""/>
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: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="465170">NO</clin_shared:radiation_therapy>
173
+ <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="465171">YES</clin_shared:postoperative_rx_tx>
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 Available" preferred_name="new_tumor_event_dx_days_to" display_order="89" cde_ver="1.000"/>
175
+ <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="465865"/>
176
+ <nte:days_to_additional_surgery_locoregional_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408572" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_loco" display_order="9999" cde_ver="1.000"/>
177
+ <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="Not Available" restricted="false" source_system_identifier="465869"/>
178
+ <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="465870"/>
179
+ <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="465871"/>
180
+ <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="465872"/>
181
+ <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="465873"/>
182
+ <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="Not Available" restricted="false" source_system_identifier="465874"/>
183
+ <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="465875"/>
184
+ <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="465876"/>
185
+ <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="465877"/>
186
+ <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="465878"/>
187
+ <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="465879"/>
188
+ <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="465880"/>
189
+ <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="465881"/>
190
+ <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="465882"/>
191
+ <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="465883"/>
192
+ <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="465884"/>
193
+ <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="465885"/>
194
+ <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="465886"/>
195
+ <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="465887"/>
196
+ <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="465888"/>
197
+ <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="465889"/>
198
+ <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="465890"/>
199
+ <nte:additional_surgery_metastatic_procedure preferred_name="new_tumor_event_surgery_met" display_order="999" cde="3008757" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="465891"/>
200
+ <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"/>
201
+ <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="465895"/>
202
+ <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="465896"/>
203
+ <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="465897"/>
204
+ <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="465898"/>
205
+ <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="465899"/>
206
+ <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="465900"/>
207
+ <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="465901"/>
208
+ <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="465902"/>
209
+ <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="465903"/>
210
+ <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="465904"/>
211
+ <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="465905"/>
212
+ <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="465906"/>
213
+ <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="465907"/>
214
+ <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="465908"/>
215
+ <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="465909"/>
216
+ <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="465910"/>
217
+ <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="465911"/>
218
+ <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="465912"/>
219
+ <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="465913"/>
220
+ <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="465914"/>
221
+ <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="465915"/>
222
+ <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="465916"/>
223
+ <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="465917"/>
224
+ <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="465918"/>
225
+ <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="465157">9</clin_shared:day_of_form_completion>
226
+ <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="465156">1</clin_shared:month_of_form_completion>
227
+ <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="465158">2011</clin_shared:year_of_form_completion>
228
+ </follow_up_v1.5:follow_up>
229
+ <follow_up_v2.1:follow_up version="2.1" sequence="2">
230
+ <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-AO-A03M-F30186</clin_shared:bcr_followup_barcode>
231
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">62767797-1CEB-468B-A320-FB552F1B6627</clin_shared:bcr_followup_uuid>
232
+ <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="1837780">Scheduled Follow-up Submission</clin_shared:followup_case_report_form_submission_reason>
233
+ <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="1837797">NO</clin_shared:radiation_therapy>
234
+ <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="1837798">YES</clin_shared:postoperative_rx_tx>
235
+ <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="1837799">Alive</clin_shared:vital_status>
236
+ <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">1866</clin_shared:days_to_last_followup>
237
+ <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"/>
238
+ <clin_shared:person_neoplasm_cancer_status preferred_name="tumor_status" display_order="16" cde="2759550" cde_ver="1.000" xsd_ver="1.9" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1837806"/>
239
+ <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="1837807">NO</nte:new_tumor_event_after_initial_treatment>
240
+ <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"/>
241
+ <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="1837811"/>
242
+ <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="1837812"/>
243
+ <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="1837813"/>
244
+ <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="1837814"/>
245
+ <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"/>
246
+ <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="1837818"/>
247
+ <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="1837819"/>
248
+ <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="1837820"/>
249
+ <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="1837821"/>
250
+ <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="1837822"/>
251
+ <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="1837823"/>
252
+ <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="1837824"/>
253
+ <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="1837825"/>
254
+ <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="1837826"/>
255
+ <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="1837827"/>
256
+ <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="1837828"/>
257
+ <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="1837829"/>
258
+ <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="1837830"/>
259
+ <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="1837831"/>
260
+ <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="1837832"/>
261
+ <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="1837833"/>
262
+ <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="1837834"/>
263
+ <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="1837835"/>
264
+ <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="1837836"/>
265
+ <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="1837837"/>
266
+ <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="1837838"/>
267
+ <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="1837839"/>
268
+ <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="1837840"/>
269
+ <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="1837841"/>
270
+ <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="1837842"/>
271
+ <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="1837843"/>
272
+ <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="1837778">4</clin_shared:day_of_form_completion>
273
+ <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="1837777">4</clin_shared:month_of_form_completion>
274
+ <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="1837779">2012</clin_shared:year_of_form_completion>
275
+ </follow_up_v2.1:follow_up>
276
+ </brca:follow_ups>
277
+ <rx:drugs>
278
+ <rx:drug>
279
+ <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"/>
280
+ <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="473714">1</rx:regimen_number>
281
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-AO-A03M-D5995</rx:bcr_drug_barcode>
282
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">20c31de8-d96e-4867-8335-719ccb5806a3</rx:bcr_drug_uuid>
283
+ <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="473723">1100</rx:total_dose>
284
+ <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="473724">mg</rx:total_dose_units>
285
+ <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="473721">175</rx:prescribed_dose>
286
+ <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="473722">mg/m2</rx:prescribed_dose_units>
287
+ <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="Completed" restricted="false" source_system_identifier="473720">4</rx:number_cycles>
288
+ <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">119</rx:days_to_drug_therapy_start>
289
+ <rx:days_to_drug_therapy_end precision="day" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">161</rx:days_to_drug_therapy_end>
290
+ <rx:therapy_types>
291
+ <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="473717">Chemotherapy</rx:therapy_type>
292
+ <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="473718"/>
293
+ </rx:therapy_types>
294
+ <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="473719">Paclitaxel</rx:drug_name>
295
+ <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"/>
296
+ <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="473715">ADJUVANT</clin_shared:regimen_indication>
297
+ <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="473716"/>
298
+ <rx:route_of_administrations>
299
+ <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="473725">IV</rx:route_of_administration>
300
+ </rx:route_of_administrations>
301
+ <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="473729">NO</rx:therapy_ongoing>
302
+ <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"/>
303
+ <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="473712">10</clin_shared:day_of_form_completion>
304
+ <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="473711">1</clin_shared:month_of_form_completion>
305
+ <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="473713">2011</clin_shared:year_of_form_completion>
306
+ </rx:drug>
307
+ <rx:drug>
308
+ <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"/>
309
+ <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="473783">2</rx:regimen_number>
310
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-AO-A03M-D5996</rx:bcr_drug_barcode>
311
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">c13d0b89-a948-4f3f-ac88-4e9387d555db</rx:bcr_drug_uuid>
312
+ <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="473792"/>
313
+ <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="473793"/>
314
+ <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="473790">20</rx:prescribed_dose>
315
+ <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="473791">mg/day</rx:prescribed_dose_units>
316
+ <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="473789"/>
317
+ <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">161</rx:days_to_drug_therapy_start>
318
+ <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"/>
319
+ <rx:therapy_types>
320
+ <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="473786">Hormone Therapy</rx:therapy_type>
321
+ <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="473787"/>
322
+ </rx:therapy_types>
323
+ <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="473788">Tamoxifen</rx:drug_name>
324
+ <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"/>
325
+ <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="473784">ADJUVANT</clin_shared:regimen_indication>
326
+ <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="473785"/>
327
+ <rx:route_of_administrations>
328
+ <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="473794">PO</rx:route_of_administration>
329
+ </rx:route_of_administrations>
330
+ <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="473798">YES</rx:therapy_ongoing>
331
+ <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"/>
332
+ <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="473781">10</clin_shared:day_of_form_completion>
333
+ <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="473780">1</clin_shared:month_of_form_completion>
334
+ <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="473782">2011</clin_shared:year_of_form_completion>
335
+ </rx:drug>
336
+ <rx:drug>
337
+ <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"/>
338
+ <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="473690">1</rx:regimen_number>
339
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-AO-A03M-D5994</rx:bcr_drug_barcode>
340
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">9bdbaaed-6f6d-4d45-a7c0-dd1366b813db</rx:bcr_drug_uuid>
341
+ <rx:total_dose preferred_name="total_dose" display_order="999" cde="1515" cde_ver="4.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="473699">3768</rx:total_dose>
342
+ <rx:total_dose_units preferred_name="pharmaceutical_tx_total_dose_units" display_order="999" cde="3088785" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="473700">mg</rx:total_dose_units>
343
+ <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="473697">600</rx:prescribed_dose>
344
+ <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="473698">mg/m2</rx:prescribed_dose_units>
345
+ <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="Completed" restricted="false" source_system_identifier="473696">4</rx:number_cycles>
346
+ <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">63</rx:days_to_drug_therapy_start>
347
+ <rx:days_to_drug_therapy_end precision="day" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">105</rx:days_to_drug_therapy_end>
348
+ <rx:therapy_types>
349
+ <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="473693">Chemotherapy</rx:therapy_type>
350
+ <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="473694"/>
351
+ </rx:therapy_types>
352
+ <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="473695">Cyclophosphamide</rx:drug_name>
353
+ <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"/>
354
+ <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="473691">ADJUVANT</clin_shared:regimen_indication>
355
+ <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="473692"/>
356
+ <rx:route_of_administrations>
357
+ <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="473701">IV</rx:route_of_administration>
358
+ </rx:route_of_administrations>
359
+ <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="473705">NO</rx:therapy_ongoing>
360
+ <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"/>
361
+ <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="473617">10</clin_shared:day_of_form_completion>
362
+ <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="473616">1</clin_shared:month_of_form_completion>
363
+ <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="473618">2011</clin_shared:year_of_form_completion>
364
+ </rx:drug>
365
+ <rx:drug>
366
+ <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"/>
367
+ <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="473595">1</rx:regimen_number>
368
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-AO-A03M-D5992</rx:bcr_drug_barcode>
369
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">e5a69005-a19c-4fc9-a8f2-9a2c939cb391</rx:bcr_drug_uuid>
370
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1875
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1876
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1877
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1878
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1879
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1880
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1882
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data/gdc_data_organized/128d198e-9b22-427c-90db-3714455f3a17/SHAWM_p_TCGAb72_SNP_N_GenomeWideSNP_6_C07_698036.nocnv_grch38.seg.v2.txt ADDED
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51
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:portion_number>
52
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
53
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A21W</bio:plate_id>
54
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">30</bio:center_id>
55
+ <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3</bio:shipment_portion_day_of_shipment>
56
+ <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">4</bio:shipment_portion_month_of_shipment>
57
+ <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2012</bio:shipment_portion_year_of_shipment>
58
+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-13-A21W-30</bio:shipment_portion_bcr_aliquot_barcode>
59
+ <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">77E6014F-D836-444D-BBE5-4C8216A190AF</bio:bcr_shipment_portion_uuid>
60
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
61
+ </bio:shipment_portion>
62
+ <bio:shipment_portion>
63
+ <admin:additional_studies/>
64
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">21</bio:portion_number>
65
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:portion_sequence>
66
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A13D</bio:plate_id>
67
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">20</bio:center_id>
68
+ <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">22</bio:shipment_portion_day_of_shipment>
69
+ <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3</bio:shipment_portion_month_of_shipment>
70
+ <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2011</bio:shipment_portion_year_of_shipment>
71
+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-21-A13D-20</bio:shipment_portion_bcr_aliquot_barcode>
72
+ <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">73634c23-d25e-4268-a1bb-f8270a5d1d00</bio:bcr_shipment_portion_uuid>
73
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
74
+ </bio:shipment_portion>
75
+ <bio:portion>
76
+ <admin:additional_studies/>
77
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
78
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
79
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:day_of_creation>
80
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_creation>
81
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
82
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
83
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11</bio:bcr_portion_barcode>
84
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d609fbf1-909e-4350-898a-490acbd535a0</bio:bcr_portion_uuid>
85
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
86
+ <bio:analytes>
87
+ <bio:analyte>
88
+ <admin:additional_studies/>
89
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
90
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
91
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
92
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
93
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.92</bio:a260_a280_ratio>
94
+ <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>
95
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
96
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D</bio:bcr_analyte_barcode>
97
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9cd08677-1afd-46ee-bf7e-501643d81fe5</bio:bcr_analyte_uuid>
98
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
99
+ <bio:aliquots>
100
+ <bio:aliquot>
101
+ <admin:additional_studies/>
102
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A086</bio:plate_id>
103
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
104
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
105
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
106
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
107
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D-A086-02</bio:bcr_aliquot_barcode>
108
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9517240d-e0d5-47ee-a655-7315bd0b83ca</bio:bcr_aliquot_uuid>
109
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
110
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
111
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
112
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
113
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
114
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100470394</bio:biospecimen_barcode_bottom>
115
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
116
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
117
+ </bio:aliquot>
118
+ <bio:aliquot>
119
+ <admin:additional_studies/>
120
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A087</bio:plate_id>
121
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
122
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
123
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
124
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
125
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D-A087-01</bio:bcr_aliquot_barcode>
126
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">eaf1eb18-1568-459d-be40-71e5e92df673</bio:bcr_aliquot_uuid>
127
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
128
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
129
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
130
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
131
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
132
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100472122</bio:biospecimen_barcode_bottom>
133
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
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="">A088</bio:plate_id>
139
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
140
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
141
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
142
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
143
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D-A088-05</bio:bcr_aliquot_barcode>
144
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">952831ef-d68e-4007-b96c-1ff612623bfe</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="">3.74</bio:quantity>
147
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</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="">5</bio:plate_column>
150
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100471162</bio:biospecimen_barcode_bottom>
151
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
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="">A099</bio:plate_id>
157
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</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="">10</bio:month_of_shipment>
160
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
161
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D-A099-09</bio:bcr_aliquot_barcode>
162
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">147489f2-c34b-4ee1-a9ab-cb8469278af9</bio:bcr_aliquot_uuid>
163
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
164
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.82</bio:quantity>
165
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.00</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="">5</bio:plate_column>
168
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100475482</bio:biospecimen_barcode_bottom>
169
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
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:aliquot>
173
+ <admin:additional_studies/>
174
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A10P</bio:plate_id>
175
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
176
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">20</bio:day_of_shipment>
177
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_shipment>
178
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
179
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11D-A10P-05</bio:bcr_aliquot_barcode>
180
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6f1aeadb-fd0a-4ea0-89a6-cc6222d789f8</bio:bcr_aliquot_uuid>
181
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.14</bio:concentration>
182
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.74</bio:quantity>
183
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
184
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">A</bio:plate_row>
185
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9</bio:plate_column>
186
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100477278</bio:biospecimen_barcode_bottom>
187
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
188
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
189
+ </bio:aliquot>
190
+ </bio:aliquots>
191
+ <bio:protocols>
192
+ <bio:protocol>
193
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
194
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
195
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
196
+ </bio:protocol>
197
+ </bio:protocols>
198
+ <bio:dna>
199
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
200
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
201
+ </bio:dna>
202
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
203
+ </bio:analyte>
204
+ <bio:analyte>
205
+ <admin:additional_studies/>
206
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
207
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
208
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
209
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
210
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.84</bio:a260_a280_ratio>
211
+ <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>
212
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
213
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11R</bio:bcr_analyte_barcode>
214
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4c7b924a-b6eb-4b30-9de4-b45d502bcabc</bio:bcr_analyte_uuid>
215
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
216
+ <bio:aliquots>
217
+ <bio:aliquot>
218
+ <admin:additional_studies/>
219
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A084</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="">29</bio:day_of_shipment>
222
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
223
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
224
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11R-A084-07</bio:bcr_aliquot_barcode>
225
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">491c6c41-d1c5-4be7-bb7c-9df7275aa388</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="">C</bio:plate_row>
230
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
231
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100471882</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:aliquot>
236
+ <admin:additional_studies/>
237
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A085</bio:plate_id>
238
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
239
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
240
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:month_of_shipment>
241
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
242
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11R-A085-13</bio:bcr_aliquot_barcode>
243
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3f27e873-4e3c-402f-9435-f87ec9f0203d</bio:bcr_aliquot_uuid>
244
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
245
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
246
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
247
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
248
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
249
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100471594</bio:biospecimen_barcode_bottom>
250
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
251
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
252
+ </bio:aliquot>
253
+ </bio:aliquots>
254
+ <bio:protocols>
255
+ <bio:protocol>
256
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
257
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
258
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
259
+ </bio:protocol>
260
+ </bio:protocols>
261
+ <bio:rna>
262
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.50</bio:ratio_28s_18s>
263
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.50</bio:rinvalue>
264
+ </bio:rna>
265
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
266
+ </bio:analyte>
267
+ <bio:analyte>
268
+ <admin:additional_studies/>
269
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
270
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
271
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
272
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
273
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
274
+ <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>
275
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
276
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11W</bio:bcr_analyte_barcode>
277
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">06B145BB-316C-4F0D-BD8A-5A9F4D4CD87F</bio:bcr_analyte_uuid>
278
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
279
+ <bio:aliquots>
280
+ <bio:aliquot>
281
+ <admin:additional_studies/>
282
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A097</bio:plate_id>
283
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
284
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
285
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:month_of_shipment>
286
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
287
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11W-A097-09</bio:bcr_aliquot_barcode>
288
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">c7918143-dbce-45b3-8d24-2993a9e2b7f4</bio:bcr_aliquot_uuid>
289
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
290
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
291
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
292
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
293
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
294
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100479322</bio:biospecimen_barcode_bottom>
295
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
296
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
297
+ </bio:aliquot>
298
+ </bio:aliquots>
299
+ <bio:protocols>
300
+ <bio:protocol>
301
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
302
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
303
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
304
+ </bio:protocol>
305
+ </bio:protocols>
306
+ <bio:dna>
307
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
308
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
309
+ </bio:dna>
310
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
311
+ </bio:analyte>
312
+ <bio:analyte>
313
+ <admin:additional_studies/>
314
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
315
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
316
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
317
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
318
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
319
+ <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>
320
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
321
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11X</bio:bcr_analyte_barcode>
322
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8134DCBD-A55D-4987-97BC-98AE3BCB7421</bio:bcr_analyte_uuid>
323
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
324
+ <bio:aliquots>
325
+ <bio:aliquot>
326
+ <admin:additional_studies/>
327
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A098</bio:plate_id>
328
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
329
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_shipment>
330
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:month_of_shipment>
331
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
332
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-11X-A098-09</bio:bcr_aliquot_barcode>
333
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">77a8681d-9db3-4a01-b43a-96aa7c0d1490</bio:bcr_aliquot_uuid>
334
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
335
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
336
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
337
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
338
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
339
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100473850</bio:biospecimen_barcode_bottom>
340
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
341
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
342
+ </bio:aliquot>
343
+ </bio:aliquots>
344
+ <bio:protocols>
345
+ <bio:protocol>
346
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G X</bio:experimental_protocol_type>
347
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
348
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
349
+ </bio:protocol>
350
+ </bio:protocols>
351
+ <bio:dna>
352
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
353
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
354
+ </bio:dna>
355
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
356
+ </bio:analyte>
357
+ </bio:analytes>
358
+ <bio:slides>
359
+ <bio:slide>
360
+ <admin:additional_studies/>
361
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
362
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
363
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_cells>
364
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_nuclei>
365
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
366
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
367
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_stromal_cells>
368
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
369
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_lymphocyte_infiltration>
370
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_monocyte_infiltration>
371
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
372
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:percent_neutrophil_infiltration>
373
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
374
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-01-BSA</shared:bcr_slide_barcode>
375
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3613219b-687b-419f-ac8f-33b668b72446</shared:bcr_slide_uuid>
376
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-01-BSA.3613219b-687b-419f-ac8f-33b668b72446.svs</shared:image_file_name>
377
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
378
+ </bio:slide>
379
+ <bio:slide>
380
+ <admin:additional_studies/>
381
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
382
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
383
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
384
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
385
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
386
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">5</bio:percent_necrosis>
387
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_stromal_cells>
388
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
389
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_lymphocyte_infiltration>
390
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_monocyte_infiltration>
391
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
392
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:percent_neutrophil_infiltration>
393
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
394
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-01-TSA</shared:bcr_slide_barcode>
395
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8595967b-5bf7-447f-9310-10b53a1c1dfa</shared:bcr_slide_uuid>
396
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A2-A0T2-01A-01-TSA.8595967b-5bf7-447f-9310-10b53a1c1dfa.svs</shared:image_file_name>
397
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
398
+ </bio:slide>
399
+ </bio:slides>
400
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
401
+ </bio:portion>
402
+ </bio:portions>
403
+ <bio:tumor_pathology/>
404
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
405
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
406
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
407
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">0DCD80E1-173E-4A1B-BDD8-74C7D12C1313</bio:pathology_report_uuid>
408
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A2-A0T2.0DCD80E1-173E-4A1B-BDD8-74C7D12C1313.pdf</bio:pathology_report_file_name>
409
+ <bio:diagnostic_slides>
410
+ <admin:additional_studies/>
411
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">29A5C4C8-6AE8-44EE-98C2-ACBCBFBE9D60</bio:ffpe_slide_uuid>
412
+ </bio:diagnostic_slides>
413
+ </bio:sample>
414
+ <bio:sample>
415
+ <admin:additional_studies/>
416
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
417
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
418
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
419
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
420
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
421
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
422
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
423
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
424
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
425
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
426
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
427
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
428
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
429
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
430
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
431
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">261</bio:days_to_collection>
432
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
433
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
434
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-10A</bio:bcr_sample_barcode>
435
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">cb711bf0-eb99-4925-893d-485ac8beef1d</bio:bcr_sample_uuid>
436
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
437
+ <bio:portions>
438
+ <bio:portion>
439
+ <admin:additional_studies/>
440
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
441
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
442
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">21</bio:day_of_creation>
443
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">07</bio:month_of_creation>
444
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
445
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
446
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-10A-01</bio:bcr_portion_barcode>
447
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2a8dc4cc-c987-49b8-beac-11cb2414d2ed</bio:bcr_portion_uuid>
448
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
449
+ <bio:analytes>
450
+ <bio:analyte>
451
+ <admin:additional_studies/>
452
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
453
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
454
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
455
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
456
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.84</bio:a260_a280_ratio>
457
+ <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>
458
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
459
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A2-A0T2-10A-01D</bio:bcr_analyte_barcode>
460
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">b0a32fab-3da7-43e4-af07-c541d242df58</bio:bcr_analyte_uuid>
461
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
462
+ <bio:aliquots>
463
+ <bio:aliquot>
464
+ <admin:additional_studies/>
465
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A086</bio:plate_id>
466
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
467
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471
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472
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480
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481
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482
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483
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485
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486
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487
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488
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489
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493
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497
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498
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499
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500
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501
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503
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504
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506
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507
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508
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510
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511
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515
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516
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517
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518
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519
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520
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521
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522
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523
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524
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
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542
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543
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544
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545
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546
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548
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549
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551
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552
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562
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563
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564
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565
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566
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567
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568
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569
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570
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571
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572
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573
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574
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575
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576
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577
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578
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580
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581
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584
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590
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610
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The diff for this file is too large to render. See raw diff
 
data/gdc_data_organized/182c4bdf-2c58-4303-b034-459da86b9d90/TCGA-E9-A54Y-01A-21-A321-20_RPPA_data.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 0.11855
3
+ AGID00111 913 sc-23957 Old 1433EPSILON 0.11685
4
+ AGID00101 883 sc-1019 Old 1433ZETA 0.43831
5
+ AGID00001 2 9452 Old 4EBP1 0.31351
6
+ AGID00002 3 9456 Old 4EBP1_pS65 -0.60609
7
+ AGID00003 6 9459 Old 4EBP1_pT37T46 0.1334
8
+ AGID00443 8 9455 Old 4EBP1_pT70 0.10205
9
+ AGID00120 985 4937 Old 53BP1 -0.60773
10
+ AGID00004 13 3661 Old ACC_pS79 1.1894
11
+ AGID00005 14 1768-1/ab45174 Old ACC1 0.96979
12
+ AGID00408 2372 3658 Set163 AceCS1 -0.2510704
13
+ AGID00473 1182 5335 Old ACETYLATUBULINLYS40 -0.20312
14
+ AGID00404 2367 9189 Set163 ACSL1 -0.07280998
15
+ AGID02144 2450 PA5-27081 Old ACVRL1 0.15155
16
+ AGID00186 1198 ab88574 Old ADAR1 0.30172
17
+ AGID00146 1084 4691 Old AKT -0.30898
18
+ AGID00028 230 9271 Old AKT_pS473 -1.4319
19
+ AGID00170 1154 2965 Old AKT_pT308 -1.427
20
+ AGID00316 1800 3063 Set163 Akt2 -0.3014649
21
+ AGID00347 2009 8599 Set163 Akt2_pS474 -0.4763405
22
+ AGID02215 2577 ab195377 Set163 ALKBH5 -0.5050451
23
+ AGID00498 924 CA1030 Old ALPHACATENIN NA
24
+ AGID00287 1630 ABC80 Set163 Ambra1_pS52 -0.06949578
25
+ AGID00236 1351 ab129081 Set163 AMPK-a2_pS345 0.04812497
26
+ AGID00006 39 2532 Old AMPKALPHA -0.46963
27
+ AGID00007 40 2535 Old AMPKALPHA_pT172 -0.50256
28
+ AGID00193 1208 610066 Old ANNEXIN1 -0.73612
29
+ AGID00166 1142 610668 Old ANNEXINVII 0.14483
30
+ AGID00371 756 1852-1/ab52615 Old AR 0.40242
31
+ AGID00194 1217 4432 Old ARAF 0.34428
32
+ AGID02191 2507 PA5-39728 Old ARAF_pS299 0.067981
33
+ AGID00260 1053 sc-32761 Old ARID1A 0.26273
34
+ AGID00264 1560 HPA029318 Old ASNS -0.86435
35
+ AGID00276 1612 3415 Set163 Atg3 0
36
+ AGID00309 1775 13507 Set163 Atg4B -0.1731005
37
+ AGID00310 1776 12994 Set163 Atg5 -0.23961
38
+ AGID00277 1613 8558 Set163 Atg7 0.4424901
39
+ AGID00242 1363 2873 Old ATM 0.52353
40
+ AGID02142 2447 13050 Set163 ATM_pS1981 -0.05063508
41
+ AGID00217 1289 ab14748 Set163 ATP5A -0.09777058
42
+ AGID02145 2451 PA5-43776 Set163 ATP5H 0.08273504
43
+ AGID02150 2456 13934 Set163 ATR 0.176387
44
+ AGID00315 1795 ab178407 Set163 ATR_pS428 0.1535038
45
+ AGID00268 1569 ab97508 Set163 ATRX 0.5559474
46
+ AGID00391 2332 14475 Set163 Aurora-A 0.05009006
47
+ AGID00392 2333 2914 Set163 Aurora-ABC_pT288_pT232_pT198 -0.1998399
48
+ AGID02195 2512 MA5-27890 Set163 Aurora-B -0.5736062
49
+ AGID00215 1271 8661 Old AXL NA
50
+ AGID02143 2449 8457 Set163 b-Actin -0.5842202
51
+ AGID00179 1170 9565 Set163 b-Catenin_pT41_S45 -0.2026149
52
+ AGID00301 1725 14058 Set163 B7-H3 0.6483191
53
+ AGID00302 1726 14572 Set163 B7-H4 -0.03157527
54
+ AGID00008 63 9291 Old BAD_pS112 -0.37305
55
+ AGID00009 71 1542-1/ab32371 Old BAK 0.49224
56
+ AGID00192 1207 sc-28383 Old BAP1C4 0.29364
57
+ AGID00010 73 2772 Old BAX 0.055021
58
+ AGID00433 80 M0887 Old BCL2 0.48936
59
+ AGID00219 1299 PAB8528 Old BCL2A1 0.11259
60
+ AGID00012 84 1018-1 Old BCLXL -0.16298
61
+ AGID00377 87 sc-10086 Old BECLIN 0.41502
62
+ AGID00011 75 9562 Old BETACATENIN -2.4339
63
+ AGID00013 88 1008-1/ab32060 Old BID 0.0063536
64
+ AGID00180 90 1036-1/ab32158 Old BIM -0.11631
65
+ AGID00221 1311 610978 Set163 BiP-GRP78 0.08824451
66
+ AGID00373 2194 07-507 Set163 BMK1-Erk5_pT218_Y220 -0.0404899
67
+ AGID00355 92 1647/ab33899 Old BRAF 0.18628
68
+ AGID00014 94 2696 Old BRAF_pS445 0.35124
69
+ AGID00445 761 9012 Old BRCA2 0.073373
70
+ AGID00266 1567 13440 Old BRD4 -0.54104
71
+ AGID00168 1146 2865 Set163 c-Abl_pY412 -0.03572067
72
+ AGID00278 1615 3130 Set163 c-IAP2 0.03945495
73
+ AGID00345 1990 5649 Old CA9 NA
74
+ AGID00265 1565 2862 Old CABL -0.013232
75
+ AGID00429 2407 2679 Set163 Calnexin 0.08064981
76
+ AGID00176 1165 9496 Set163 Caspase-8-cleaved 0.204585
77
+ AGID00623 111 9665 Old CASPASE3 0.15686
78
+ AGID00015 109 9491 Old CASPASE7CLEAVEDD198 0.023183
79
+ AGID00118 951 9746 Old CASPASE8 -0.21738
80
+ AGID00537 935 551246 Old CASPASE9 NA
81
+ AGID00016 114 3238 Old CAVEOLIN1 -0.72006
82
+ AGID00358 2100 ab76000 Set163 CD134 -0.03135137
83
+ AGID00303 1737 826701 Set163 CD171 -0.57785
84
+ AGID00410 125 1632-1/ab78237 Old CD20 0.19743
85
+ AGID00220 1308 ab28340 Old CD26 -0.020423
86
+ AGID00191 1206 610467 Set163 CD29 0.06686971
87
+ AGID00017 127 M0823 Old CD31 0.26299
88
+ AGID00369 2174 ab108403 Set163 CD38 -0.1041999
89
+ AGID00359 2104 ab133616 Set163 CD4 0.1408388
90
+ AGID00411 1398 3570 Set163 CD44 -0.2535551
91
+ AGID00237 1352 M070101-2 Set163 CD45 -0.0270001
92
+ AGID00115 937 611016 Old CD49B 0.23602
93
+ AGID02171 2482 91882 Set163 CD86 -0.1969899
94
+ AGID00329 1873 4688 Set163 cdc25C 0.1651951
95
+ AGID00227 1332 4651 Set163 Cdc42 0.08875984
96
+ AGID00422 2396 3387 Set163 Cdc6 0.09884995
97
+ AGID00501 1007 9112 Old CDK1 0.020599
98
+ AGID00293 1658 ab32384 Set163 CDK1_pT14 1.0416
99
+ AGID00314 1783 4539 Old CDK1_pY15 -0.18103
100
+ AGID00423 2397 8064 Set163 CDT1 -0.3189654
101
+ AGID02101 2348 15102 Set163 cGAS -0.03548993
102
+ AGID00447 2410 13460 Set163 CHD1L 0.6803282
103
+ AGID00189 1203 2360 Old CHK1 0.070491
104
+ AGID00234 1348 ab79758 Old CHK1_pS296 0.12079
105
+ AGID00107 903 2348 Old CHK1_pS345 -0.39039
106
+ AGID00018 146 3440 Old CHK2 0.053796
107
+ AGID00019 147 2197 Old CHK2_pT68 0.15601
108
+ AGID00527 2078 4952 Old CIAP 0.45656
109
+ AGID00350 2018 3793 Set163 CIITA -0.006939933
110
+ AGID00434 155 9164 Old CJUN_pS73 -0.13295
111
+ AGID00020 157 1522-1/ab32363 Old CKIT -0.05433
112
+ AGID00400 852 NB100-91714 Old CLAUDIN7 0.2344
113
+ AGID00466 726 3127 Old CMET 0.14566
114
+ AGID00079 727 3129 Old CMET_pY1235 0.040553
115
+ AGID00167 161 9402 Old CMYC 0.096923
116
+ AGID00292 1656 11130-1-AP Old COG3 0.4438
117
+ AGID00021 171 sc-20649 Old COLLAGENVI 0.45374
118
+ AGID00141 1069 459230 Old COMPLEXIISUBUNIT30 NA
119
+ AGID00267 1568 3512 Set163 Connexin-43 0.7769598
120
+ AGID00269 1571 6434 Set163 Coup-TFII 0.6636801
121
+ AGID00150 1116 4850 Set163 Cox-IV 0.2616994
122
+ AGID00195 1218 4842 Set163 Cox2 -0.1788399
123
+ AGID00188 803 05-739 Old CRAF -0.29351
124
+ AGID00022 179 9427 Old CRAF_pS338 -0.017583
125
+ AGID00023 181 9197 Set163 Creb -0.2019811
126
+ AGID00393 2334 9198 Set163 CREB_pS133 -1.216248
127
+ AGID00365 2155 4980 Set163 CSK 0.04818003
128
+ AGID00367 2160 9201 Set163 CtIP -0.2328853
129
+ AGID00536 2096 ab107198 Old CTLA4 NA
130
+ AGID00025 198 2936 Set163 Cyclin-D3 0.6573399
131
+ AGID00024 192 1495-1/ab32053 Old CYCLINB1 0.24214
132
+ AGID00382 194 sc-718 Old CYCLIND1 -0.18027
133
+ AGID00437 199 sc-25303 Old CYCLINE1 -0.90158
134
+ AGID00449 202 1142-1 Old CYCLINE2 0.41185
135
+ AGID00209 1257 ab110324 Set163 Cyclophilin-F 0.4327798
136
+ AGID00247 1379 ab48389 Set163 D-a-Tubulin 0.3530351
137
+ AGID00308 1770 GTX10524 Set163 DAPK1_pS308 -0.15184
138
+ AGID00304 1744 ab51601 Set163 DAPK2 0.2024948
139
+ AGID00343 1980 6998 Set163 DDB-1 0.83651
140
+ AGID00427 2402 5583 Set163 DDR1 1.986894
141
+ AGID00428 2403 SAB4504671 Set163 DDR1_pY513 0.06013004
142
+ AGID00532 1273 Bast Lab Old DIRAS3 0.1498
143
+ AGID00104 891 ab76008 Old DJ1 0.20733
144
+ AGID02146 2452 4658 Set163 DM-Histone-H3 -0.1207853
145
+ AGID00386 1397 ab32521 Set163 DM-K9-Histone-H3 0.05412503
146
+ AGID00352 2030 14649 Set163 DNA-Ligase-IV 0.2897248
147
+ AGID00407 2371 13609 Set163 DNA_POLG 0.63227
148
+ AGID00399 2344 5032 Set163 DNMT1 0.4964499
149
+ AGID00409 2373 5391 Set163 DRP1 -0.0239315
150
+ AGID00253 1406 5149 Old DUSP4 0.40794
151
+ AGID00334 1936 ab76310 Set163 DUSP6 -0.3864203
152
+ AGID00116 940 3218 Old DVL3 -0.60913
153
+ AGID00211 1261 sc-251 Old E2F1 NA
154
+ AGID00148 1099 3195 Old ECADHERIN -3.522
155
+ AGID00135 1060 2332 Old EEF2 -0.94329
156
+ AGID00136 1061 3692 Old EEF2K 0.45322
157
+ AGID00152 1120 2232 Old EGFR -0.35832
158
+ AGID00450 217 2234 Old EGFR_pY1068 0.00013589
159
+ AGID00026 221 1124-1/ab32578 Old EGFR_pY1173 0.18507
160
+ AGID00078 722 9742 Old EIF4E -0.23193
161
+ AGID00328 1871 ab76256 Set163 eIF4E_pS209 -0.1396803
162
+ AGID00154 1124 2498 Old EIF4G -0.58096
163
+ AGID00027 228 9181 Set163 Elk1_pS383 -0.1850349
164
+ AGID00235 1350 M061329-2 Set163 EMA 1.36305
165
+ AGID00394 2337 3810 Set163 Enolase-1 -0.1254752
166
+ AGID00395 2338 8171 Set163 Enolase-2 0.1503851
167
+ AGID00196 1219 GTX629542 Old ENY2 NA
168
+ AGID00438 1849 A302-024A Set163 EphA2 -0.06953993
169
+ AGID00552 2422 6347 Set163 EphA2_pS897 -0.4215399
170
+ AGID00553 2423 12677 Set163 EphA2_pY588 -0.2176184
171
+ AGID00075 693 556347 Old EPPK1 4.7489
172
+ AGID00335 238 RM-9101 Old ERALPHA 3.4392
173
+ AGID00029 241 1091-1/ab32396 Old ERALPHA_pS118 0.037391
174
+ AGID00240 247 MS-671 Old ERCC1 0.10386
175
+ AGID00239 1355 11331-1-AP Old ERCC5 -0.27397
176
+ AGID00484 249 sc-154 Old ERK2 -0.36648
177
+ AGID00372 2193 3552 Set163 Erk5 -0.6140299
178
+ AGID00405 2369 13826 Set163 ERRalpha -0.1495351
179
+ AGID00187 1200 A303-501A Old ETS1 -0.70174
180
+ AGID00511 2492 2593 Set163 EVI1 0.3216045
181
+ AGID00485 1284 4905 Old EZH2 NA
182
+ AGID00030 252 1700-1/ab40794 Set163 FAK 0.3081401
183
+ AGID02151 2457 8556 Set163 FAK_pY397 -0.5778665
184
+ AGID00171 1156 3180 Old FASN 2.0859
185
+ AGID00356 2085 500-P18/10775-082 Set163 FGF-basic -0.6338549
186
+ AGID00031 262 1574-1/ab45688 Old FIBRONECTIN 0.6878
187
+ AGID00339 1959 4403 Set163 FN14 0.08252507
188
+ AGID02152 2458 20459 Old FOXM1 0.15565
189
+ AGID00378 269 9467 Old FOXO3A -0.055308
190
+ AGID02197 2515 orb6051 Old FOXO3A_pS318S321 0.12451
191
+ AGID02167 2475 PA5-64616 Set163 FRS2-alpha_pY196 -0.1308899
192
+ AGID02213 2575 ab124892 Set163 FTO -0.2029399
193
+ AGID02141 2446 12263 Old G6PD -0.049409
194
+ AGID00117 943 3239 Old GAB2 -0.0059415
195
+ AGID00412 274 AM4300 Old GAPDH -0.31607
196
+ AGID00086 764 558686 Old GATA3 2.7065
197
+ AGID00383 1578 4253 Old GATA6 NA
198
+ AGID00289 1634 12601-1-AP Set163 GCLC 0.519165
199
+ AGID00305 1745 ab124827 Set163 GCLM 0.05777007
200
+ AGID00212 1263 3305 Old GCN5L2 NA
201
+ AGID00270 1579 3538 Set163 Gli1 0.2031597
202
+ AGID00263 1520 ab69838 Set163 Gli3 0.2079589
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor -1.038965
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 0.4785689
205
+ AGID00262 1491 ab156876 Set163 Glutaminase -0.05107999
206
+ AGID00319 1807 4275 Set163 Granzyme-B -0.0009750299
207
+ AGID00368 2169 ab183737 Set163 GRB7 0.04665929
208
+ AGID00396 2339 3593 Set163 Grp75 0.817785
209
+ AGID00174 1163 9315 Set163 GSK-3B 0.1602592
210
+ AGID00502 1082 9336 Old GSK3_pS9 -1.2507
211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA 0.31744
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 -1.3684
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
+ AGID01354 1342 9718 Set163 H2AX_pS139 0.22615
216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 0.159545
217
+ AGID00131 1038 MS-325-P1 Old HER2 0.8651
218
+ AGID00142 299 06-229 Old HER2_pY1248 0.090608
219
+ AGID00110 911 sc-285 Old HER3 0.81297
220
+ AGID00080 728 4791 Old HER3_pY1289 0.22526
221
+ AGID00103 890 2573 Old HEREGULIN 0.07671
222
+ AGID00271 1582 11988 Set163 HES1 0.6854598
223
+ AGID00397 2340 2024 Set163 Hexokinase-I 0.1369298
224
+ AGID00442 1023 2867 Set163 Hexokinase-II 1.004959
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
+ AGID00205 1250 ab1791 Set163 Histone-H3 0.6061099
227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 0.1748349
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 0.6197387
229
+ AGID00333 1902 14832-1-AP Set163 HMHA1 -0.6104904
230
+ AGID00035 321 2402 Set163 HSP27 0.257025
231
+ AGID00036 323 2401 Set163 HSP27_pS82 0.4350301
232
+ AGID00320 1808 12165 Set163 HSP60 -0.05005515
233
+ AGID00037 325 4872 Old HSP70 -0.21987
234
+ AGID00366 2158 86630 Set163 IDO -0.4600854
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.22674
236
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237
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238
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239
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240
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241
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242
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243
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244
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245
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246
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247
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248
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249
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250
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251
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252
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253
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254
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255
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256
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257
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258
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259
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260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.16282
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 0.122345
263
+ AGID00439 2424 2796 Set163 Lyn -0.173085
264
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265
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266
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267
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268
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269
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270
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271
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272
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273
+ AGID00337 1951 12711 Set163 MERIT40 0.2765644
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 0.2670401
275
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276
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277
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278
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279
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280
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281
+ AGID00322 1810 11925 Set163 Mitofusin-2 0.5250199
282
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283
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284
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285
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286
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287
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288
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289
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290
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291
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292
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293
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294
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295
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296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 0.1468749
297
+ AGID00401 1139 21370002 Old MYH11 1.2221
298
+ AGID00291 1647 3403 Old MYOSINIIA NA
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 -0.12997
300
+ AGID00318 1803 4282 Set163 Myt1 0.1782298
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN -0.15199
303
+ AGID00156 1126 3217 Old NDRG1_pT346 1.4793
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 -0.04490993
305
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306
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307
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308
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309
+ AGID00087 767 sc-5593 Set163 Notch3 0.14182
310
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311
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312
+ AGID00257 1419 12721 Old NRF2 NA
313
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314
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315
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316
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317
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318
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319
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320
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321
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322
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323
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324
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325
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326
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327
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328
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329
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330
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331
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332
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333
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334
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335
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336
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337
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338
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339
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340
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341
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342
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343
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344
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345
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346
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347
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348
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349
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350
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351
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352
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353
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354
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355
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356
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357
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358
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359
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360
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361
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362
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363
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364
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365
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366
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367
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368
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369
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370
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371
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372
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373
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374
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375
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376
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377
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378
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379
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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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389
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390
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391
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392
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393
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394
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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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401
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402
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403
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404
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405
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406
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407
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408
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409
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410
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411
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413
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414
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415
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416
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417
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422
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424
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425
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426
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428
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429
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436
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437
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438
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439
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440
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466
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467
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468
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469
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471
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475
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476
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477
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478
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479
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480
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481
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482
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483
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484
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485
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486
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487
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488
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+ <shared:patient_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A54Y</shared:patient_id>
19
+ <shared:gender cde="2200604" xsd_ver="1.8" procurement_status="Completed" owner="">FEMALE</shared:gender>
20
+ <bio:days_to_index precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">0</bio:days_to_index>
21
+ <bio:bcr_canonical_check>
22
+ <bio:bcr_patient_canonical_status cde="" xsd_ver="2.6" procurement_status="Completed" owner="">Canonical</bio:bcr_patient_canonical_status>
23
+ </bio:bcr_canonical_check>
24
+ <bio:samples>
25
+ <bio:sample>
26
+ <admin:additional_studies/>
27
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:sample_type_id>
28
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
29
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
30
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Primary Tumor</bio:sample_type>
31
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
32
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
33
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
34
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">370</bio:initial_weight>
35
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
36
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
37
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">true</bio:oct_embedded>
38
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
39
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
40
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
41
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
42
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">76</bio:days_to_collection>
43
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
44
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
45
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A</bio:bcr_sample_barcode>
46
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4C42EC4C-0EBD-41FF-8758-1E6A69CF7EB3</bio:bcr_sample_uuid>
47
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
48
+ <bio:portions>
49
+ <bio:shipment_portion>
50
+ <admin:additional_studies/>
51
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">21</bio:portion_number>
52
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2</bio:portion_sequence>
53
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A321</bio:plate_id>
54
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">20</bio:center_id>
55
+ <bio:shipment_portion_day_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">16</bio:shipment_portion_day_of_shipment>
56
+ <bio:shipment_portion_month_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">9</bio:shipment_portion_month_of_shipment>
57
+ <bio:shipment_portion_year_of_shipment cde="" xsd_ver="2.4" procurement_status="Completed" owner="">2013</bio:shipment_portion_year_of_shipment>
58
+ <bio:shipment_portion_bcr_aliquot_barcode cde="" xsd_ver="2.4" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-21-A321-20</bio:shipment_portion_bcr_aliquot_barcode>
59
+ <bio:bcr_shipment_portion_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">190643C9-D8A9-4E20-AC54-DE58928DDFAF</bio:bcr_shipment_portion_uuid>
60
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
61
+ </bio:shipment_portion>
62
+ <bio:portion>
63
+ <admin:additional_studies/>
64
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">11</bio:portion_number>
65
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
66
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">11</bio:day_of_creation>
67
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_creation>
68
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2012</bio:year_of_creation>
69
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30.00</bio:weight>
70
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11</bio:bcr_portion_barcode>
71
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D0DE7CEF-1B12-4FF0-B106-9655E5FEE457</bio:bcr_portion_uuid>
72
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
73
+ <bio:analytes>
74
+ <bio:analyte>
75
+ <admin:additional_studies/>
76
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
77
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
78
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
79
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
80
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
81
+ <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>
82
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
83
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11D</bio:bcr_analyte_barcode>
84
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6E35E47B-ED8D-4456-9992-042E0CE673D3</bio:bcr_analyte_uuid>
85
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
86
+ <bio:aliquots>
87
+ <bio:aliquot>
88
+ <admin:additional_studies/>
89
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A25N</bio:plate_id>
90
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
91
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
92
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
93
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
94
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11D-A25N-01</bio:bcr_aliquot_barcode>
95
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">FC728459-51DA-4BED-8F19-89C724E2139F</bio:bcr_aliquot_uuid>
96
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
97
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
98
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.70</bio:volume>
99
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
100
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
101
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132159366</bio:biospecimen_barcode_bottom>
102
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
103
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
104
+ </bio:aliquot>
105
+ <bio:aliquot>
106
+ <admin:additional_studies/>
107
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A25Q</bio:plate_id>
108
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
109
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
110
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
111
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
112
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11D-A25Q-09</bio:bcr_aliquot_barcode>
113
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">FAFDB0F0-8793-4FA5-AAD9-7EDB0FE378A3</bio:bcr_aliquot_uuid>
114
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
115
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
116
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:volume>
117
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
118
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
119
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158694</bio:biospecimen_barcode_bottom>
120
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
121
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
122
+ </bio:aliquot>
123
+ <bio:aliquot>
124
+ <admin:additional_studies/>
125
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A268</bio:plate_id>
126
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
127
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
128
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
129
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
130
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11D-A268-05</bio:bcr_aliquot_barcode>
131
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B8B14EA5-AB85-4B95-9DEC-812143577B40</bio:bcr_aliquot_uuid>
132
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
133
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
134
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
135
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
136
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
137
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0128923932</bio:biospecimen_barcode_bottom>
138
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
139
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
140
+ </bio:aliquot>
141
+ </bio:aliquots>
142
+ <bio:protocols>
143
+ <bio:protocol>
144
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
145
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
146
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
147
+ </bio:protocol>
148
+ </bio:protocols>
149
+ <bio:dna>
150
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
151
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
152
+ </bio:dna>
153
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">PicoGreen</bio:spectrophotometer_method>
154
+ </bio:analyte>
155
+ <bio:analyte>
156
+ <admin:additional_studies/>
157
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
158
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
159
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
160
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
161
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.88</bio:a260_a280_ratio>
162
+ <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>
163
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
164
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11R</bio:bcr_analyte_barcode>
165
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">60909771-FB57-4CCB-85D5-BE7D98DB5405</bio:bcr_analyte_uuid>
166
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
167
+ <bio:aliquots>
168
+ <bio:aliquot>
169
+ <admin:additional_studies/>
170
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A25Z</bio:plate_id>
171
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
172
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
173
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
174
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
175
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11R-A25Z-13</bio:bcr_aliquot_barcode>
176
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">FB486C7C-8666-4E1A-9242-318170BEB512</bio:bcr_aliquot_uuid>
177
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
178
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
179
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
180
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
181
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
182
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0128924906</bio:biospecimen_barcode_bottom>
183
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
184
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
185
+ </bio:aliquot>
186
+ <bio:aliquot>
187
+ <admin:additional_studies/>
188
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A266</bio:plate_id>
189
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
190
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
191
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
192
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
193
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11R-A266-07</bio:bcr_aliquot_barcode>
194
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">966EB273-B61B-46CE-BC5F-3DDD6BD2167A</bio:bcr_aliquot_uuid>
195
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
196
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">2.08</bio:quantity>
197
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
198
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">B</bio:plate_row>
199
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
200
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0128925194</bio:biospecimen_barcode_bottom>
201
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
202
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
203
+ </bio:aliquot>
204
+ <bio:aliquot>
205
+ <admin:additional_studies/>
206
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A466</bio:plate_id>
207
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
208
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">09</bio:day_of_shipment>
209
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:month_of_shipment>
210
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2014</bio:year_of_shipment>
211
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11R-A466-07</bio:bcr_aliquot_barcode>
212
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C11FFCD0-8E82-4815-B30B-2D08945CE0BC</bio:bcr_aliquot_uuid>
213
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
214
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.06</bio:quantity>
215
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.60</bio:volume>
216
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">F</bio:plate_row>
217
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4</bio:plate_column>
218
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0167812923</bio:biospecimen_barcode_bottom>
219
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
220
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
221
+ </bio:aliquot>
222
+ </bio:aliquots>
223
+ <bio:protocols>
224
+ <bio:protocol>
225
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
226
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
227
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
228
+ </bio:protocol>
229
+ </bio:protocols>
230
+ <bio:rna>
231
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.65</bio:ratio_28s_18s>
232
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">7.20</bio:rinvalue>
233
+ </bio:rna>
234
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
235
+ </bio:analyte>
236
+ <bio:analyte>
237
+ <admin:additional_studies/>
238
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
239
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
240
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
241
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
242
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
243
+ <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>
244
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
245
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11W</bio:bcr_analyte_barcode>
246
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">786C6B3A-1AB9-4325-9CC0-CB8C90CF942B</bio:bcr_analyte_uuid>
247
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
248
+ <bio:aliquots>
249
+ <bio:aliquot>
250
+ <admin:additional_studies/>
251
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A292</bio:plate_id>
252
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
253
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:day_of_shipment>
254
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_shipment>
255
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
256
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-11W-A292-09</bio:bcr_aliquot_barcode>
257
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C1AC38C2-BFEE-4E4C-99EB-C7A64CCE3F36</bio:bcr_aliquot_uuid>
258
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
259
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
260
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
261
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
262
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3</bio:plate_column>
263
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132269186</bio:biospecimen_barcode_bottom>
264
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
265
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
266
+ </bio:aliquot>
267
+ </bio:aliquots>
268
+ <bio:protocols>
269
+ <bio:protocol>
270
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
271
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
272
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
273
+ </bio:protocol>
274
+ </bio:protocols>
275
+ <bio:dna>
276
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
277
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
278
+ </bio:dna>
279
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
280
+ </bio:analyte>
281
+ </bio:analytes>
282
+ <bio:slides>
283
+ <bio:slide>
284
+ <admin:additional_studies/>
285
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
286
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
287
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">40</bio:percent_tumor_cells>
288
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">70</bio:percent_tumor_nuclei>
289
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_normal_cells>
290
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
291
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">60</bio:percent_stromal_cells>
292
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
293
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_lymphocyte_infiltration>
294
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
295
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
296
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
297
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
298
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-01-TSA</shared:bcr_slide_barcode>
299
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7EF6FC52-B788-4ACD-B92A-A59BE4F11BDD</shared:bcr_slide_uuid>
300
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-E9-A54Y-01A-01-TSA.7EF6FC52-B788-4ACD-B92A-A59BE4F11BDD.svs</shared:image_file_name>
301
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
302
+ </bio:slide>
303
+ </bio:slides>
304
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
305
+ </bio:portion>
306
+ </bio:portions>
307
+ <bio:tumor_pathology/>
308
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
309
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
310
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
311
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">3F43AE57-0EB8-4F40-980F-6E2C8C2B3A74</bio:pathology_report_uuid>
312
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-E9-A54Y.3F43AE57-0EB8-4F40-980F-6E2C8C2B3A74.pdf</bio:pathology_report_file_name>
313
+ <bio:diagnostic_slides>
314
+ <admin:additional_studies/>
315
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">5FD70369-6514-4E5E-8BEF-65DAC5671E1A</bio:ffpe_slide_uuid>
316
+ </bio:diagnostic_slides>
317
+ </bio:sample>
318
+ <bio:sample>
319
+ <admin:additional_studies/>
320
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
321
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
322
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
323
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
324
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
325
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
326
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
327
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
328
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
329
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
330
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
331
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
332
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
333
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
334
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
335
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">76</bio:days_to_collection>
336
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
337
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
338
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A</bio:bcr_sample_barcode>
339
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3C4EE0B4-7992-48A2-BE0B-EE5F54068466</bio:bcr_sample_uuid>
340
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
341
+ <bio:portions>
342
+ <bio:portion>
343
+ <admin:additional_studies/>
344
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
345
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:portion_sequence>
346
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:day_of_creation>
347
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_creation>
348
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_creation>
349
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2.00</bio:weight>
350
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01</bio:bcr_portion_barcode>
351
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">242572B4-7120-46F5-A70F-06000EC54736</bio:bcr_portion_uuid>
352
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
353
+ <bio:analytes>
354
+ <bio:analyte>
355
+ <admin:additional_studies/>
356
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
357
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
358
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
359
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
360
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
361
+ <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>
362
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
363
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01D</bio:bcr_analyte_barcode>
364
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0F5B044C-D199-4F26-AB64-55863AA91A1F</bio:bcr_analyte_uuid>
365
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
366
+ <bio:aliquots>
367
+ <bio:aliquot>
368
+ <admin:additional_studies/>
369
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A25N</bio:plate_id>
370
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
371
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
372
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
373
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
374
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01D-A25N-01</bio:bcr_aliquot_barcode>
375
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3AE6A742-012F-48F6-A8EC-73941AA2CA5D</bio:bcr_aliquot_uuid>
376
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
377
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.07</bio:quantity>
378
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.70</bio:volume>
379
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
380
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
381
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158510</bio:biospecimen_barcode_bottom>
382
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
383
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
384
+ </bio:aliquot>
385
+ <bio:aliquot>
386
+ <admin:additional_studies/>
387
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A25Q</bio:plate_id>
388
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
389
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">30</bio:day_of_shipment>
390
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">01</bio:month_of_shipment>
391
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
392
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01D-A25Q-09</bio:bcr_aliquot_barcode>
393
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">DD45289A-3543-448A-AD91-B35D282448F5</bio:bcr_aliquot_uuid>
394
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.08</bio:concentration>
395
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</bio:quantity>
396
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:volume>
397
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
398
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
399
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132158699</bio:biospecimen_barcode_bottom>
400
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
401
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
402
+ </bio:aliquot>
403
+ </bio:aliquots>
404
+ <bio:protocols>
405
+ <bio:protocol>
406
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
407
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
408
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
409
+ </bio:protocol>
410
+ </bio:protocols>
411
+ <bio:dna>
412
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
413
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
414
+ </bio:dna>
415
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">PicoGreen</bio:spectrophotometer_method>
416
+ </bio:analyte>
417
+ <bio:analyte>
418
+ <admin:additional_studies/>
419
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
420
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
421
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
422
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
423
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
424
+ <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>
425
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
426
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01W</bio:bcr_analyte_barcode>
427
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9AC7E780-DB46-4817-BA4F-A09A27D86C52</bio:bcr_analyte_uuid>
428
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
429
+ <bio:aliquots>
430
+ <bio:aliquot>
431
+ <admin:additional_studies/>
432
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A292</bio:plate_id>
433
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
434
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:day_of_shipment>
435
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_shipment>
436
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2013</bio:year_of_shipment>
437
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-E9-A54Y-10A-01W-A292-09</bio:bcr_aliquot_barcode>
438
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1A97BED5-F00A-4CCD-86E1-2DE82EACB387</bio:bcr_aliquot_uuid>
439
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
440
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
441
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
442
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">D</bio:plate_row>
443
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7</bio:plate_column>
444
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0132269269</bio:biospecimen_barcode_bottom>
445
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
446
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
447
+ </bio:aliquot>
448
+ </bio:aliquots>
449
+ <bio:protocols>
450
+ <bio:protocol>
451
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
452
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
453
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
454
+ </bio:protocol>
455
+ </bio:protocols>
456
+ <bio:dna>
457
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
458
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
459
+ </bio:dna>
460
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
461
+ </bio:analyte>
462
+ </bio:analytes>
463
+ <bio:slides/>
464
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
465
+ </bio:portion>
466
+ </bio:portions>
467
+ <bio:tumor_pathology/>
468
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
469
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
470
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
471
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
472
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
473
+ <bio:diagnostic_slides>
474
+ <admin:additional_studies/>
475
+ </bio:diagnostic_slides>
476
+ </bio:sample>
477
+ </bio:samples>
478
+ </bio:patient>
479
+ </bio:tcga_bcr>
data/gdc_data_organized/182c4bdf-2c58-4303-b034-459da86b9d90/nationwidechildrens.org_ssf.TCGA-E9-A54Y.xml ADDED
@@ -0,0 +1,88 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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">5840D5A2-88EF-44B7-94B0-B63A2AA068AF</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">271.57.0</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-E9-A54Y</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">182C4BDF-2C58-4303-B034-459DA86B9D90</shared:bcr_patient_uuid>
22
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">E9</shared:tissue_source_site>
23
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A54Y</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">4C42EC4C-0EBD-41FF-8758-1E6A69CF7EB3</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="">7</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="2211898">Modified Radical Mastectomy</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="Not Applicable" restricted="false" source_system_identifier="2211899" xsi:nil="true"/>
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="2211903">Cassette</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="2211904"/>
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="2211910">530</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="2211906">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="2211911">97</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="2211912">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">61</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="2211977">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="2211978">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="2211979">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="2211981">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" source_system_identifier="2211982"/>
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="2211907">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">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="2211983">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="2211984">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="2211985">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">6</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="2211900">Ukraine</shared:country>
53
+ <ssf_disease:disease_details/>
54
+ <ssf:tumor_histologies>
55
+ <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="2211890">Infiltrating Lobular 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"/>
60
+ </ssf:tumor_histology>
61
+ </ssf:tumor_histologies>
62
+ <ssf:tumor_locations>
63
+ <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"/>
64
+ <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="2211893">Right</ssf:laterality>
65
+ <ssf:tumor_location>
66
+ <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="2211893">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="2211893"/>
69
+ </ssf:tumor_location>
70
+ </ssf:tumor_locations>
71
+ </ssf:tumor_sample>
72
+ </ssf:tumor_samples>
73
+ <ssf:normal_controls>
74
+ <ssf:normal_control>
75
+ <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">3C4EE0B4-7992-48A2-BE0B-EE5F54068466</ssf:bcr_sample_uuid>
76
+ <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="2211919">Blood Draw</ssf:method_of_normal_sample_procurement>
77
+ <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"/>
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">7</ssf:days_to_normal_sample_procurement>
79
+ <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"/>
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="Not Available" restricted="false"/>
81
+ <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"/>
82
+ <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"/>
83
+ <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"/>
84
+ <ssf:normal_control_locations/>
85
+ </ssf:normal_control>
86
+ </ssf:normal_controls>
87
+ </ssf:patient>
88
+ </ssf:tcga_bcr>
data/gdc_data_organized/1f99e4d4-4e8b-4cc1-a129-227a2a82780e/JOUAL_p_TCGA_b96_SNP_N_GenomeWideSNP_6_G04_747978.grch38.seg.v2.txt ADDED
@@ -0,0 +1,412 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ GDC_Aliquot Chromosome Start End Num_Probes Segment_Mean
2
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 62920 462894 19 0.4751
3
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 599171 3134030 642 -0.1045
4
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5
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8
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9
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 30274729 37307167 3975 0.0047
10
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11
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12
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13
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14
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15
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16
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17
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 73181704 81422917 5254 0.0109
18
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19
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20
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21
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 87710295 102350985 9346 0.0069
22
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 102353061 102353130 2 -1.2645
23
+ 9c918c56-fd45-443d-8137-00685de9f0c3 1 102353146 105476583 1569 0.0088
24
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+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
130
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21D-A12Q-09</bio:bcr_aliquot_barcode>
131
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8495c66e-dc95-4eae-909b-b51b8bc84889</bio:bcr_aliquot_uuid>
132
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.09</bio:concentration>
133
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.60</bio:quantity>
134
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:volume>
135
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
136
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
137
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108431831</bio:biospecimen_barcode_bottom>
138
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
139
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
140
+ </bio:aliquot>
141
+ <bio:aliquot>
142
+ <admin:additional_studies/>
143
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12R</bio:plate_id>
144
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">05</bio:center_id>
145
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:day_of_shipment>
146
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
147
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
148
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21D-A12R-05</bio:bcr_aliquot_barcode>
149
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">08358ec0-a233-44c5-b00a-5148a5f1f03c</bio:bcr_aliquot_uuid>
150
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.17</bio:concentration>
151
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.54</bio:quantity>
152
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
153
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
154
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
155
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108431639</bio:biospecimen_barcode_bottom>
156
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
157
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
158
+ </bio:aliquot>
159
+ </bio:aliquots>
160
+ <bio:protocols>
161
+ <bio:protocol>
162
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
163
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
164
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
165
+ </bio:protocol>
166
+ </bio:protocols>
167
+ <bio:dna>
168
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
169
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
170
+ </bio:dna>
171
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
172
+ </bio:analyte>
173
+ <bio:analyte>
174
+ <admin:additional_studies/>
175
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
176
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">R</bio:analyte_type_id>
177
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
178
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
179
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.79</bio:a260_a280_ratio>
180
+ <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>
181
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
182
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21R</bio:bcr_analyte_barcode>
183
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ec363471-8a55-4bb3-aa97-5d51344303d4</bio:bcr_analyte_uuid>
184
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
185
+ <bio:aliquots>
186
+ <bio:aliquot>
187
+ <admin:additional_studies/>
188
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12O</bio:plate_id>
189
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
190
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:day_of_shipment>
191
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
192
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
193
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21R-A12O-13</bio:bcr_aliquot_barcode>
194
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2d0b6c55-ccd0-4da9-bb6c-997b4aff97f2</bio:bcr_aliquot_uuid>
195
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
196
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.60</bio:quantity>
197
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
198
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
199
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
200
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0108431729</bio:biospecimen_barcode_bottom>
201
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
202
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
203
+ </bio:aliquot>
204
+ <bio:aliquot>
205
+ <admin:additional_studies/>
206
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A12P</bio:plate_id>
207
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">07</bio:center_id>
208
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">22</bio:day_of_shipment>
209
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
210
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
211
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21R-A12P-07</bio:bcr_aliquot_barcode>
212
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ad602633-fdd7-4bf1-b3ac-e1c8e0a02934</bio:bcr_aliquot_uuid>
213
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.18</bio:concentration>
214
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.81</bio:quantity>
215
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
216
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
217
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
218
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0094929337</bio:biospecimen_barcode_bottom>
219
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
220
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
221
+ </bio:aliquot>
222
+ </bio:aliquots>
223
+ <bio:protocols>
224
+ <bio:protocol>
225
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
226
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
227
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
228
+ </bio:protocol>
229
+ </bio:protocols>
230
+ <bio:rna>
231
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.40</bio:ratio_28s_18s>
232
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.40</bio:rinvalue>
233
+ </bio:rna>
234
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
235
+ </bio:analyte>
236
+ <bio:analyte>
237
+ <admin:additional_studies/>
238
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
239
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
240
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
241
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
242
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
243
+ <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>
244
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
245
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21W</bio:bcr_analyte_barcode>
246
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">3C2506B3-FFB9-4137-93DE-E17136594ADF</bio:bcr_analyte_uuid>
247
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
248
+ <bio:aliquots>
249
+ <bio:aliquot>
250
+ <admin:additional_studies/>
251
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A14O</bio:plate_id>
252
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
253
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">03</bio:day_of_shipment>
254
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">05</bio:month_of_shipment>
255
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2011</bio:year_of_shipment>
256
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-21W-A14O-09</bio:bcr_aliquot_barcode>
257
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2dfeec26-8264-4552-890e-190b281579f5</bio:bcr_aliquot_uuid>
258
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
259
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
260
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
261
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
262
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1</bio:plate_column>
263
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0100477118</bio:biospecimen_barcode_bottom>
264
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
265
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
266
+ </bio:aliquot>
267
+ </bio:aliquots>
268
+ <bio:protocols>
269
+ <bio:protocol>
270
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">Repli-G</bio:experimental_protocol_type>
271
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
272
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
273
+ </bio:protocol>
274
+ </bio:protocols>
275
+ <bio:dna>
276
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
277
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
278
+ </bio:dna>
279
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
280
+ </bio:analyte>
281
+ </bio:analytes>
282
+ <bio:slides>
283
+ <bio:slide>
284
+ <admin:additional_studies/>
285
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
286
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
287
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_cells>
288
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
289
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">5</bio:percent_normal_cells>
290
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
291
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">10</bio:percent_stromal_cells>
292
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
293
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_lymphocyte_infiltration>
294
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
295
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
296
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
297
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
298
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-02-TSB</shared:bcr_slide_barcode>
299
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a5a169e3-b2b7-4a89-95fb-ee01621d32ee</shared:bcr_slide_uuid>
300
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-AR-A1AL-01A-02-TSB.a5a169e3-b2b7-4a89-95fb-ee01621d32ee.svs</shared:image_file_name>
301
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
302
+ </bio:slide>
303
+ </bio:slides>
304
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
305
+ </bio:portion>
306
+ </bio:portions>
307
+ <bio:tumor_pathology/>
308
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
309
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
310
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
311
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">E3D44C6B-4497-4212-8CA1-AC9444B4CC54</bio:pathology_report_uuid>
312
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-AR-A1AL.E3D44C6B-4497-4212-8CA1-AC9444B4CC54.pdf</bio:pathology_report_file_name>
313
+ <bio:diagnostic_slides>
314
+ <admin:additional_studies/>
315
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">0970370F-6D4B-449A-AF33-76355DD99F91</bio:ffpe_slide_uuid>
316
+ </bio:diagnostic_slides>
317
+ </bio:sample>
318
+ <bio:sample>
319
+ <admin:additional_studies/>
320
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
321
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
322
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
323
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
324
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
325
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
326
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
327
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
328
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
329
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
330
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
331
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
332
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
333
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
334
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
335
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">1528</bio:days_to_collection>
336
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
337
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
338
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-AR-A1AL-10A</bio:bcr_sample_barcode>
339
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a69155d1-f490-4e2e-9c94-7236ad66e15a</bio:bcr_sample_uuid>
340
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
341
+ <bio:portions>
342
+ <bio:portion>
343
+ <admin:additional_studies/>
344
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
345
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346
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data/gdc_data_organized/27dfb9d4-3a2c-44bc-9acf-8f638d3f3004/TCGA-BRCA.833793a9-9708-4363-ac40-ce7960a5e13d.ascat3.gene_level_copy_number.v36.tsv ADDED
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data/gdc_data_organized/27dfb9d4-3a2c-44bc-9acf-8f638d3f3004/nationwidechildrens.org_clinical.TCGA-BH-A0GZ.xml ADDED
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <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_v1.5="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/1.5" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
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+ <admin:admin>
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+ <admin:batch_number xsd_ver="1.17">61.89.0</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:admin>
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+ <brca:patient>
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+ <admin:additional_studies/>
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+ <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="368612">Breast</clin_shared:tumor_tissue_site>
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+ <clin_shared:tumor_tissue_site_other preferred_name="site_of_primary_tumor_other" display_order="999" cde="2584114" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="368613" xsi:nil="true"/>
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+ <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="368601">No</shared:other_dx>
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+ <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="368592">FEMALE</shared:gender>
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+ <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="368597">Alive</clin_shared:vital_status>
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+ <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">-22714</clin_shared:days_to_birth>
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+ <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=""/>
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+ <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
28
+ <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">328</clin_shared:days_to_last_followup>
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+ <clin_shared:race_list>
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+ <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="368599">WHITE</clin_shared:race>
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+ </clin_shared:race_list>
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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-BH-A0GZ</shared:bcr_patient_barcode>
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+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">BH</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">A0GZ</shared:patient_id>
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+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">27dfb9d4-3a2c-44bc-9acf-8f638d3f3004</shared:bcr_patient_uuid>
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+ <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="368602">No</shared:history_of_neoadjuvant_treatment>
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+ <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>
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+ <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">62</clin_shared:age_at_initial_pathologic_diagnosis>
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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="368619">2009</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="Not Available" restricted="false" source_system_identifier="368600"/>
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="368598">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="Not Available" restricted="false"/>
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="368631">14</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="Completed" restricted="false" source_system_identifier="368644">H-SCORE 300</brca_shared:er_detection_method_text>
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="Completed" restricted="false" source_system_identifier="368649">H-SCORE 280</brca_shared:pgr_detection_method_text>
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="368614">Left Upper Inner Quadrant</clin_shared:anatomic_neoplasm_subdivision>
52
+ <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="368614">Left</clin_shared:anatomic_neoplasm_subdivision>
53
+ </brca:anatomic_neoplasm_subdivisions>
54
+ <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="368659">1.05</brca_shared:her2_neu_chromosone_17_signal_ratio_value>
55
+ <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="368628">Sentinel lymph node biopsy plus axillary dissection</brca:axillary_lymph_node_stage_method_type>
56
+ <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="368629"/>
57
+ <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="368622">Other</brca:breast_carcinoma_surgical_procedure_name>
58
+ <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="368626" xsi:nil="true"/>
59
+ <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 Evaluated" restricted="false" source_system_identifier="368625"/>
60
+ <brca:surgical_procedure_purpose_other_text preferred_name="first_surgical_procedure_other" display_order="39" cde="3020338" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368623">Segmental mastectomy</brca:surgical_procedure_purpose_other_text>
61
+ <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="368615">Infiltrating Ductal Carcinoma</shared:histological_type>
62
+ <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="368616" xsi:nil="true"/>
63
+ <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="368596">Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)</clin_shared:menopause_status>
64
+ <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="368645">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
65
+ <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="368630">NO</brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator>
66
+ <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"/>
67
+ <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368642">3+</brca_shared:immunohistochemistry_positive_cell_score>
68
+ <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="368652">2+</brca_shared:her2_immunohistochemistry_level_result>
69
+ <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="Completed" restricted="false" source_system_identifier="368627">Negative</brca:breast_cancer_surgery_margin_status>
70
+ <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="368624">Negative</clin_shared:margin_status>
71
+ <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="368620">Core needle biopsy</clin_shared:initial_pathologic_diagnosis_method>
72
+ <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="368621" xsi:nil="true"/>
73
+ <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="368655">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
74
+ <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="368640">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
75
+ <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="368650">Equivocal</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
76
+ <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="368633"/>
77
+ <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="368632">1</clin_shared:number_of_lymphnodes_positive_by_he>
78
+ <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368648">H-SCORE</brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text>
79
+ <brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text preferred_name="er_positivity_scale_other" display_order="62" cde="3086851" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368643">H-SCORE</brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text>
80
+ <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="368651"/>
81
+ <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="368653"/>
82
+ <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="368654"/>
83
+ <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="Completed" restricted="false" source_system_identifier="368658">40</brca_shared:her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count>
84
+ <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="368660"/>
85
+ <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="368661"/>
86
+ <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="368566">NO</clin_shared:tissue_prospective_collection_indicator>
87
+ <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="368567">YES</clin_shared:tissue_retrospective_collection_indicator>
88
+ <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="Completed" restricted="false" source_system_identifier="368657">2.08</brca_shared:fluorescence_in_situ_hybridization_diagnostic_procedure_chromosome_17_signal_result_range>
89
+ <brca:first_nonlymph_node_metastasis_anatomic_sites>
90
+ <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="368638"/>
91
+ <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="368639"/>
92
+ </brca:first_nonlymph_node_metastasis_anatomic_sites>
93
+ <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="368641">90-99%</brca_shared:er_level_cell_percentage_category>
94
+ <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="368646">80-89%</brca_shared:progesterone_receptor_level_cell_percent_category>
95
+ <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"/>
96
+ <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 Evaluated" restricted="false" source_system_identifier="368662"/>
97
+ <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="368663"/>
98
+ <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="368664"/>
99
+ <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="368665"/>
100
+ <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="368666"/>
101
+ <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 Evaluated" restricted="false" source_system_identifier="368667"/>
102
+ <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 Evaluated" restricted="false" source_system_identifier="368672"/>
103
+ <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="368668"/>
104
+ <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="368669"/>
105
+ <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="368670"/>
106
+ <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="368671"/>
107
+ <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="368673"/>
108
+ <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="368674"/>
109
+ <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="368675"/>
110
+ <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="368676"/>
111
+ <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 Evaluated" restricted="false" source_system_identifier="368677"/>
112
+ <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="368679"/>
113
+ <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="368680"/>
114
+ <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="368681"/>
115
+ <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="368682"/>
116
+ <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="368683"/>
117
+ <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="368678"/>
118
+ <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="Completed" restricted="false" source_system_identifier="368656">2.2</brca_shared:her2_neu_breast_carcinoma_copy_analysis_input_total_number>
119
+ <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"/>
120
+ <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368647">3+</brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score>
121
+ <shared_stage:stage_event system="AJCC">
122
+ <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="1080002"/>
123
+ <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"/>
124
+ <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="368637">Stage IIA</shared_stage:pathologic_stage>
125
+ <shared_stage:tnm_categories>
126
+ <shared_stage:clinical_categories>
127
+ <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"/>
128
+ <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"/>
129
+ <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"/>
130
+ </shared_stage:clinical_categories>
131
+ <shared_stage:pathologic_categories>
132
+ <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="368634">T1c</shared_stage:pathologic_T>
133
+ <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="368635">N1a</shared_stage:pathologic_N>
134
+ <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="368636">M0</shared_stage:pathologic_M>
135
+ </shared_stage:pathologic_categories>
136
+ </shared_stage:tnm_categories>
137
+ <shared_stage:psa>
138
+ <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"/>
139
+ <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"/>
140
+ </shared_stage:psa>
141
+ <shared_stage:gleason_grading>
142
+ <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"/>
143
+ <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"/>
144
+ <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"/>
145
+ <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"/>
146
+ </shared_stage:gleason_grading>
147
+ <shared_stage:ann_arbor>
148
+ <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"/>
149
+ <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"/>
150
+ </shared_stage:ann_arbor>
151
+ <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"/>
152
+ <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"/>
153
+ <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"/>
154
+ </shared_stage:stage_event>
155
+ <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"/>
156
+ <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"/>
157
+ <brca_nte:new_tumor_events>
158
+ <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"/>
159
+ <brca_nte:new_tumor_event>
160
+ <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"/>
161
+ <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"/>
162
+ <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"/>
163
+ <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"/>
164
+ <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"/>
165
+ <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"/>
166
+ <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"/>
167
+ <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"/>
168
+ <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 Evaluated" restricted="false" source_system_identifier="368662"/>
169
+ <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="368663"/>
170
+ <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"/>
171
+ <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="368664"/>
172
+ <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="368665"/>
173
+ <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="368666"/>
174
+ <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 Evaluated" restricted="false" source_system_identifier="368667"/>
175
+ <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="368668"/>
176
+ <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"/>
177
+ <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="368669"/>
178
+ <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="368670"/>
179
+ <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="368671"/>
180
+ <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 Evaluated" restricted="false" source_system_identifier="368672"/>
181
+ <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="368673"/>
182
+ <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="368674"/>
183
+ <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="368675"/>
184
+ <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="368676"/>
185
+ <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 Evaluated" restricted="false" source_system_identifier="368677"/>
186
+ <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="368678"/>
187
+ <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="368679"/>
188
+ <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="368680"/>
189
+ <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="368681"/>
190
+ <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="368682"/>
191
+ <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="368683"/>
192
+ </brca_nte:new_tumor_event>
193
+ </brca_nte:new_tumor_events>
194
+ <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="368564">10</clin_shared:day_of_form_completion>
195
+ <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="368563">11</clin_shared:month_of_form_completion>
196
+ <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="368565">2010</clin_shared:year_of_form_completion>
197
+ <brca:follow_ups>
198
+ <follow_up_v1.5:follow_up version="1.5" sequence="1">
199
+ <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-BH-A0GZ-F4697</clin_shared:bcr_followup_barcode>
200
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">6B3FE8B6-3E78-48C6-8CE0-77EFFD2F5DF5</clin_shared:bcr_followup_uuid>
201
+ <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">328</clin_shared:days_to_last_followup>
202
+ <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="368828">Alive</clin_shared:vital_status>
203
+ <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="368829">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
204
+ <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=""/>
205
+ <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"/>
206
+ <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="368836">YES</clin_shared:radiation_therapy>
207
+ <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="368837">YES</clin_shared:postoperative_rx_tx>
208
+ <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"/>
209
+ <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="Completed" restricted="false" source_system_identifier="368841">NO</nte:additional_surgery_locoregional_procedure>
210
+ <nte:days_to_additional_surgery_locoregional_procedure precision="day" xsd_ver="2.2" tier="2" cde="3408572" owner="TSS" procurement_status="Not Available" preferred_name="new_tumor_event_surgery_days_to_loco" display_order="9999" cde_ver="1.000"/>
211
+ <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="Not Available" restricted="false" source_system_identifier="368845"/>
212
+ <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="368846"/>
213
+ <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="368847"/>
214
+ <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="368848"/>
215
+ <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="368849"/>
216
+ <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="Not Available" restricted="false" source_system_identifier="368850"/>
217
+ <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="368851"/>
218
+ <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="368852"/>
219
+ <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="368853"/>
220
+ <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="368854"/>
221
+ <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368855"/>
222
+ <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="368856"/>
223
+ <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368857"/>
224
+ <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="368858"/>
225
+ <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="368859"/>
226
+ <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368860"/>
227
+ <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="368861"/>
228
+ <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="368862"/>
229
+ <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="368863"/>
230
+ <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="368864"/>
231
+ <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="368865"/>
232
+ <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="368866"/>
233
+ <nte:additional_surgery_metastatic_procedure preferred_name="new_tumor_event_surgery_met" display_order="999" cde="3008757" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368867">NO</nte:additional_surgery_metastatic_procedure>
234
+ <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"/>
235
+ <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="368871"/>
236
+ <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="368872"/>
237
+ <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="368873"/>
238
+ <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="368874"/>
239
+ <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="368875"/>
240
+ <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="368876"/>
241
+ <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="368877"/>
242
+ <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="368878"/>
243
+ <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="368879"/>
244
+ <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="368880"/>
245
+ <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="368881"/>
246
+ <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="368882"/>
247
+ <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="368883"/>
248
+ <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="368884"/>
249
+ <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="368885"/>
250
+ <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="368886"/>
251
+ <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="368887"/>
252
+ <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="368888"/>
253
+ <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="368889"/>
254
+ <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="368890"/>
255
+ <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="368891"/>
256
+ <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="368892"/>
257
+ <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="Completed" restricted="false" source_system_identifier="368893">NO</nte:additional_radiation_therapy>
258
+ <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="Completed" restricted="false" source_system_identifier="368894">NO</nte:additional_pharmaceutical_therapy>
259
+ <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="368823">16</clin_shared:day_of_form_completion>
260
+ <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="368822">11</clin_shared:month_of_form_completion>
261
+ <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="368824">2010</clin_shared:year_of_form_completion>
262
+ </follow_up_v1.5:follow_up>
263
+ </brca:follow_ups>
264
+ <rx:drugs>
265
+ <rx:drug>
266
+ <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"/>
267
+ <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="368713">1</rx:regimen_number>
268
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-BH-A0GZ-D4691</rx:bcr_drug_barcode>
269
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">DF515EB3-0AC1-4BBE-B0F5-D74BBA8B245C</rx:bcr_drug_uuid>
270
+ <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="368722"/>
271
+ <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="368723"/>
272
+ <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="368720">1</rx:prescribed_dose>
273
+ <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="368721">mg/day</rx:prescribed_dose_units>
274
+ <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="368719"/>
275
+ <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">157</rx:days_to_drug_therapy_start>
276
+ <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"/>
277
+ <rx:therapy_types>
278
+ <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="368716">Hormone Therapy</rx:therapy_type>
279
+ <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="368717"/>
280
+ </rx:therapy_types>
281
+ <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="368718">ARIMIDEX</rx:drug_name>
282
+ <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"/>
283
+ <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="368714">ADJUVANT</clin_shared:regimen_indication>
284
+ <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="368715"/>
285
+ <rx:route_of_administrations>
286
+ <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="368724">PO</rx:route_of_administration>
287
+ </rx:route_of_administrations>
288
+ <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="368728">YES</rx:therapy_ongoing>
289
+ <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"/>
290
+ <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="368706">17</clin_shared:day_of_form_completion>
291
+ <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="368705">11</clin_shared:month_of_form_completion>
292
+ <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="368707">2010</clin_shared:year_of_form_completion>
293
+ </rx:drug>
294
+ </rx:drugs>
295
+ <rad:radiations>
296
+ <rad:radiation>
297
+ <rad:bcr_radiation_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-BH-A0GZ-R4693</rad:bcr_radiation_barcode>
298
+ <rad:bcr_radiation_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">2C0E7F31-3FAC-443E-BBDB-9DDEF10114BA</rad:bcr_radiation_uuid>
299
+ <rad:days_to_radiation_therapy_start floored="false" restricted="false" xsd_ver="" tier="" cde="3008313" owner="TSS" procurement_status="Not Available" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000"/>
300
+ <rad:days_to_radiation_therapy_end floored="false" restricted="false" xsd_ver="" tier="" cde="3008333" owner="TSS" procurement_status="Not Available" preferred_name="radiation_therapy_ended_days_to" display_order="17" cde_ver="1.000"/>
301
+ <rad:radiation_type preferred_name="radiation_therapy_type" display_order="4" cde="2842944" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368764">EXTERNAL BEAM</rad:radiation_type>
302
+ <rad:radiation_type_notes preferred_name="radiation_type_other" display_order="999" cde="2195477" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="368765"/>
303
+ <rad:radiation_dosage preferred_name="radiation_total_dose" display_order="6" cde="2721441" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368767"/>
304
+ <rad:units preferred_name="radiation_adjuvant_units" display_order="7" cde="61446" cde_ver="3.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368768"/>
305
+ <rad:numfractions preferred_name="radiation_adjuvant_fractions_total" display_order="8" cde="61465" cde_ver="3.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368769"/>
306
+ <rad:anatomic_treatment_site preferred_name="radiation_therapy_site" display_order="5" cde="2793522" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368766">Primary Tumor Field</rad:anatomic_treatment_site>
307
+ <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="368762">ADJUVANT</clin_shared:regimen_indication>
308
+ <clin_shared:regimen_indication_notes preferred_name="therapy_regimen_other" display_order="999" cde="2793516" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="368763"/>
309
+ <rad:radiation_treatment_ongoing preferred_name="radiation_therapy_ongoing_indicator" display_order="13" cde="2842745" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368773">NO</rad:radiation_treatment_ongoing>
310
+ <rad:course_number preferred_name="course_number" display_order="999" cde="2732184" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="368761">1</rad:course_number>
311
+ <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"/>
312
+ <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="368754">17</clin_shared:day_of_form_completion>
313
+ <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="368753">11</clin_shared:month_of_form_completion>
314
+ <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="368755">2010</clin_shared:year_of_form_completion>
315
+ </rad:radiation>
316
+ </rad:radiations>
317
+ </brca:patient>
318
+ </brca:tcga_bcr>