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  1. .gitattributes +100 -0
  2. data/__notebook__.ipynb +3265 -0
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  27. data/gdc_data_organized/0a017f15-1c6b-45e7-8d55-e0a71df1b2e8/CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D02_628264.grch38.seg.v2.txt +1169 -0
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+ "[2267/10000] (0.33GB) Downloading: 732ee0df-c0fa-4fa3-aa77-989a11172285.mirbase21.isoforms.quantification.txt (0.35 MB)... "
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+ ]
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+ },
18739
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18742
+ "text": [
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+ "OK\n",
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+ "[2268/10000] (0.33GB) Downloading: f1fd6980-0dce-47ea-893d-47c65502a2c7.methylation_array.sesame.level3betas.txt (12.58 MB)... "
18745
+ ]
18746
+ },
18747
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18750
+ "text": [
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+ "OK\n",
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+ "[2269/10000] (0.34GB) Downloading: TCGA-BRCA.ae2856f4-dafc-45b6-96af-6c6615cf9475.gene_level_copy_number.v36.tsv (3.29 MB)... "
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+ ]
18754
+ },
18755
+ {
18756
+ "name": "stdout",
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+ "output_type": "stream",
18758
+ "text": [
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+ "OK\n",
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+ "[2270/10000] (0.34GB) Downloading: TCGA-BRCA.ae2856f4-dafc-45b6-96af-6c6615cf9475.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
18761
+ ]
18762
+ },
18763
+ {
18764
+ "name": "stdout",
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+ "output_type": "stream",
18766
+ "text": [
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+ "OK\n",
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+ "[2271/10000] (0.34GB) Downloading: nationwidechildrens.org_clinical_drug_brca.txt (0.92 MB)... "
18769
+ ]
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+ },
18771
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18774
+ "text": [
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+ "OK\n",
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+ "[2272/10000] (0.35GB) Downloading: TCGA-BRCA.ae2856f4-dafc-45b6-96af-6c6615cf9475.ascat2.allelic_specific.seg.txt (0.01 MB)... "
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+ ]
18778
+ },
18779
+ {
18780
+ "name": "stdout",
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+ "output_type": "stream",
18782
+ "text": [
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+ "OK\n",
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+ "[2273/10000] (0.35GB) Downloading: TCGA-A8-A09E-01A-01-TS1.cd6ea8c1-5427-4be5-9ccf-8fdc40249000.svs (475.57 MB)... "
18785
+ ]
18786
+ },
18787
+ {
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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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+ "[2274/10000] (0.81GB) Downloading: 60ea9ace-996e-40d4-98a7-1f05a1df00de.methylation_array.sesame.level3betas.txt (0.73 MB)... "
18793
+ ]
18794
+ },
18795
+ {
18796
+ "name": "stdout",
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+ "output_type": "stream",
18798
+ "text": [
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+ "OK\n",
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+ "[2275/10000] (0.81GB) Downloading: TCGA-BRCA.70b9ece6-dedc-44c7-8f35-b78d9bac626e.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
18801
+ ]
18802
+ },
18803
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18806
+ "text": [
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+ "OK\n",
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+ "[2276/10000] (0.81GB) Downloading: TCGA-BRCA.70b9ece6-dedc-44c7-8f35-b78d9bac626e.ascat3.allelic_specific.seg.txt (0.01 MB)... "
18809
+ ]
18810
+ },
18811
+ {
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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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+ "[2277/10000] (0.81GB) Downloading: TCGA-A8-A09E-01Z-00-DX1.239A8E03-49EA-4C29-AF86-FC1BD8A9DB20.svs (284.14 MB)... "
18817
+ ]
18818
+ },
18819
+ {
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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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+ "[2278/10000] (1.09GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A09E.xml (0.09 MB)... "
18825
+ ]
18826
+ },
18827
+ {
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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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+ "[2279/10000] (1.09GB) Downloading: TCGA-BRCA.70b9ece6-dedc-44c7-8f35-b78d9bac626e.gene_level_copy_number.v36.tsv (3.29 MB)... "
18833
+ ]
18834
+ },
18835
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18838
+ "text": [
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+ "OK\n",
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+ "[2280/10000] (1.09GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_A08_628448.grch38.seg.v2.txt (0.02 MB)... "
18841
+ ]
18842
+ },
18843
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18846
+ "text": [
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+ "OK\n",
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+ "[2281/10000] (1.09GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A09E.xml (0.06 MB)... "
18849
+ ]
18850
+ },
18851
+ {
18852
+ "name": "stdout",
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+ "output_type": "stream",
18854
+ "text": [
18855
+ "OK\n",
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+ "[2282/10000] (1.09GB) Downloading: 31fa9bfd-dc91-4e27-be93-db7df8df2cd8.mirbase21.isoforms.quantification.txt (0.31 MB)... "
18857
+ ]
18858
+ },
18859
+ {
18860
+ "name": "stdout",
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+ "output_type": "stream",
18862
+ "text": [
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+ "OK\n",
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+ "[2283/10000] (1.09GB) Downloading: TCGA-A8-A09E-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
18865
+ ]
18866
+ },
18867
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
18870
+ "text": [
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+ "OK\n",
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+ "[2284/10000] (1.09GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G09_628500.nocnv_grch38.seg.v2.txt (0.03 MB)... "
18873
+ ]
18874
+ },
18875
+ {
18876
+ "name": "stdout",
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+ "output_type": "stream",
18878
+ "text": [
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+ "OK\n",
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+ "[2285/10000] (1.09GB) Downloading: e35fa380-07ac-45e1-9adc-4351675c6ccf.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
18881
+ ]
18882
+ },
18883
+ {
18884
+ "name": "stdout",
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+ "output_type": "stream",
18886
+ "text": [
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+ "OK\n",
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+ "[2286/10000] (1.09GB) Downloading: TCGA-BRCA.70b9ece6-dedc-44c7-8f35-b78d9bac626e.ascat2.allelic_specific.seg.txt (0.01 MB)... "
18889
+ ]
18890
+ },
18891
+ {
18892
+ "name": "stdout",
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+ "output_type": "stream",
18894
+ "text": [
18895
+ "OK\n",
18896
+ "[2287/10000] (1.09GB) Downloading: TCGA-A8-A09E.C55B6F4B-1248-4FBF-83C2-B0A1B33DEA03.PDF (0.06 MB)... "
18897
+ ]
18898
+ },
18899
+ {
18900
+ "name": "stdout",
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+ "output_type": "stream",
18902
+ "text": [
18903
+ "OK\n",
18904
+ "[2288/10000] (1.10GB) Downloading: TCGA-A8-A09E-01A-11D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.16 MB)... "
18905
+ ]
18906
+ },
18907
+ {
18908
+ "name": "stdout",
18909
+ "output_type": "stream",
18910
+ "text": [
18911
+ "OK\n",
18912
+ "[2289/10000] (1.10GB) Downloading: 60ea9ace-996e-40d4-98a7-1f05a1df00de_noid_Grn.idat (0.69 MB)... "
18913
+ ]
18914
+ },
18915
+ {
18916
+ "name": "stdout",
18917
+ "output_type": "stream",
18918
+ "text": [
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+ "OK\n",
18920
+ "[2290/10000] (1.10GB) Downloading: TCGA-BRCA.70b9ece6-dedc-44c7-8f35-b78d9bac626e.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
18921
+ ]
18922
+ },
18923
+ {
18924
+ "name": "stdout",
18925
+ "output_type": "stream",
18926
+ "text": [
18927
+ "OK\n",
18928
+ "[2291/10000] (1.10GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G09_628500.grch38.seg.v2.txt (0.06 MB)... "
18929
+ ]
18930
+ },
18931
+ {
18932
+ "name": "stdout",
18933
+ "output_type": "stream",
18934
+ "text": [
18935
+ "OK\n",
18936
+ "[2292/10000] (1.10GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A09E.xml (0.01 MB)... "
18937
+ ]
18938
+ },
18939
+ {
18940
+ "name": "stdout",
18941
+ "output_type": "stream",
18942
+ "text": [
18943
+ "OK\n",
18944
+ "[2293/10000] (1.10GB) Downloading: ca4ba8e9-dac8-468b-998c-f4ec259c472d.mirbase21.mirnas.quantification.txt (0.05 MB)... "
18945
+ ]
18946
+ },
18947
+ {
18948
+ "name": "stdout",
18949
+ "output_type": "stream",
18950
+ "text": [
18951
+ "OK\n",
18952
+ "[2294/10000] (1.10GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A7-A0DC.xml (0.16 MB)... "
18953
+ ]
18954
+ },
18955
+ {
18956
+ "name": "stdout",
18957
+ "output_type": "stream",
18958
+ "text": [
18959
+ "OK\n",
18960
+ "[2295/10000] (1.10GB) Downloading: c2ab5465-6a15-4122-8100-f40b5af388e9.methylation_array.sesame.level3betas.txt (12.37 MB)... "
18961
+ ]
18962
+ },
18963
+ {
18964
+ "name": "stdout",
18965
+ "output_type": "stream",
18966
+ "text": [
18967
+ "OK\n",
18968
+ "[2296/10000] (1.11GB) Downloading: TCGA-A7-A0DC-11A-04-TS4.6041f153-cc5a-44d8-9e04-f082918268e6.svs (135.84 MB)... "
18969
+ ]
18970
+ },
18971
+ {
18972
+ "name": "stdout",
18973
+ "output_type": "stream",
18974
+ "text": [
18975
+ "OK\n",
18976
+ "[2297/10000] (1.24GB) Downloading: nationwidechildrens.org_ssf.TCGA-A7-A0DC.xml (0.02 MB)... "
18977
+ ]
18978
+ },
18979
+ {
18980
+ "name": "stdout",
18981
+ "output_type": "stream",
18982
+ "text": [
18983
+ "OK\n",
18984
+ "[2298/10000] (1.24GB) Downloading: c6a90de3-979b-46b0-9f84-2875c1e38742.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
18985
+ ]
18986
+ },
18987
+ {
18988
+ "name": "stdout",
18989
+ "output_type": "stream",
18990
+ "text": [
18991
+ "OK\n",
18992
+ "[2299/10000] (1.25GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_H08_628250.nocnv_grch38.seg.v2.txt (0.01 MB)... "
18993
+ ]
18994
+ },
18995
+ {
18996
+ "name": "stdout",
18997
+ "output_type": "stream",
18998
+ "text": [
18999
+ "OK\n",
19000
+ "[2300/10000] (1.25GB) Downloading: c2ab5465-6a15-4122-8100-f40b5af388e9_noid_Grn.idat (7.72 MB)... "
19001
+ ]
19002
+ },
19003
+ {
19004
+ "name": "stdout",
19005
+ "output_type": "stream",
19006
+ "text": [
19007
+ "OK\n",
19008
+ "[2301/10000] (1.26GB) Downloading: TCGA-A7-A0DC-01Z-00-DX1.C770781E-83E4-47DD-B658-25BBBBB32066.svs (195.52 MB)... "
19009
+ ]
19010
+ },
19011
+ {
19012
+ "name": "stdout",
19013
+ "output_type": "stream",
19014
+ "text": [
19015
+ "OK\n",
19016
+ "[2302/10000] (1.45GB) Downloading: CHILE_p_TCGASNP_230_231_FFPE_N_GenomeWideSNP_6_A10_1147968.grch38.seg.v2.txt (0.12 MB)... "
19017
+ ]
19018
+ },
19019
+ {
19020
+ "name": "stdout",
19021
+ "output_type": "stream",
19022
+ "text": [
19023
+ "OK\n",
19024
+ "[2303/10000] (1.45GB) Downloading: ca4ba8e9-dac8-468b-998c-f4ec259c472d.mirbase21.isoforms.quantification.txt (0.36 MB)... "
19025
+ ]
19026
+ },
19027
+ {
19028
+ "name": "stdout",
19029
+ "output_type": "stream",
19030
+ "text": [
19031
+ "OK\n",
19032
+ "[2304/10000] (1.45GB) Downloading: 727d2856-09cb-4131-9052-f3cd85136cef.methylation_array.sesame.level3betas.txt (12.48 MB)... "
19033
+ ]
19034
+ },
19035
+ {
19036
+ "name": "stdout",
19037
+ "output_type": "stream",
19038
+ "text": [
19039
+ "OK\n",
19040
+ "[2305/10000] (1.46GB) Downloading: TCGA-A7-A0DC-01B-04-BS4.7F68E084-12C4-4591-AD2C-8DADE9DF09F1.svs (89.16 MB)... "
19041
+ ]
19042
+ },
19043
+ {
19044
+ "name": "stdout",
19045
+ "output_type": "stream",
19046
+ "text": [
19047
+ "OK\n",
19048
+ "[2306/10000] (1.55GB) Downloading: 0c814cd9-5b2c-4764-9e6a-6ad0403fcd7d.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
19049
+ ]
19050
+ },
19051
+ {
19052
+ "name": "stdout",
19053
+ "output_type": "stream",
19054
+ "text": [
19055
+ "OK\n",
19056
+ "[2307/10000] (1.55GB) Downloading: TCGA-A7-A0DC-01A-01-BS1.1129f718-410c-4fb7-9eeb-7a04d76487b6.svs (374.22 MB)... "
19057
+ ]
19058
+ },
19059
+ {
19060
+ "name": "stdout",
19061
+ "output_type": "stream",
19062
+ "text": [
19063
+ "OK\n",
19064
+ "[2308/10000] (1.92GB) Downloading: 22ae1265-0ef4-439e-ab8a-46abd4c8f3b2.mirbase21.isoforms.quantification.txt (0.19 MB)... "
19065
+ ]
19066
+ },
19067
+ {
19068
+ "name": "stdout",
19069
+ "output_type": "stream",
19070
+ "text": [
19071
+ "OK\n",
19072
+ "[2309/10000] (1.92GB) Downloading: c2ab5465-6a15-4122-8100-f40b5af388e9_noid_Red.idat (7.72 MB)... "
19073
+ ]
19074
+ },
19075
+ {
19076
+ "name": "stdout",
19077
+ "output_type": "stream",
19078
+ "text": [
19079
+ "OK\n",
19080
+ "[2310/10000] (1.92GB) Downloading: CHILE_p_TCGASNP_230_231_FFPE_N_GenomeWideSNP_6_A10_1147968.nocnv_grch38.seg.v2.txt (0.07 MB)... "
19081
+ ]
19082
+ },
19083
+ {
19084
+ "name": "stdout",
19085
+ "output_type": "stream",
19086
+ "text": [
19087
+ "OK\n",
19088
+ "[2311/10000] (1.92GB) Downloading: db5dab56-838e-4784-a7cf-f05296e356f7.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
19089
+ ]
19090
+ },
19091
+ {
19092
+ "name": "stdout",
19093
+ "output_type": "stream",
19094
+ "text": [
19095
+ "OK\n",
19096
+ "[2312/10000] (1.93GB) Downloading: TCGA-BRCA.e781547e-415c-4656-b656-c1df8cc22fc3.ascat2.allelic_specific.seg.txt (0.02 MB)... "
19097
+ ]
19098
+ },
19099
+ {
19100
+ "name": "stdout",
19101
+ "output_type": "stream",
19102
+ "text": [
19103
+ "OK\n",
19104
+ "[2313/10000] (1.93GB) Downloading: 7919dd79-9e3e-43ea-81da-cace56edfc1b_noid_Grn.idat (0.69 MB)... "
19105
+ ]
19106
+ },
19107
+ {
19108
+ "name": "stdout",
19109
+ "output_type": "stream",
19110
+ "text": [
19111
+ "OK\n",
19112
+ "[2314/10000] (1.93GB) Downloading: TCGA-BRCA.5bfd4ac0-78fb-4ee5-ac75-7e20a268685c.gene_level_copy_number.v36.tsv (3.29 MB)... "
19113
+ ]
19114
+ },
19115
+ {
19116
+ "name": "stdout",
19117
+ "output_type": "stream",
19118
+ "text": [
19119
+ "OK\n",
19120
+ "[2315/10000] (1.93GB) Downloading: TCGA-A7-A0DC-01B-03-BS3.318D8EA4-41EC-4D62-927B-5B40E5448E86.svs (95.65 MB)... "
19121
+ ]
19122
+ },
19123
+ {
19124
+ "name": "stdout",
19125
+ "output_type": "stream",
19126
+ "text": [
19127
+ "OK\n",
19128
+ "[2316/10000] (2.02GB) Downloading: TCGA-BRCA.e781547e-415c-4656-b656-c1df8cc22fc3.gene_level_copy_number.v36.tsv (3.29 MB)... "
19129
+ ]
19130
+ },
19131
+ {
19132
+ "name": "stdout",
19133
+ "output_type": "stream",
19134
+ "text": [
19135
+ "OK\n",
19136
+ "[2317/10000] (2.03GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_H11_628226.nocnv_grch38.seg.v2.txt (0.00 MB)... "
19137
+ ]
19138
+ },
19139
+ {
19140
+ "name": "stdout",
19141
+ "output_type": "stream",
19142
+ "text": [
19143
+ "OK\n",
19144
+ "[2318/10000] (2.03GB) Downloading: 727d2856-09cb-4131-9052-f3cd85136cef_noid_Grn.idat (7.72 MB)... "
19145
+ ]
19146
+ },
19147
+ {
19148
+ "name": "stdout",
19149
+ "output_type": "stream",
19150
+ "text": [
19151
+ "OK\n",
19152
+ "[2319/10000] (2.04GB) Downloading: 22ae1265-0ef4-439e-ab8a-46abd4c8f3b2.mirbase21.mirnas.quantification.txt (0.05 MB)... "
19153
+ ]
19154
+ },
19155
+ {
19156
+ "name": "stdout",
19157
+ "output_type": "stream",
19158
+ "text": [
19159
+ "OK\n",
19160
+ "[2320/10000] (2.04GB) Downloading: TCGA-A7-A0DC-01Z-00-DX2.795FD529-D7C2-407D-9E8A-5DCE1EF49029.svs (503.30 MB)... "
19161
+ ]
19162
+ },
19163
+ {
19164
+ "name": "stdout",
19165
+ "output_type": "stream",
19166
+ "text": [
19167
+ "OK\n",
19168
+ "[2321/10000] (2.53GB) Downloading: TCGA-BRCA.5bfd4ac0-78fb-4ee5-ac75-7e20a268685c.ascat2.allelic_specific.seg.txt (0.01 MB)... "
19169
+ ]
19170
+ },
19171
+ {
19172
+ "name": "stdout",
19173
+ "output_type": "stream",
19174
+ "text": [
19175
+ "OK\n",
19176
+ "[2322/10000] (2.53GB) Downloading: 7919dd79-9e3e-43ea-81da-cace56edfc1b_noid_Red.idat (0.69 MB)... "
19177
+ ]
19178
+ },
19179
+ {
19180
+ "name": "stdout",
19181
+ "output_type": "stream",
19182
+ "text": [
19183
+ "OK\n",
19184
+ "[2323/10000] (2.53GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_H08_628250.grch38.seg.v2.txt (0.04 MB)... "
19185
+ ]
19186
+ },
19187
+ {
19188
+ "name": "stdout",
19189
+ "output_type": "stream",
19190
+ "text": [
19191
+ "OK\n",
19192
+ "[2324/10000] (2.53GB) Downloading: TCGA-A7-A0DC.43D912CD-BD3C-4E69-B28B-AB2E173C0BC2.PDF (0.28 MB)... "
19193
+ ]
19194
+ },
19195
+ {
19196
+ "name": "stdout",
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+ "output_type": "stream",
19198
+ "text": [
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+ "OK\n",
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+ "[2325/10000] (2.53GB) Downloading: TCGA-BRCA.5bfd4ac0-78fb-4ee5-ac75-7e20a268685c.ascat3.allelic_specific.seg.txt (0.00 MB)... "
19201
+ ]
19202
+ },
19203
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19206
+ "text": [
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+ "OK\n",
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+ "[2326/10000] (2.53GB) Downloading: nationwidechildrens.org_clinical.TCGA-A7-A0DC.xml (0.11 MB)... "
19209
+ ]
19210
+ },
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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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+ "[2327/10000] (2.53GB) Downloading: db537846-eb1b-4954-aa74-81afd11f694e.mirbase21.mirnas.quantification.txt (0.05 MB)... "
19217
+ ]
19218
+ },
19219
+ {
19220
+ "name": "stdout",
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+ "output_type": "stream",
19222
+ "text": [
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+ "OK\n",
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+ "[2328/10000] (2.53GB) Downloading: TCGA-BRCA.5bfd4ac0-78fb-4ee5-ac75-7e20a268685c.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
19225
+ ]
19226
+ },
19227
+ {
19228
+ "name": "stdout",
19229
+ "output_type": "stream",
19230
+ "text": [
19231
+ "OK\n",
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+ "[2329/10000] (2.53GB) Downloading: db537846-eb1b-4954-aa74-81afd11f694e.mirbase21.isoforms.quantification.txt (0.26 MB)... "
19233
+ ]
19234
+ },
19235
+ {
19236
+ "name": "stdout",
19237
+ "output_type": "stream",
19238
+ "text": [
19239
+ "OK\n",
19240
+ "[2330/10000] (2.53GB) Downloading: MAPLE_p_TCGAb78_BrstRedo_SNP_N_GenomeWideSNP_6_F07_729628.grch38.seg.v2.txt (0.03 MB)... "
19241
+ ]
19242
+ },
19243
+ {
19244
+ "name": "stdout",
19245
+ "output_type": "stream",
19246
+ "text": [
19247
+ "OK\n",
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+ "[2331/10000] (2.53GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_H11_628226.grch38.seg.v2.txt (0.04 MB)... "
19249
+ ]
19250
+ },
19251
+ {
19252
+ "name": "stdout",
19253
+ "output_type": "stream",
19254
+ "text": [
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+ "OK\n",
19256
+ "[2332/10000] (2.53GB) Downloading: TCGA-A7-A0DC-01A-21-A13C-20_RPPA_data.tsv (0.02 MB)... "
19257
+ ]
19258
+ },
19259
+ {
19260
+ "name": "stdout",
19261
+ "output_type": "stream",
19262
+ "text": [
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+ "OK\n",
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+ "[2333/10000] (2.53GB) Downloading: MAPLE_p_TCGAb78_BrstRedo_SNP_N_GenomeWideSNP_6_F07_729628.nocnv_grch38.seg.v2.txt (0.01 MB)... "
19265
+ ]
19266
+ },
19267
+ {
19268
+ "name": "stdout",
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+ "output_type": "stream",
19270
+ "text": [
19271
+ "OK\n",
19272
+ "[2334/10000] (2.53GB) Downloading: 727d2856-09cb-4131-9052-f3cd85136cef_noid_Red.idat (7.72 MB)... "
19273
+ ]
19274
+ },
19275
+ {
19276
+ "name": "stdout",
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+ "output_type": "stream",
19278
+ "text": [
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+ "OK\n",
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+ "[2335/10000] (2.54GB) Downloading: TCGA-A7-A0DC-01A-01-TS1.19dd493c-9563-416b-8e3f-71c6ef3e8e95.svs (400.71 MB)... "
19281
+ ]
19282
+ },
19283
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19286
+ "text": [
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+ "OK\n",
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+ "[2336/10000] (2.93GB) Downloading: 7919dd79-9e3e-43ea-81da-cace56edfc1b.methylation_array.sesame.level3betas.txt (0.73 MB)... "
19289
+ ]
19290
+ },
19291
+ {
19292
+ "name": "stdout",
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+ "output_type": "stream",
19294
+ "text": [
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+ "OK\n",
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+ "[2337/10000] (2.93GB) Downloading: 7b135e51-3f69-496d-8668-bb19e2b793d8_noid_Red.idat (0.69 MB)... "
19297
+ ]
19298
+ },
19299
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19302
+ "text": [
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+ "OK\n",
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+ "[2338/10000] (2.93GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D02_628264.nocnv_grch38.seg.v2.txt (0.05 MB)... "
19305
+ ]
19306
+ },
19307
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19310
+ "text": [
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+ "OK\n",
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+ "[2339/10000] (2.93GB) Downloading: TCGA-BRCA.91094862-5aee-4304-b503-12a163a52532.gene_level_copy_number.v36.tsv (3.29 MB)... "
19313
+ ]
19314
+ },
19315
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19318
+ "text": [
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+ "OK\n",
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+ "[2340/10000] (2.94GB) Downloading: TCGA-A8-A08F-01A-01-TS1.e2b24767-1df7-431b-bba2-45d1b4e767d8.svs (221.26 MB)... "
19321
+ ]
19322
+ },
19323
+ {
19324
+ "name": "stdout",
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+ "output_type": "stream",
19326
+ "text": [
19327
+ "OK\n",
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+ "[2341/10000] (3.15GB) Downloading: nationwidechildrens.org_omf.TCGA-A8-A08F.xml (0.01 MB)... "
19329
+ ]
19330
+ },
19331
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
19334
+ "text": [
19335
+ "OK\n",
19336
+ "[2342/10000] (3.15GB) Downloading: TCGA-BRCA.91094862-5aee-4304-b503-12a163a52532.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
19337
+ ]
19338
+ },
19339
+ {
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+ "name": "stdout",
19341
+ "output_type": "stream",
19342
+ "text": [
19343
+ "OK\n",
19344
+ "[2343/10000] (3.15GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_C06_628334.grch38.seg.v2.txt (0.01 MB)... "
19345
+ ]
19346
+ },
19347
+ {
19348
+ "name": "stdout",
19349
+ "output_type": "stream",
19350
+ "text": [
19351
+ "OK\n",
19352
+ "[2344/10000] (3.15GB) Downloading: TCGA-A8-A08F-01Z-00-DX1.9D2222F6-1425-46FD-BC94-728EF835FAC2.svs (518.48 MB)... "
19353
+ ]
19354
+ },
19355
+ {
19356
+ "name": "stdout",
19357
+ "output_type": "stream",
19358
+ "text": [
19359
+ "OK\n",
19360
+ "[2345/10000] (3.66GB) Downloading: TCGA-A8-A08F.683AAF99-3B91-4501-B701-C3A4E8439647.PDF (0.07 MB)... "
19361
+ ]
19362
+ },
19363
+ {
19364
+ "name": "stdout",
19365
+ "output_type": "stream",
19366
+ "text": [
19367
+ "OK\n",
19368
+ "[2346/10000] (3.66GB) Downloading: TCGA-A8-A08F-01A-11D-A88Z-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.21 MB)... "
19369
+ ]
19370
+ },
19371
+ {
19372
+ "name": "stdout",
19373
+ "output_type": "stream",
19374
+ "text": [
19375
+ "OK\n",
19376
+ "[2347/10000] (3.66GB) Downloading: 616b6b60-8c4a-4d85-9a24-f47df6ad497e.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
19377
+ ]
19378
+ },
19379
+ {
19380
+ "name": "stdout",
19381
+ "output_type": "stream",
19382
+ "text": [
19383
+ "OK\n",
19384
+ "[2348/10000] (3.67GB) Downloading: TCGA-BRCA.91094862-5aee-4304-b503-12a163a52532.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
19385
+ ]
19386
+ },
19387
+ {
19388
+ "name": "stdout",
19389
+ "output_type": "stream",
19390
+ "text": [
19391
+ "OK\n",
19392
+ "[2349/10000] (3.67GB) Downloading: 7b135e51-3f69-496d-8668-bb19e2b793d8_noid_Grn.idat (0.69 MB)... "
19393
+ ]
19394
+ },
19395
+ {
19396
+ "name": "stdout",
19397
+ "output_type": "stream",
19398
+ "text": [
19399
+ "OK\n",
19400
+ "[2350/10000] (3.67GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A08F.xml (0.08 MB)... "
19401
+ ]
19402
+ },
19403
+ {
19404
+ "name": "stdout",
19405
+ "output_type": "stream",
19406
+ "text": [
19407
+ "OK\n",
19408
+ "[2351/10000] (3.67GB) Downloading: nationwidechildrens.org_ssf.TCGA-A8-A08F.xml (0.02 MB)... "
19409
+ ]
19410
+ },
19411
+ {
19412
+ "name": "stdout",
19413
+ "output_type": "stream",
19414
+ "text": [
19415
+ "OK\n",
19416
+ "[2352/10000] (3.67GB) Downloading: TCGA-BRCA.91094862-5aee-4304-b503-12a163a52532.ascat2.allelic_specific.seg.txt (0.02 MB)... "
19417
+ ]
19418
+ },
19419
+ {
19420
+ "name": "stdout",
19421
+ "output_type": "stream",
19422
+ "text": [
19423
+ "OK\n",
19424
+ "[2353/10000] (3.67GB) Downloading: a329335e-2962-485d-af32-1f6adf48cf7f.wxs.aliquot_ensemble_masked.maf.gz (0.04 MB)... "
19425
+ ]
19426
+ },
19427
+ {
19428
+ "name": "stdout",
19429
+ "output_type": "stream",
19430
+ "text": [
19431
+ "OK\n",
19432
+ "[2354/10000] (3.67GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_D02_628264.grch38.seg.v2.txt (0.08 MB)... "
19433
+ ]
19434
+ },
19435
+ {
19436
+ "name": "stdout",
19437
+ "output_type": "stream",
19438
+ "text": [
19439
+ "OK\n",
19440
+ "[2355/10000] (3.67GB) Downloading: TCGA-A8-A08F-01A-01-BS1.efa980a8-9019-4413-94a1-72f68fe860e9.svs (213.71 MB)... "
19441
+ ]
19442
+ },
19443
+ {
19444
+ "name": "stdout",
19445
+ "output_type": "stream",
19446
+ "text": [
19447
+ "OK\n",
19448
+ "[2356/10000] (3.88GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A08F.xml (0.09 MB)... "
19449
+ ]
19450
+ },
19451
+ {
19452
+ "name": "stdout",
19453
+ "output_type": "stream",
19454
+ "text": [
19455
+ "OK\n",
19456
+ "[2357/10000] (3.88GB) Downloading: TCGA-BRCA.91094862-5aee-4304-b503-12a163a52532.ascat3.allelic_specific.seg.txt (0.02 MB)... "
19457
+ ]
19458
+ },
19459
+ {
19460
+ "name": "stdout",
19461
+ "output_type": "stream",
19462
+ "text": [
19463
+ "OK\n",
19464
+ "[2358/10000] (3.88GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_C06_628334.nocnv_grch38.seg.v2.txt (0.00 MB)... "
19465
+ ]
19466
+ },
19467
+ {
19468
+ "name": "stdout",
19469
+ "output_type": "stream",
19470
+ "text": [
19471
+ "OK\n",
19472
+ "[2359/10000] (3.88GB) Downloading: 7b135e51-3f69-496d-8668-bb19e2b793d8.methylation_array.sesame.level3betas.txt (0.74 MB)... "
19473
+ ]
19474
+ },
19475
+ {
19476
+ "name": "stdout",
19477
+ "output_type": "stream",
19478
+ "text": [
19479
+ "OK\n",
19480
+ "[2360/10000] (3.88GB) Downloading: TCGA-LL-A6FP.D318A0F0-38B2-4DFA-8326-E362603AAC5E.PDF (0.19 MB)... "
19481
+ ]
19482
+ },
19483
+ {
19484
+ "name": "stdout",
19485
+ "output_type": "stream",
19486
+ "text": [
19487
+ "OK\n",
19488
+ "[2361/10000] (3.88GB) Downloading: TCGA-BRCA.23353deb-8af1-474e-8654-70d444529e5e.gene_level_copy_number.v36.tsv (3.29 MB)... "
19489
+ ]
19490
+ },
19491
+ {
19492
+ "name": "stdout",
19493
+ "output_type": "stream",
19494
+ "text": [
19495
+ "OK\n",
19496
+ "[2362/10000] (3.88GB) Downloading: TCGA-A7-A0CD-01A-11D-A930-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.15 MB)... "
19497
+ ]
19498
+ },
19499
+ {
19500
+ "name": "stdout",
19501
+ "output_type": "stream",
19502
+ "text": [
19503
+ "OK\n",
19504
+ "[2363/10000] (3.88GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_B07_628378.grch38.seg.v2.txt (0.04 MB)... "
19505
+ ]
19506
+ },
19507
+ {
19508
+ "name": "stdout",
19509
+ "output_type": "stream",
19510
+ "text": [
19511
+ "OK\n",
19512
+ "[2364/10000] (3.88GB) Downloading: TCGA-A7-A0CD.DEB67EB8-155C-4ACF-B3D4-595E4CBE2E5C.PDF (0.14 MB)... "
19513
+ ]
19514
+ },
19515
+ {
19516
+ "name": "stdout",
19517
+ "output_type": "stream",
19518
+ "text": [
19519
+ "OK\n",
19520
+ "[2365/10000] (3.88GB) Downloading: 93655b20-9109-4c7e-afd7-7bc76ca61578.methylation_array.sesame.level3betas.txt (0.73 MB)... "
19521
+ ]
19522
+ },
19523
+ {
19524
+ "name": "stdout",
19525
+ "output_type": "stream",
19526
+ "text": [
19527
+ "OK\n",
19528
+ "[2366/10000] (3.88GB) Downloading: TCGA-BRCA.a82e297d-8342-44f1-b7e8-e42872c834fa.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
19529
+ ]
19530
+ },
19531
+ {
19532
+ "name": "stdout",
19533
+ "output_type": "stream",
19534
+ "text": [
19535
+ "OK\n",
19536
+ "[2367/10000] (3.89GB) Downloading: TCGA-A7-A0CD-01A-21-A13A-20_RPPA_data.tsv (0.02 MB)... "
19537
+ ]
19538
+ },
19539
+ {
19540
+ "name": "stdout",
19541
+ "output_type": "stream",
19542
+ "text": [
19543
+ "OK\n",
19544
+ "[2368/10000] (3.89GB) Downloading: d9a51484-0d7f-423c-a3b2-93df9ce5da76_noid_Grn.idat (7.72 MB)... "
19545
+ ]
19546
+ },
19547
+ {
19548
+ "name": "stdout",
19549
+ "output_type": "stream",
19550
+ "text": [
19551
+ "OK\n",
19552
+ "[2369/10000] (3.89GB) Downloading: 2a181635-ab97-4384-8293-60802f45d9b5.mirbase21.isoforms.quantification.txt (0.21 MB)... "
19553
+ ]
19554
+ },
19555
+ {
19556
+ "name": "stdout",
19557
+ "output_type": "stream",
19558
+ "text": [
19559
+ "OK\n",
19560
+ "[2370/10000] (3.89GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_H03_1365130.grch38.seg.v2.txt (0.03 MB)... "
19561
+ ]
19562
+ },
19563
+ {
19564
+ "name": "stdout",
19565
+ "output_type": "stream",
19566
+ "text": [
19567
+ "OK\n",
19568
+ "[2371/10000] (3.89GB) Downloading: 2d82bb16-80f2-4c1e-9283-ff3d0afdb5f5_noid_Grn.idat (0.69 MB)... "
19569
+ ]
19570
+ },
19571
+ {
19572
+ "name": "stdout",
19573
+ "output_type": "stream",
19574
+ "text": [
19575
+ "OK\n",
19576
+ "[2372/10000] (3.89GB) Downloading: bdc9b6cc-c666-4f89-a993-d77e229d9f8b.mirbase21.mirnas.quantification.txt (0.05 MB)... "
19577
+ ]
19578
+ },
19579
+ {
19580
+ "name": "stdout",
19581
+ "output_type": "stream",
19582
+ "text": [
19583
+ "OK\n",
19584
+ "[2373/10000] (3.89GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G01_628418.grch38.seg.v2.txt (0.03 MB)... "
19585
+ ]
19586
+ },
19587
+ {
19588
+ "name": "stdout",
19589
+ "output_type": "stream",
19590
+ "text": [
19591
+ "OK\n",
19592
+ "[2374/10000] (3.89GB) Downloading: HAULS_p_TCGAb47_SNP_2N_GenomeWideSNP_6_G01_628418.nocnv_grch38.seg.v2.txt (0.00 MB)... "
19593
+ ]
19594
+ },
19595
+ {
19596
+ "name": "stdout",
19597
+ "output_type": "stream",
19598
+ "text": [
19599
+ "OK\n",
19600
+ "[2375/10000] (3.89GB) Downloading: TCGA-BRCA.7cd3f9f8-20a8-468e-aaca-9a49a32d250f.ascat2.allelic_specific.seg.txt (0.01 MB)... "
19601
+ ]
19602
+ },
19603
+ {
19604
+ "name": "stdout",
19605
+ "output_type": "stream",
19606
+ "text": [
19607
+ "OK\n",
19608
+ "[2376/10000] (3.89GB) Downloading: 465c6270-2bfa-410a-b282-e7cc7b7b028c.methylation_array.sesame.level3betas.txt (0.73 MB)... "
19609
+ ]
19610
+ },
19611
+ {
19612
+ "name": "stdout",
19613
+ "output_type": "stream",
19614
+ "text": [
19615
+ "OK\n",
19616
+ "[2377/10000] (3.90GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A091.xml (0.09 MB)... "
19617
+ ]
19618
+ },
19619
+ {
19620
+ "name": "stdout",
19621
+ "output_type": "stream",
19622
+ "text": [
19623
+ "OK\n",
19624
+ "[2378/10000] (3.90GB) Downloading: TCGA-A7-A0CD-01Z-00-DX2.609CED8D-5947-4753-A75B-73A8343B47EC.svs (233.59 MB)... "
19625
+ ]
19626
+ },
19627
+ {
19628
+ "name": "stdout",
19629
+ "output_type": "stream",
19630
+ "text": [
19631
+ "OK\n",
19632
+ "[2379/10000] (4.12GB) Downloading: 2a181635-ab97-4384-8293-60802f45d9b5.mirbase21.mirnas.quantification.txt (0.05 MB)... "
19633
+ ]
19634
+ },
19635
+ {
19636
+ "name": "stdout",
19637
+ "output_type": "stream",
19638
+ "text": [
19639
+ "OK\n",
19640
+ "[2380/10000] (4.12GB) Downloading: TCGA-LL-A6FP-01A-11D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.15 MB)... "
19641
+ ]
19642
+ },
19643
+ {
19644
+ "name": "stdout",
19645
+ "output_type": "stream",
19646
+ "text": [
19647
+ "OK\n",
19648
+ "[2381/10000] (4.12GB) Downloading: nationwidechildrens.org_omf.TCGA-A8-A091.xml (0.01 MB)... "
19649
+ ]
19650
+ },
19651
+ {
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+ "name": "stdout",
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19673
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+ "OK\n",
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+ "OK\n",
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19706
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+ "OK\n",
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+ "OK\n",
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+ "OK\n",
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+ "name": "stdout",
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+ "name": "stdout",
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19825
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19826
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19827
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+ "name": "stdout",
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19833
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19834
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19835
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19841
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19842
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19843
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19849
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19850
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19851
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19857
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19858
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19859
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19862
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19866
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19867
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19873
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19874
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19875
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19878
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19881
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19882
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19883
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19884
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19885
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19886
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19889
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19890
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19891
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19892
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19893
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19894
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19897
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19898
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19899
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19902
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19905
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19906
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19907
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19914
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19921
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19922
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19923
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19929
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19930
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19931
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19934
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19937
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19938
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19939
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19940
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19941
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19942
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19945
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19946
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19947
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19948
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19949
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19950
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19951
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19953
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19954
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19956
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19958
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19961
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19962
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19963
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19964
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19966
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19969
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19970
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19971
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+ "name": "stdout",
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19978
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19979
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19980
+ "name": "stdout",
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+ "OK\n",
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19985
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19986
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19987
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19988
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19990
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19991
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19992
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19993
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19994
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19996
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19998
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19999
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20001
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20009
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20010
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+ "OK\n",
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20017
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20018
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20019
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20020
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20021
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20022
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+ "OK\n",
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20026
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20027
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20030
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+ "OK\n",
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+ "[2429/10000] (5.68GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_B12_799974.nocnv_grch38.seg.v2.txt (0.04 MB)... "
20033
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20034
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20035
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20036
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20037
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20038
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+ "[2430/10000] (5.68GB) Downloading: TCGA-GI-A2C8-01A-01-TSA.3b6ee8f0-86dc-47bc-b5ab-fa0b1c6e8a59.svs (157.42 MB)... "
20041
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20042
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20043
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20044
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20045
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20046
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+ "OK\n",
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+ "[2431/10000] (5.84GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_H08_870982.nocnv_grch38.seg.v2.txt (0.00 MB)... "
20049
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20050
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20051
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20052
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+ "text": [
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+ "OK\n",
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+ "[2432/10000] (5.84GB) Downloading: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_A09_799960.grch38.seg.v2.txt (0.02 MB)... "
20057
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20058
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20059
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+ "name": "stdout",
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+ "OK\n",
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20065
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20066
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20067
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+ "OK\n",
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20074
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20075
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20081
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20082
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20083
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+ "name": "stdout",
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+ "OK\n",
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20098
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20099
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20100
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20107
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+ "name": "stdout",
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20110
+ "text": [
20111
+ "OK\n",
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+ "[2439/10000] (6.22GB) Downloading: TCGA-AR-A2LR.C310F4EC-D8B1-45C4-8D55-705A9EE35902.PDF (0.07 MB)... "
20113
+ ]
20114
+ },
20115
+ {
20116
+ "name": "stdout",
20117
+ "output_type": "stream",
20118
+ "text": [
20119
+ "OK\n",
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+ "[2440/10000] (6.22GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_D11_666934.nocnv_grch38.seg.v2.txt (0.03 MB)... "
20121
+ ]
20122
+ },
20123
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20126
+ "text": [
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+ "OK\n",
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+ "[2441/10000] (6.22GB) Downloading: TCGA-A8-A09I.AF12859A-D67A-488D-8BC2-ED28698F2ACA.PDF (0.05 MB)... "
20129
+ ]
20130
+ },
20131
+ {
20132
+ "name": "stdout",
20133
+ "output_type": "stream",
20134
+ "text": [
20135
+ "OK\n",
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+ "[2442/10000] (6.22GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_H08_870982.grch38.seg.v2.txt (0.02 MB)... "
20137
+ ]
20138
+ },
20139
+ {
20140
+ "name": "stdout",
20141
+ "output_type": "stream",
20142
+ "text": [
20143
+ "OK\n",
20144
+ "[2443/10000] (6.22GB) Downloading: TCGA-BRCA.bd4d930e-0848-48c1-8b03-c04a986f22d8.gene_level_copy_number.v36.tsv (3.29 MB)... "
20145
+ ]
20146
+ },
20147
+ {
20148
+ "name": "stdout",
20149
+ "output_type": "stream",
20150
+ "text": [
20151
+ "OK\n",
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+ "[2444/10000] (6.22GB) Downloading: TCGA-A8-A06U-01A-11D-A894-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.27 MB)... "
20153
+ ]
20154
+ },
20155
+ {
20156
+ "name": "stdout",
20157
+ "output_type": "stream",
20158
+ "text": [
20159
+ "OK\n",
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+ "[2445/10000] (6.22GB) Downloading: TCGA-BRCA.714b3b2b-ad91-483d-8754-2afc96067e5e.ascat2.allelic_specific.seg.txt (0.04 MB)... "
20161
+ ]
20162
+ },
20163
+ {
20164
+ "name": "stdout",
20165
+ "output_type": "stream",
20166
+ "text": [
20167
+ "OK\n",
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+ "[2446/10000] (6.22GB) Downloading: nationwidechildrens.org_ssf.TCGA-AO-A0J5.xml (0.01 MB)... "
20169
+ ]
20170
+ },
20171
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20174
+ "text": [
20175
+ "OK\n",
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+ "[2447/10000] (6.22GB) Downloading: TCGA-BRCA.714b3b2b-ad91-483d-8754-2afc96067e5e.ascat3.allelic_specific.seg.txt (0.03 MB)... "
20177
+ ]
20178
+ },
20179
+ {
20180
+ "name": "stdout",
20181
+ "output_type": "stream",
20182
+ "text": [
20183
+ "OK\n",
20184
+ "[2448/10000] (6.22GB) Downloading: 89c06b7b-8adc-449c-8de5-d8190b0f8c4d_noid_Red.idat (0.69 MB)... "
20185
+ ]
20186
+ },
20187
+ {
20188
+ "name": "stdout",
20189
+ "output_type": "stream",
20190
+ "text": [
20191
+ "OK\n",
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+ "[2449/10000] (6.22GB) Downloading: TCGA-A8-A06U-01A-01-TS1.078F5623-AB8A-455E-919E-41AD2575FA91.svs (310.55 MB)... "
20193
+ ]
20194
+ },
20195
+ {
20196
+ "name": "stdout",
20197
+ "output_type": "stream",
20198
+ "text": [
20199
+ "OK\n",
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+ "[2450/10000] (6.53GB) Downloading: COZEN_p_TCGAb56_SNP_2N_GenomeWideSNP_6_H02_667102.grch38.seg.v2.txt (0.04 MB)... "
20201
+ ]
20202
+ },
20203
+ {
20204
+ "name": "stdout",
20205
+ "output_type": "stream",
20206
+ "text": [
20207
+ "OK\n",
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+ "[2451/10000] (6.53GB) Downloading: 987d41ee-6bab-490c-b0f2-bf28c0089de9_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.14 MB)... "
20209
+ ]
20210
+ },
20211
+ {
20212
+ "name": "stdout",
20213
+ "output_type": "stream",
20214
+ "text": [
20215
+ "OK\n",
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+ "[2452/10000] (6.53GB) Downloading: TCGA-A8-A06U-01A-01-TS1.DFD8B445-C7A5-4247-A39F-222591C6D7E2.svs (121.32 MB)... "
20217
+ ]
20218
+ },
20219
+ {
20220
+ "name": "stdout",
20221
+ "output_type": "stream",
20222
+ "text": [
20223
+ "OK\n",
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+ "[2453/10000] (6.65GB) Downloading: 4f9ab944-ee29-4f43-ac5d-61cee10483ac.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20225
+ ]
20226
+ },
20227
+ {
20228
+ "name": "stdout",
20229
+ "output_type": "stream",
20230
+ "text": [
20231
+ "OK\n",
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+ "[2454/10000] (6.65GB) Downloading: 29644452-cc56-4895-a959-c7a1c344444a.methylation_array.sesame.level3betas.txt (12.53 MB)... "
20233
+ ]
20234
+ },
20235
+ {
20236
+ "name": "stdout",
20237
+ "output_type": "stream",
20238
+ "text": [
20239
+ "OK\n",
20240
+ "[2455/10000] (6.66GB) Downloading: 2912470e-ef3f-40fa-8a9b-f77aae0afa2d_noid_Grn.idat (0.69 MB)... "
20241
+ ]
20242
+ },
20243
+ {
20244
+ "name": "stdout",
20245
+ "output_type": "stream",
20246
+ "text": [
20247
+ "OK\n",
20248
+ "[2456/10000] (6.66GB) Downloading: nationwidechildrens.org_ssf.TCGA-C8-A1HO.xml (0.01 MB)... "
20249
+ ]
20250
+ },
20251
+ {
20252
+ "name": "stdout",
20253
+ "output_type": "stream",
20254
+ "text": [
20255
+ "OK\n",
20256
+ "[2457/10000] (6.66GB) Downloading: 92e64d91-88d8-4b1f-ab56-b593748b9f19.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
20257
+ ]
20258
+ },
20259
+ {
20260
+ "name": "stdout",
20261
+ "output_type": "stream",
20262
+ "text": [
20263
+ "OK\n",
20264
+ "[2458/10000] (6.66GB) Downloading: 6f4bdfe5-0f49-4b67-8d61-6acb4b024998.wxs.aliquot_ensemble_masked.maf.gz (0.02 MB)... "
20265
+ ]
20266
+ },
20267
+ {
20268
+ "name": "stdout",
20269
+ "output_type": "stream",
20270
+ "text": [
20271
+ "OK\n",
20272
+ "[2459/10000] (6.66GB) Downloading: TCGA-A8-A09I-01Z-00-DX1.B738E479-8766-4766-B012-B32AC2F27533.svs (553.81 MB)... "
20273
+ ]
20274
+ },
20275
+ {
20276
+ "name": "stdout",
20277
+ "output_type": "stream",
20278
+ "text": [
20279
+ "OK\n",
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+ "[2460/10000] (7.20GB) Downloading: e2edf21d-dcdb-49e6-a65b-bd1e555339ac.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20281
+ ]
20282
+ },
20283
+ {
20284
+ "name": "stdout",
20285
+ "output_type": "stream",
20286
+ "text": [
20287
+ "OK\n",
20288
+ "[2461/10000] (7.20GB) Downloading: TCGA-BRCA.bd4d930e-0848-48c1-8b03-c04a986f22d8.ascat3.allelic_specific.seg.txt (0.02 MB)... "
20289
+ ]
20290
+ },
20291
+ {
20292
+ "name": "stdout",
20293
+ "output_type": "stream",
20294
+ "text": [
20295
+ "OK\n",
20296
+ "[2462/10000] (7.20GB) Downloading: TCGA-C8-A1HO-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
20297
+ ]
20298
+ },
20299
+ {
20300
+ "name": "stdout",
20301
+ "output_type": "stream",
20302
+ "text": [
20303
+ "OK\n",
20304
+ "[2463/10000] (7.20GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_G04_666952.nocnv_grch38.seg.v2.txt (0.02 MB)... "
20305
+ ]
20306
+ },
20307
+ {
20308
+ "name": "stdout",
20309
+ "output_type": "stream",
20310
+ "text": [
20311
+ "OK\n",
20312
+ "[2464/10000] (7.20GB) Downloading: TCGA-A8-A09I-01A-11-A13A-20_RPPA_data.tsv (0.02 MB)... "
20313
+ ]
20314
+ },
20315
+ {
20316
+ "name": "stdout",
20317
+ "output_type": "stream",
20318
+ "text": [
20319
+ "OK\n",
20320
+ "[2465/10000] (7.20GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-A8-A06U.xml (0.10 MB)... "
20321
+ ]
20322
+ },
20323
+ {
20324
+ "name": "stdout",
20325
+ "output_type": "stream",
20326
+ "text": [
20327
+ "OK\n",
20328
+ "[2466/10000] (7.20GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A06U.xml (0.05 MB)... "
20329
+ ]
20330
+ },
20331
+ {
20332
+ "name": "stdout",
20333
+ "output_type": "stream",
20334
+ "text": [
20335
+ "OK\n",
20336
+ "[2467/10000] (7.20GB) Downloading: TCGA-A8-A09I-01A-02-BS2.ca9aacf2-573b-4af2-bc50-5213526eb3a3.svs (504.24 MB)... "
20337
+ ]
20338
+ },
20339
+ {
20340
+ "name": "stdout",
20341
+ "output_type": "stream",
20342
+ "text": [
20343
+ "OK\n",
20344
+ "[2468/10000] (7.70GB) Downloading: 4f9ab944-ee29-4f43-ac5d-61cee10483ac.mirbase21.isoforms.quantification.txt (0.34 MB)... "
20345
+ ]
20346
+ },
20347
+ {
20348
+ "name": "stdout",
20349
+ "output_type": "stream",
20350
+ "text": [
20351
+ "OK\n",
20352
+ "[2469/10000] (7.70GB) Downloading: 68b4a573-7a51-46d6-8c43-8ef46826b7d4.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20353
+ ]
20354
+ },
20355
+ {
20356
+ "name": "stdout",
20357
+ "output_type": "stream",
20358
+ "text": [
20359
+ "OK\n",
20360
+ "[2470/10000] (7.70GB) Downloading: TCGA-A8-A06U-01Z-00-DX1.56070AB9-A73E-44B8-8051-D93E8F881BBE.svs (404.69 MB)... "
20361
+ ]
20362
+ },
20363
+ {
20364
+ "name": "stdout",
20365
+ "output_type": "stream",
20366
+ "text": [
20367
+ "OK\n",
20368
+ "[2471/10000] (8.09GB) Downloading: 1a41dd5b-27b3-4032-8d76-93dc053b5940.mirbase21.isoforms.quantification.txt (0.43 MB)... "
20369
+ ]
20370
+ },
20371
+ {
20372
+ "name": "stdout",
20373
+ "output_type": "stream",
20374
+ "text": [
20375
+ "OK\n",
20376
+ "[2472/10000] (8.09GB) Downloading: TCGA-BRCA.80ffdd30-9845-4ee5-8f68-f272c0b0b1f5.ascat3.allelic_specific.seg.txt (0.01 MB)... "
20377
+ ]
20378
+ },
20379
+ {
20380
+ "name": "stdout",
20381
+ "output_type": "stream",
20382
+ "text": [
20383
+ "OK\n",
20384
+ "[2473/10000] (8.09GB) Downloading: TCGA-B6-A1KC-01B-01-TS1.af22665c-5cc1-4c93-a95c-65580c40e7e1.svs (266.74 MB)... "
20385
+ ]
20386
+ },
20387
+ {
20388
+ "name": "stdout",
20389
+ "output_type": "stream",
20390
+ "text": [
20391
+ "OK\n",
20392
+ "[2474/10000] (8.35GB) Downloading: 89d822a3-6577-46b6-8cca-5600e88a56a3.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20393
+ ]
20394
+ },
20395
+ {
20396
+ "name": "stdout",
20397
+ "output_type": "stream",
20398
+ "text": [
20399
+ "OK\n",
20400
+ "[2475/10000] (8.35GB) Downloading: 2912470e-ef3f-40fa-8a9b-f77aae0afa2d_noid_Red.idat (0.69 MB)... "
20401
+ ]
20402
+ },
20403
+ {
20404
+ "name": "stdout",
20405
+ "output_type": "stream",
20406
+ "text": [
20407
+ "OK\n",
20408
+ "[2476/10000] (8.35GB) Downloading: TCGA-C8-A1HO.24B1FA5C-7D84-4CE5-B094-2358ECE73C10.PDF (0.33 MB)... "
20409
+ ]
20410
+ },
20411
+ {
20412
+ "name": "stdout",
20413
+ "output_type": "stream",
20414
+ "text": [
20415
+ "OK\n",
20416
+ "[2477/10000] (8.35GB) Downloading: RANDS_p_TCGA_b109_SNP_1N_GenomeWideSNP_6_A07_771954.nocnv_grch38.seg.v2.txt (0.01 MB)... "
20417
+ ]
20418
+ },
20419
+ {
20420
+ "name": "stdout",
20421
+ "output_type": "stream",
20422
+ "text": [
20423
+ "OK\n",
20424
+ "[2478/10000] (8.35GB) Downloading: 9bc2055b-86f4-4ab7-80db-568b8d65b9f3.methylation_array.sesame.level3betas.txt (12.54 MB)... "
20425
+ ]
20426
+ },
20427
+ {
20428
+ "name": "stdout",
20429
+ "output_type": "stream",
20430
+ "text": [
20431
+ "OK\n",
20432
+ "[2479/10000] (8.37GB) Downloading: cb3b3878-adfb-41e0-9f1a-971f38df16dd_noid_Red.idat (7.72 MB)... "
20433
+ ]
20434
+ },
20435
+ {
20436
+ "name": "stdout",
20437
+ "output_type": "stream",
20438
+ "text": [
20439
+ "OK\n",
20440
+ "[2480/10000] (8.37GB) Downloading: TCGA-BRCA.89a93ef7-73a7-451f-9c83-251b827f02c6.ascat2.allelic_specific.seg.txt (0.01 MB)... "
20441
+ ]
20442
+ },
20443
+ {
20444
+ "name": "stdout",
20445
+ "output_type": "stream",
20446
+ "text": [
20447
+ "OK\n",
20448
+ "[2481/10000] (8.37GB) Downloading: d0207ef8-9ffc-4ba5-abb2-57fac81b5c38_noid_Grn.idat (0.69 MB)... "
20449
+ ]
20450
+ },
20451
+ {
20452
+ "name": "stdout",
20453
+ "output_type": "stream",
20454
+ "text": [
20455
+ "OK\n",
20456
+ "[2482/10000] (8.37GB) Downloading: TCGA-BRCA.80ffdd30-9845-4ee5-8f68-f272c0b0b1f5.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
20457
+ ]
20458
+ },
20459
+ {
20460
+ "name": "stdout",
20461
+ "output_type": "stream",
20462
+ "text": [
20463
+ "OK\n",
20464
+ "[2483/10000] (8.38GB) Downloading: a6c14ebc-81a2-44f7-af87-2b7ec85e5696_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.18 MB)... "
20465
+ ]
20466
+ },
20467
+ {
20468
+ "name": "stdout",
20469
+ "output_type": "stream",
20470
+ "text": [
20471
+ "OK\n",
20472
+ "[2484/10000] (8.38GB) Downloading: b09dddaf-f343-4e50-b324-178d456cfe50.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
20473
+ ]
20474
+ },
20475
+ {
20476
+ "name": "stdout",
20477
+ "output_type": "stream",
20478
+ "text": [
20479
+ "OK\n",
20480
+ "[2485/10000] (8.38GB) Downloading: d0207ef8-9ffc-4ba5-abb2-57fac81b5c38.methylation_array.sesame.level3betas.txt (0.73 MB)... "
20481
+ ]
20482
+ },
20483
+ {
20484
+ "name": "stdout",
20485
+ "output_type": "stream",
20486
+ "text": [
20487
+ "OK\n",
20488
+ "[2486/10000] (8.38GB) Downloading: dd3ab228-1c35-4710-aae3-68458bf959db.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20489
+ ]
20490
+ },
20491
+ {
20492
+ "name": "stdout",
20493
+ "output_type": "stream",
20494
+ "text": [
20495
+ "OK\n",
20496
+ "[2487/10000] (8.38GB) Downloading: 96a6ae98-0eb2-45aa-b7ce-b948012705d0.mirbase21.isoforms.quantification.txt (0.33 MB)... "
20497
+ ]
20498
+ },
20499
+ {
20500
+ "name": "stdout",
20501
+ "output_type": "stream",
20502
+ "text": [
20503
+ "OK\n",
20504
+ "[2488/10000] (8.38GB) Downloading: TCGA-BRCA.fdc086da-5ae1-4600-9039-4ea5c1fb7655.ascat3.allelic_specific.seg.txt (0.00 MB)... "
20505
+ ]
20506
+ },
20507
+ {
20508
+ "name": "stdout",
20509
+ "output_type": "stream",
20510
+ "text": [
20511
+ "OK\n",
20512
+ "[2489/10000] (8.38GB) Downloading: f7e81ca6-5c0e-4fc1-bdcf-9ddc0749fd01.methylation_array.sesame.level3betas.txt (12.46 MB)... "
20513
+ ]
20514
+ },
20515
+ {
20516
+ "name": "stdout",
20517
+ "output_type": "stream",
20518
+ "text": [
20519
+ "OK\n",
20520
+ "[2490/10000] (8.39GB) Downloading: 96a6ae98-0eb2-45aa-b7ce-b948012705d0.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20521
+ ]
20522
+ },
20523
+ {
20524
+ "name": "stdout",
20525
+ "output_type": "stream",
20526
+ "text": [
20527
+ "OK\n",
20528
+ "[2491/10000] (8.39GB) Downloading: cb3b3878-adfb-41e0-9f1a-971f38df16dd.methylation_array.sesame.level3betas.txt (12.29 MB)... "
20529
+ ]
20530
+ },
20531
+ {
20532
+ "name": "stdout",
20533
+ "output_type": "stream",
20534
+ "text": [
20535
+ "OK\n",
20536
+ "[2492/10000] (8.40GB) Downloading: TCGA-BRCA.8c976a66-2f34-4441-8f79-a13136e1dbe7.gene_level_copy_number.v36.tsv (3.29 MB)... "
20537
+ ]
20538
+ },
20539
+ {
20540
+ "name": "stdout",
20541
+ "output_type": "stream",
20542
+ "text": [
20543
+ "OK\n",
20544
+ "[2493/10000] (8.41GB) Downloading: 0633890f-584c-43d9-aa3f-7a6555533dd8.rna_seq.augmented_star_gene_counts.tsv (4.06 MB)... "
20545
+ ]
20546
+ },
20547
+ {
20548
+ "name": "stdout",
20549
+ "output_type": "stream",
20550
+ "text": [
20551
+ "OK\n",
20552
+ "[2494/10000] (8.41GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_A03_697148.grch38.seg.v2.txt (0.04 MB)... "
20553
+ ]
20554
+ },
20555
+ {
20556
+ "name": "stdout",
20557
+ "output_type": "stream",
20558
+ "text": [
20559
+ "OK\n",
20560
+ "[2495/10000] (8.41GB) Downloading: TCGA-AO-A0JI.468411B5-1719-46B4-835D-E469D6AEFF12.PDF (0.59 MB)... "
20561
+ ]
20562
+ },
20563
+ {
20564
+ "name": "stdout",
20565
+ "output_type": "stream",
20566
+ "text": [
20567
+ "OK\n",
20568
+ "[2496/10000] (8.41GB) Downloading: TCGA-BRCA.fdc086da-5ae1-4600-9039-4ea5c1fb7655.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
20569
+ ]
20570
+ },
20571
+ {
20572
+ "name": "stdout",
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+ "output_type": "stream",
20574
+ "text": [
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+ "OK\n",
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+ "[2497/10000] (8.41GB) Downloading: 89d822a3-6577-46b6-8cca-5600e88a56a3.mirbase21.isoforms.quantification.txt (0.22 MB)... "
20577
+ ]
20578
+ },
20579
+ {
20580
+ "name": "stdout",
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+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
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+ "[2498/10000] (8.41GB) Downloading: TCGA-BRCA.80ffdd30-9845-4ee5-8f68-f272c0b0b1f5.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
20585
+ ]
20586
+ },
20587
+ {
20588
+ "name": "stdout",
20589
+ "output_type": "stream",
20590
+ "text": [
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+ "OK\n",
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+ "[2499/10000] (8.42GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_A03_697148.nocnv_grch38.seg.v2.txt (0.01 MB)... "
20593
+ ]
20594
+ },
20595
+ {
20596
+ "name": "stdout",
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+ "output_type": "stream",
20598
+ "text": [
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+ "OK\n",
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+ "[2500/10000] (8.42GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_F04_628376.grch38.seg.v2.txt (0.06 MB)... "
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+ ]
20602
+ },
20603
+ {
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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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+ "[2501/10000] (8.42GB) Downloading: TCGA-BRCA.80ffdd30-9845-4ee5-8f68-f272c0b0b1f5.ascat2.allelic_specific.seg.txt (0.02 MB)... "
20609
+ ]
20610
+ },
20611
+ {
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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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+ "[2502/10000] (8.42GB) Downloading: TCGA-A8-A07I-01Z-00-DX1.37E7BB2E-8210-4216-B75F-0FD06D6C9AE3.svs (856.08 MB)... "
20617
+ ]
20618
+ },
20619
+ {
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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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+ "[2503/10000] (9.25GB) Downloading: TCGA-D8-A146-01A-03-TSC.b6b31df5-0bf0-47fb-9806-b99e1357af43.svs (344.54 MB)... "
20625
+ ]
20626
+ },
20627
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20630
+ "text": [
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+ "OK\n",
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+ "[2504/10000] (9.59GB) Downloading: PITON_p_TCGA_b162_167_SNP_N_GenomeWideSNP_6_F07_844842.nocnv_grch38.seg.v2.txt (0.01 MB)... "
20633
+ ]
20634
+ },
20635
+ {
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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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+ "[2505/10000] (9.59GB) Downloading: nationwidechildrens.org_biospecimen_protocol_brca.txt (0.75 MB)... "
20641
+ ]
20642
+ },
20643
+ {
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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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+ "[2506/10000] (9.59GB) Downloading: a3595c7e-948b-4d93-a623-477d7af84e15.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
20649
+ ]
20650
+ },
20651
+ {
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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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+ "[2507/10000] (9.59GB) Downloading: a61b373c-3cc9-46af-8b16-e3c1594ad9a7_noid_Grn.idat (0.69 MB)... "
20657
+ ]
20658
+ },
20659
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20662
+ "text": [
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+ "OK\n",
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+ "[2508/10000] (9.59GB) Downloading: b773c30d-f37b-4aee-8330-a159d42d3019.rna_seq.augmented_star_gene_counts.tsv (4.05 MB)... "
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+ ]
20666
+ },
20667
+ {
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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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+ "[2509/10000] (9.60GB) Downloading: nationwidechildrens.org_clinical.TCGA-BH-A0C0.xml (0.09 MB)... "
20673
+ ]
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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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+ "[2510/10000] (9.60GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_C09_697084.grch38.seg.v2.txt (0.04 MB)... "
20681
+ ]
20682
+ },
20683
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20686
+ "text": [
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+ "OK\n",
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+ "[2511/10000] (9.60GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_H04_697174.grch38.seg.v2.txt (0.07 MB)... "
20689
+ ]
20690
+ },
20691
+ {
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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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+ "[2512/10000] (9.60GB) Downloading: TCGA-BRCA.e0a41bf9-0af4-4a94-9b08-724a938ae4ae.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
20697
+ ]
20698
+ },
20699
+ {
20700
+ "name": "stdout",
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+ "output_type": "stream",
20702
+ "text": [
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+ "OK\n",
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+ "[2513/10000] (9.60GB) Downloading: MAPLE_p_TCGAb78_BrstRedo_SNP_N_GenomeWideSNP_6_G10_729670.nocnv_grch38.seg.v2.txt (0.00 MB)... "
20705
+ ]
20706
+ },
20707
+ {
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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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+ "[2514/10000] (9.60GB) Downloading: TCGA-A8-A07G-01Z-00-DX1.37E8A762-8141-4BE6-935A-B3DCB712BB4A.svs (441.31 MB)... "
20713
+ ]
20714
+ },
20715
+ {
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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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+ "[2515/10000] (10.03GB) Downloading: TCGA-B6-A0IK-01Z-00-DX1.1640DB44-4AC0-4A34-9E21-4673C4289A99.svs (631.48 MB)... "
20721
+ ]
20722
+ },
20723
+ {
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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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+ "[2516/10000] (10.65GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A07G.xml (0.07 MB)... "
20729
+ ]
20730
+ },
20731
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20734
+ "text": [
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+ "OK\n",
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+ "[2517/10000] (10.65GB) Downloading: TCGA-BRCA.37240e3a-9340-4509-a5e9-c7877ed93f52.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
20737
+ ]
20738
+ },
20739
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
20742
+ "text": [
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+ "OK\n",
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+ "[2518/10000] (10.65GB) Downloading: TCGA-BRCA.acf17ee7-c238-4602-9ec3-855c8d334089.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
20745
+ ]
20746
+ },
20747
+ {
20748
+ "name": "stdout",
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+ "output_type": "stream",
20750
+ "text": [
20751
+ "OK\n",
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+ "[2519/10000] (10.66GB) Downloading: TCGA-BRCA.37240e3a-9340-4509-a5e9-c7877ed93f52.ascat2.allelic_specific.seg.txt (0.02 MB)... "
20753
+ ]
20754
+ },
20755
+ {
20756
+ "name": "stdout",
20757
+ "output_type": "stream",
20758
+ "text": [
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+ "OK\n",
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+ "[2520/10000] (10.66GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_A12_667004.nocnv_grch38.seg.v2.txt (0.01 MB)... "
20761
+ ]
20762
+ },
20763
+ {
20764
+ "name": "stdout",
20765
+ "output_type": "stream",
20766
+ "text": [
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+ "OK\n",
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+ "[2521/10000] (10.66GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_C06_802374.grch38.seg.v2.txt (0.02 MB)... "
20769
+ ]
20770
+ },
20771
+ {
20772
+ "name": "stdout",
20773
+ "output_type": "stream",
20774
+ "text": [
20775
+ "OK\n",
20776
+ "[2522/10000] (10.66GB) Downloading: 435578b0-5e1b-4c59-bc82-5020c98775c2.methylation_array.sesame.level3betas.txt (12.28 MB)... "
20777
+ ]
20778
+ },
20779
+ {
20780
+ "name": "stdout",
20781
+ "output_type": "stream",
20782
+ "text": [
20783
+ "OK\n",
20784
+ "[2523/10000] (10.67GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A247.xml (0.01 MB)... "
20785
+ ]
20786
+ },
20787
+ {
20788
+ "name": "stdout",
20789
+ "output_type": "stream",
20790
+ "text": [
20791
+ "OK\n",
20792
+ "[2524/10000] (10.67GB) Downloading: TCGA-A8-A07G-01A-01-TS1.ed5520f2-535b-4bb4-b580-b2372714d3fb.svs (145.82 MB)... "
20793
+ ]
20794
+ },
20795
+ {
20796
+ "name": "stdout",
20797
+ "output_type": "stream",
20798
+ "text": [
20799
+ "OK\n",
20800
+ "[2525/10000] (10.81GB) Downloading: TCGA-BRCA.37240e3a-9340-4509-a5e9-c7877ed93f52.gene_level_copy_number.v36.tsv (3.29 MB)... "
20801
+ ]
20802
+ },
20803
+ {
20804
+ "name": "stdout",
20805
+ "output_type": "stream",
20806
+ "text": [
20807
+ "OK\n",
20808
+ "[2526/10000] (10.81GB) Downloading: TCGA-AC-A2QH.C2A0E948-2B9E-4E49-90C4-57CE4C4A95B3.PDF (0.34 MB)... "
20809
+ ]
20810
+ },
20811
+ {
20812
+ "name": "stdout",
20813
+ "output_type": "stream",
20814
+ "text": [
20815
+ "OK\n",
20816
+ "[2527/10000] (10.81GB) Downloading: TCGA-BRCA.116845a5-2178-44ff-8cac-58b95dd85081.ascat2.allelic_specific.seg.txt (0.02 MB)... "
20817
+ ]
20818
+ },
20819
+ {
20820
+ "name": "stdout",
20821
+ "output_type": "stream",
20822
+ "text": [
20823
+ "OK\n",
20824
+ "[2528/10000] (10.81GB) Downloading: TCGA-BRCA.1ffca953-dced-4469-959f-307bb3670a56.ascat3.allelic_specific.seg.txt (0.00 MB)... "
20825
+ ]
20826
+ },
20827
+ {
20828
+ "name": "stdout",
20829
+ "output_type": "stream",
20830
+ "text": [
20831
+ "OK\n",
20832
+ "[2529/10000] (10.81GB) Downloading: nationwidechildrens.org_clinical.TCGA-E9-A247.xml (0.09 MB)... "
20833
+ ]
20834
+ },
20835
+ {
20836
+ "name": "stdout",
20837
+ "output_type": "stream",
20838
+ "text": [
20839
+ "OK\n",
20840
+ "[2530/10000] (10.81GB) Downloading: TCGA-AC-A2QH-01B-03-BS3.B8CA7E1C-1D50-41C4-A2F3-130D40C86D8C.svs (566.21 MB)... "
20841
+ ]
20842
+ },
20843
+ {
20844
+ "name": "stdout",
20845
+ "output_type": "stream",
20846
+ "text": [
20847
+ "OK\n",
20848
+ "[2531/10000] (11.37GB) Downloading: CELLA_p_TCGA_177_179_Esph_SNP_N_GenomeWideSNP_6_E06_871070.grch38.seg.v2.txt (0.07 MB)... "
20849
+ ]
20850
+ },
20851
+ {
20852
+ "name": "stdout",
20853
+ "output_type": "stream",
20854
+ "text": [
20855
+ "OK\n",
20856
+ "[2532/10000] (11.37GB) Downloading: f2a6ab54-ed90-483c-9258-2ed63537bbd1.methylation_array.sesame.level3betas.txt (12.49 MB)... "
20857
+ ]
20858
+ },
20859
+ {
20860
+ "name": "stdout",
20861
+ "output_type": "stream",
20862
+ "text": [
20863
+ "OK\n",
20864
+ "[2533/10000] (11.38GB) Downloading: TCGA-AC-A2QH-01A-01-TSA.272367FE-1BB8-43F8-9304-219AAFF37D36.svs (243.67 MB)... "
20865
+ ]
20866
+ },
20867
+ {
20868
+ "name": "stdout",
20869
+ "output_type": "stream",
20870
+ "text": [
20871
+ "OK\n",
20872
+ "[2534/10000] (11.62GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_E04_802430.grch38.seg.v2.txt (0.04 MB)... "
20873
+ ]
20874
+ },
20875
+ {
20876
+ "name": "stdout",
20877
+ "output_type": "stream",
20878
+ "text": [
20879
+ "OK\n",
20880
+ "[2535/10000] (11.62GB) Downloading: TCGA-E9-A247.61E73960-32B0-413E-AF1D-2EF4582293B3.PDF (0.05 MB)... "
20881
+ ]
20882
+ },
20883
+ {
20884
+ "name": "stdout",
20885
+ "output_type": "stream",
20886
+ "text": [
20887
+ "OK\n",
20888
+ "[2536/10000] (11.62GB) Downloading: ab879a4b-4064-44a3-a69f-081e71c14d4c.wxs.aliquot_ensemble_masked.maf.gz (0.01 MB)... "
20889
+ ]
20890
+ },
20891
+ {
20892
+ "name": "stdout",
20893
+ "output_type": "stream",
20894
+ "text": [
20895
+ "OK\n",
20896
+ "[2537/10000] (11.62GB) Downloading: KEBAB_p_TCGASNP_226_227_N_GenomeWideSNP_6_D12_1151522.grch38.seg.v2.txt (0.03 MB)... "
20897
+ ]
20898
+ },
20899
+ {
20900
+ "name": "stdout",
20901
+ "output_type": "stream",
20902
+ "text": [
20903
+ "OK\n",
20904
+ "[2538/10000] (11.62GB) Downloading: nationwidechildrens.org_clinical.TCGA-AC-A2QH.xml (0.07 MB)... "
20905
+ ]
20906
+ },
20907
+ {
20908
+ "name": "stdout",
20909
+ "output_type": "stream",
20910
+ "text": [
20911
+ "OK\n",
20912
+ "[2539/10000] (11.62GB) Downloading: KEBAB_p_TCGASNP_226_227_N_GenomeWideSNP_6_D12_1151522.nocnv_grch38.seg.v2.txt (0.00 MB)... "
20913
+ ]
20914
+ },
20915
+ {
20916
+ "name": "stdout",
20917
+ "output_type": "stream",
20918
+ "text": [
20919
+ "OK\n",
20920
+ "[2540/10000] (11.62GB) Downloading: f2a6ab54-ed90-483c-9258-2ed63537bbd1_noid_Grn.idat (7.72 MB)... "
20921
+ ]
20922
+ },
20923
+ {
20924
+ "name": "stdout",
20925
+ "output_type": "stream",
20926
+ "text": [
20927
+ "OK\n",
20928
+ "[2541/10000] (11.63GB) Downloading: f7990502-632e-4fae-8218-625fe1bebdb5_noid_Red.idat (7.72 MB)... "
20929
+ ]
20930
+ },
20931
+ {
20932
+ "name": "stdout",
20933
+ "output_type": "stream",
20934
+ "text": [
20935
+ "OK\n",
20936
+ "[2542/10000] (11.63GB) Downloading: TCGA-BRCA.742b1f3f-a199-4dac-8d56-82db36855633.ascat2.allelic_specific.seg.txt (0.02 MB)... "
20937
+ ]
20938
+ },
20939
+ {
20940
+ "name": "stdout",
20941
+ "output_type": "stream",
20942
+ "text": [
20943
+ "OK\n",
20944
+ "[2543/10000] (11.63GB) Downloading: 50ab9ba6-b3c8-460d-818a-a8b5c20ddf3b.methylation_array.sesame.level3betas.txt (12.19 MB)... "
20945
+ ]
20946
+ },
20947
+ {
20948
+ "name": "stdout",
20949
+ "output_type": "stream",
20950
+ "text": [
20951
+ "OK\n",
20952
+ "[2544/10000] (11.64GB) Downloading: nationwidechildrens.org_clinical.TCGA-AN-A0XW.xml (0.05 MB)... "
20953
+ ]
20954
+ },
20955
+ {
20956
+ "name": "stdout",
20957
+ "output_type": "stream",
20958
+ "text": [
20959
+ "OK\n",
20960
+ "[2545/10000] (11.64GB) Downloading: TCGA-BRCA.86c22622-a7fb-4c73-8d6a-40be9a307dbe.gene_level_copy_number.v36.tsv (3.29 MB)... "
20961
+ ]
20962
+ },
20963
+ {
20964
+ "name": "stdout",
20965
+ "output_type": "stream",
20966
+ "text": [
20967
+ "OK\n",
20968
+ "[2546/10000] (11.65GB) Downloading: TCGA-EW-A6SD-01A-12D-A89E-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.13 MB)... "
20969
+ ]
20970
+ },
20971
+ {
20972
+ "name": "stdout",
20973
+ "output_type": "stream",
20974
+ "text": [
20975
+ "OK\n",
20976
+ "[2547/10000] (11.65GB) Downloading: TCGA-BRCA.58cceccb-40f5-4907-9e65-2e6b51f62a0a.absolute_liftover.gene_level_copy_number.v36.tsv (3.28 MB)... "
20977
+ ]
20978
+ },
20979
+ {
20980
+ "name": "stdout",
20981
+ "output_type": "stream",
20982
+ "text": [
20983
+ "OK\n",
20984
+ "[2548/10000] (11.65GB) Downloading: 676b95a0-38d6-4f95-ad71-e91e1078d90f.mirbase21.mirnas.quantification.txt (0.05 MB)... "
20985
+ ]
20986
+ },
20987
+ {
20988
+ "name": "stdout",
20989
+ "output_type": "stream",
20990
+ "text": [
20991
+ "OK\n",
20992
+ "[2549/10000] (11.65GB) Downloading: TCGA-A2-A0D4.990F5885-8EDD-42A2-AEFE-9DEE3E95A0B1.PDF (0.17 MB)... "
20993
+ ]
20994
+ },
20995
+ {
20996
+ "name": "stdout",
20997
+ "output_type": "stream",
20998
+ "text": [
20999
+ "OK\n",
21000
+ "[2550/10000] (11.65GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-AN-A0XW.xml (0.06 MB)... "
21001
+ ]
21002
+ },
21003
+ {
21004
+ "name": "stdout",
21005
+ "output_type": "stream",
21006
+ "text": [
21007
+ "OK\n",
21008
+ "[2551/10000] (11.65GB) Downloading: TCGA-BRCA.a1b53759-99b5-4470-bb22-242ab09561dd.ascat2.allelic_specific.seg.txt (0.01 MB)... "
21009
+ ]
21010
+ },
21011
+ {
21012
+ "name": "stdout",
21013
+ "output_type": "stream",
21014
+ "text": [
21015
+ "OK\n",
21016
+ "[2552/10000] (11.65GB) Downloading: TCGA-BRCA.4e237dc0-b785-4eb0-9948-a946b41dab8f.ascat3.allelic_specific.seg.txt (0.01 MB)... "
21017
+ ]
21018
+ },
21019
+ {
21020
+ "name": "stdout",
21021
+ "output_type": "stream",
21022
+ "text": [
21023
+ "OK\n",
21024
+ "[2553/10000] (11.65GB) Downloading: TCGA-BRCA.a1b53759-99b5-4470-bb22-242ab09561dd.absolute_liftover.gene_level_copy_number.v36.tsv (3.27 MB)... "
21025
+ ]
21026
+ },
21027
+ {
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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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+ "[2554/10000] (11.65GB) Downloading: TCGA-BRCA.fcd41d63-c0f1-4f8e-ad1f-ea398203a3a4.ascat3.allelic_specific.seg.txt (0.01 MB)... "
21033
+ ]
21034
+ },
21035
+ {
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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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+ "[2555/10000] (11.65GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_E02_697130.nocnv_grch38.seg.v2.txt (0.15 MB)... "
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+ ]
21042
+ },
21043
+ {
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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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+ "[2556/10000] (11.65GB) Downloading: TCGA-BRCA.a1b53759-99b5-4470-bb22-242ab09561dd.gene_level_copy_number.v36.tsv (3.29 MB)... "
21049
+ ]
21050
+ },
21051
+ {
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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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+ "[2557/10000] (11.66GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_B01_777766.grch38.seg.v2.txt (0.02 MB)... "
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+ ]
21058
+ },
21059
+ {
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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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+ "[2558/10000] (11.66GB) Downloading: CHEEP_p_TCGA_b120_121_SNP_N_GenomeWideSNP_6_G09_777598.grch38.seg.v2.txt (0.03 MB)... "
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+ ]
21066
+ },
21067
+ {
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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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+ "[2559/10000] (11.66GB) Downloading: e4d0900f-8165-4b39-82b0-8eb393684cc4_noid_Grn.idat (7.72 MB)... "
21073
+ ]
21074
+ },
21075
+ {
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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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+ "[2560/10000] (11.67GB) Downloading: nationwidechildrens.org_ssf.TCGA-BH-A0B1.xml (0.01 MB)... "
21081
+ ]
21082
+ },
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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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+ "[2561/10000] (11.67GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_B12_628398.nocnv_grch38.seg.v2.txt (0.00 MB)... "
21089
+ ]
21090
+ },
21091
+ {
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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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+ "[2562/10000] (11.67GB) Downloading: e4d0900f-8165-4b39-82b0-8eb393684cc4_noid_Red.idat (7.72 MB)... "
21097
+ ]
21098
+ },
21099
+ {
21100
+ "name": "stdout",
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+ "output_type": "stream",
21102
+ "text": [
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+ "OK\n",
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+ "[2563/10000] (11.67GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-E9-A1R4.xml (0.06 MB)... "
21105
+ ]
21106
+ },
21107
+ {
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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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+ "[2564/10000] (11.67GB) Downloading: nationwidechildrens.org_biospecimen.TCGA-BH-A0B1.xml (0.09 MB)... "
21113
+ ]
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+ },
21115
+ {
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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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+ "[2565/10000] (11.67GB) Downloading: TCGA-A2-A0D4-01Z-00-DX1.35E43827-DABC-4685-A62A-333672923349.svs (916.46 MB)... "
21121
+ ]
21122
+ },
21123
+ {
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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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+ "[2566/10000] (12.57GB) Downloading: 2b000af3-2c9d-4eaa-af3f-8101b7425c37_wgs_gdc_realn.cr.igv.reheader.seg.txt (0.18 MB)... "
21129
+ ]
21130
+ },
21131
+ {
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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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+ "[2567/10000] (12.57GB) Downloading: CUSKS_p_TCGAb47_SNP_1N_GenomeWideSNP_6_F11_628286.grch38.seg.v2.txt (0.06 MB)... "
21137
+ ]
21138
+ },
21139
+ {
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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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+ "[2568/10000] (12.57GB) Downloading: TCGA-E9-A1R4-01Z-00-DX1.B04D5A22-8CE5-49FD-8510-14444F46894D.svs (374.96 MB)... "
21145
+ ]
21146
+ },
21147
+ {
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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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+ "[2569/10000] (12.93GB) Downloading: BITES_p_TCGAb61_SNP_S_GenomeWideSNP_6_E02_697130.grch38.seg.v2.txt (0.25 MB)... "
21153
+ ]
21154
+ },
21155
+ {
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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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+ "[2570/10000] (12.94GB) Downloading: TCGA-E9-A1R2-01A-21-A17J-20_RPPA_data.tsv (0.02 MB)... "
21161
+ ]
21162
+ },
21163
+ {
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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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+ "[2571/10000] (12.94GB) Downloading: 2b67c3b5-330e-41e4-95cf-028d37fe91e1.rna_seq.augmented_star_gene_counts.tsv (4.04 MB)... "
21169
+ ]
21170
+ },
21171
+ {
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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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+ "[2572/10000] (12.94GB) Downloading: 5abd7590-46fd-4016-b38a-e334a7066e25_noid_Grn.idat (0.69 MB)... "
21177
+ ]
21178
+ },
21179
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
21182
+ "text": [
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+ "OK\n",
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+ "[2573/10000] (12.94GB) Downloading: TCGA-BRCA.fcd41d63-c0f1-4f8e-ad1f-ea398203a3a4.gene_level_copy_number.v36.tsv (3.29 MB)... "
21185
+ ]
21186
+ },
21187
+ {
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+ "name": "stdout",
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+ "output_type": "stream",
21190
+ "text": [
21191
+ "OK\n",
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+ "[2574/10000] (12.94GB) Downloading: TCGA-BRCA.fcd41d63-c0f1-4f8e-ad1f-ea398203a3a4.ascat2.allelic_specific.seg.txt (0.01 MB)... "
21193
+ ]
21194
+ },
21195
+ {
21196
+ "name": "stdout",
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+ "output_type": "stream",
21198
+ "text": [
21199
+ "OK\n",
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+ "[2575/10000] (12.94GB) Downloading: f02cebd5-5840-4c63-bdf2-af7677e112e9.wxs.aliquot_ensemble_masked.maf.gz (0.03 MB)... "
21201
+ ]
21202
+ },
21203
+ {
21204
+ "name": "stdout",
21205
+ "output_type": "stream",
21206
+ "text": [
21207
+ "OK\n",
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+ "[2576/10000] (12.94GB) Downloading: nationwidechildrens.org_ssf.TCGA-E9-A1R4.xml (0.01 MB)... "
21209
+ ]
21210
+ },
21211
+ {
21212
+ "name": "stdout",
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+ "output_type": "stream",
21214
+ "text": [
21215
+ "OK\n",
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+ "[2577/10000] (12.94GB) Downloading: nationwidechildrens.org_clinical.TCGA-A7-A4SB.xml (0.08 MB)... "
21217
+ ]
21218
+ },
21219
+ {
21220
+ "name": "stdout",
21221
+ "output_type": "stream",
21222
+ "text": [
21223
+ "OK\n",
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+ "[2578/10000] (12.94GB) Downloading: TCGA-E9-A1R4-01A-21D-A898-36.WholeGenome.RP-1657.cr.igv.reheader.seg.txt (0.06 MB)... "
21225
+ ]
21226
+ },
21227
+ {
21228
+ "name": "stdout",
21229
+ "output_type": "stream",
21230
+ "text": [
21231
+ "OK\n",
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+ "[2579/10000] (12.94GB) Downloading: nationwidechildrens.org_ssf.TCGA-AC-A62V.xml (0.01 MB)... "
21233
+ ]
21234
+ },
21235
+ {
21236
+ "name": "stdout",
21237
+ "output_type": "stream",
21238
+ "text": [
21239
+ "OK\n",
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+ "[2580/10000] (12.94GB) Downloading: TCGA-BRCA.58f16a99-4220-411d-be80-c354c3dde02f.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
21241
+ ]
21242
+ },
21243
+ {
21244
+ "name": "stdout",
21245
+ "output_type": "stream",
21246
+ "text": [
21247
+ "OK\n",
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+ "[2581/10000] (12.95GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_C09_666914.grch38.seg.v2.txt (0.08 MB)... "
21249
+ ]
21250
+ },
21251
+ {
21252
+ "name": "stdout",
21253
+ "output_type": "stream",
21254
+ "text": [
21255
+ "OK\n",
21256
+ "[2582/10000] (12.95GB) Downloading: nationwidechildrens.org_ssf.TCGA-AO-A1KQ.xml (0.02 MB)... "
21257
+ ]
21258
+ },
21259
+ {
21260
+ "name": "stdout",
21261
+ "output_type": "stream",
21262
+ "text": [
21263
+ "OK\n",
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+ "[2583/10000] (12.95GB) Downloading: nationwidechildrens.org_ssf.TCGA-A7-A4SB.xml (0.01 MB)... "
21265
+ ]
21266
+ },
21267
+ {
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+ "name": "stdout",
21269
+ "output_type": "stream",
21270
+ "text": [
21271
+ "OK\n",
21272
+ "[2584/10000] (12.95GB) Downloading: 6f51034e-ecfb-44df-9160-fb242d842de8_noid_Red.idat (7.72 MB)... "
21273
+ ]
21274
+ },
21275
+ {
21276
+ "name": "stdout",
21277
+ "output_type": "stream",
21278
+ "text": [
21279
+ "OK\n",
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+ "[2585/10000] (12.95GB) Downloading: BONZE_p_TCGAb56_SNP_1N_GenomeWideSNP_6_B07_666956.grch38.seg.v2.txt (0.07 MB)... "
21281
+ ]
21282
+ },
21283
+ {
21284
+ "name": "stdout",
21285
+ "output_type": "stream",
21286
+ "text": [
21287
+ "OK\n",
21288
+ "[2586/10000] (12.95GB) Downloading: TCGA-AO-A1KQ.EB5199BA-6164-4CFB-AFAA-B41544B83103.PDF (0.14 MB)... "
21289
+ ]
21290
+ },
21291
+ {
21292
+ "name": "stdout",
21293
+ "output_type": "stream",
21294
+ "text": [
21295
+ "OK\n",
21296
+ "[2587/10000] (12.95GB) Downloading: nationwidechildrens.org_clinical.TCGA-A8-A06Q.xml (0.03 MB)... "
21297
+ ]
21298
+ },
21299
+ {
21300
+ "name": "stdout",
21301
+ "output_type": "stream",
21302
+ "text": [
21303
+ "OK\n",
21304
+ "[2588/10000] (12.95GB) Downloading: acde14f5-60dc-4974-92e8-f66411594f64_noid_Grn.idat (7.72 MB)... "
21305
+ ]
21306
+ },
21307
+ {
21308
+ "name": "stdout",
21309
+ "output_type": "stream",
21310
+ "text": [
21311
+ "OK\n",
21312
+ "[2589/10000] (12.96GB) Downloading: 053491a2-e50a-49a4-905c-ce3a657e2d3a.mirbase21.isoforms.quantification.txt (0.31 MB)... "
21313
+ ]
21314
+ },
21315
+ {
21316
+ "name": "stdout",
21317
+ "output_type": "stream",
21318
+ "text": [
21319
+ "OK\n",
21320
+ "[2590/10000] (12.96GB) Downloading: acde14f5-60dc-4974-92e8-f66411594f64_noid_Red.idat (7.72 MB)... "
21321
+ ]
21322
+ },
21323
+ {
21324
+ "name": "stdout",
21325
+ "output_type": "stream",
21326
+ "text": [
21327
+ "OK\n",
21328
+ "[2591/10000] (12.97GB) Downloading: TCGA-BRCA.58f16a99-4220-411d-be80-c354c3dde02f.gene_level_copy_number.v36.tsv (3.29 MB)... "
21329
+ ]
21330
+ },
21331
+ {
21332
+ "name": "stdout",
21333
+ "output_type": "stream",
21334
+ "text": [
21335
+ "OK\n",
21336
+ "[2592/10000] (12.97GB) Downloading: TCGA-BRCA.0a7bfa84-8239-4d2b-8320-3d8a9db2a3ef.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
21337
+ ]
21338
+ },
21339
+ {
21340
+ "name": "stdout",
21341
+ "output_type": "stream",
21342
+ "text": [
21343
+ "OK\n",
21344
+ "[2593/10000] (12.98GB) Downloading: SHOUT_p_TCGAb_319_20_21_22_NSP_GenomeWideSNP_6_G05_1365000.grch38.seg.v2.txt (0.04 MB)... "
21345
+ ]
21346
+ },
21347
+ {
21348
+ "name": "stdout",
21349
+ "output_type": "stream",
21350
+ "text": [
21351
+ "OK\n",
21352
+ "[2594/10000] (12.98GB) Downloading: MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_C09_1320408.nocnv_grch38.seg.v2.txt (0.02 MB)... "
21353
+ ]
21354
+ },
21355
+ {
21356
+ "name": "stdout",
21357
+ "output_type": "stream",
21358
+ "text": [
21359
+ "OK\n",
21360
+ "[2595/10000] (12.98GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_C02_730904.grch38.seg.v2.txt (0.02 MB)... "
21361
+ ]
21362
+ },
21363
+ {
21364
+ "name": "stdout",
21365
+ "output_type": "stream",
21366
+ "text": [
21367
+ "OK\n",
21368
+ "[2596/10000] (12.98GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_G06_730916.grch38.seg.v2.txt (0.06 MB)... "
21369
+ ]
21370
+ },
21371
+ {
21372
+ "name": "stdout",
21373
+ "output_type": "stream",
21374
+ "text": [
21375
+ "OK\n",
21376
+ "[2597/10000] (12.98GB) Downloading: 9107ffc9-f542-4fc2-b896-b6c71c5d3a80.mirbase21.mirnas.quantification.txt (0.05 MB)... "
21377
+ ]
21378
+ },
21379
+ {
21380
+ "name": "stdout",
21381
+ "output_type": "stream",
21382
+ "text": [
21383
+ "OK\n",
21384
+ "[2598/10000] (12.98GB) Downloading: DEVEL_p_TCGAb3_73_74_75_76_NSP_GenomeWideSNP_6_C01_1438320.grch38.seg.v2.txt (0.05 MB)... "
21385
+ ]
21386
+ },
21387
+ {
21388
+ "name": "stdout",
21389
+ "output_type": "stream",
21390
+ "text": [
21391
+ "OK\n",
21392
+ "[2599/10000] (12.98GB) Downloading: TCGA-BRCA.062f01fb-85b6-4c22-bb39-1ebaeca09d82.ascat3.allelic_specific.seg.txt (0.01 MB)... "
21393
+ ]
21394
+ },
21395
+ {
21396
+ "name": "stdout",
21397
+ "output_type": "stream",
21398
+ "text": [
21399
+ "OK\n",
21400
+ "[2600/10000] (12.98GB) Downloading: 82978eff-30b4-48a0-8806-78d3d8f7ad70.methylation_array.sesame.level3betas.txt (12.42 MB)... "
21401
+ ]
21402
+ },
21403
+ {
21404
+ "name": "stdout",
21405
+ "output_type": "stream",
21406
+ "text": [
21407
+ "OK\n",
21408
+ "[2601/10000] (12.99GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_E01_780958.grch38.seg.v2.txt (0.03 MB)... "
21409
+ ]
21410
+ },
21411
+ {
21412
+ "name": "stdout",
21413
+ "output_type": "stream",
21414
+ "text": [
21415
+ "OK\n",
21416
+ "[2602/10000] (12.99GB) Downloading: EXINE_p_TCGA_b142_SNP_N_GenomeWideSNP_6_C04_802476.nocnv_grch38.seg.v2.txt (0.03 MB)... "
21417
+ ]
21418
+ },
21419
+ {
21420
+ "name": "stdout",
21421
+ "output_type": "stream",
21422
+ "text": [
21423
+ "OK\n",
21424
+ "[2603/10000] (12.99GB) Downloading: TCGA-BRCA.356ec0ad-a065-44db-8a4d-218efff4c3b4.ascat3.gene_level_copy_number.v36.tsv (3.29 MB)... "
21425
+ ]
21426
+ },
21427
+ {
21428
+ "name": "stdout",
21429
+ "output_type": "stream",
21430
+ "text": [
21431
+ "OK\n",
21432
+ "[2604/10000] (12.99GB) Downloading: nationwidechildrens.org_ssf.TCGA-AR-A24Q.xml (0.02 MB)... "
21433
+ ]
21434
+ },
21435
+ {
21436
+ "name": "stdout",
21437
+ "output_type": "stream",
21438
+ "text": [
21439
+ "OK\n",
21440
+ "[2605/10000] (12.99GB) Downloading: SHUCK_p_TCGAb74and75_SNP_N_GenomeWideSNP_6_C02_730904.nocnv_grch38.seg.v2.txt (0.00 MB)... "
21441
+ ]
21442
+ },
21443
+ {
21444
+ "name": "stdout",
21445
+ "output_type": "stream",
21446
+ "text": [
21447
+ "OK\n",
21448
+ "[2606/10000] (12.99GB) Downloading: TCGA-D8-A1XU-01Z-00-DX1.769DBC38-6F0D-425B-A904-79EBA1C119EF.svs (892.52 MB)... "
21449
+ ]
21450
+ },
21451
+ {
21452
+ "name": "stdout",
21453
+ "output_type": "stream",
21454
+ "text": [
21455
+ "OK\n",
21456
+ "[2607/10000] (13.86GB) Downloading: 816e42ac-95ac-42f3-8c9c-b60fb748d628_noid_Red.idat (7.72 MB)... "
21457
+ ]
21458
+ },
21459
+ {
21460
+ "name": "stdout",
21461
+ "output_type": "stream",
21462
+ "text": [
21463
+ "OK\n",
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+ "[2608/10000] (13.87GB) Downloading: BULGY_p_TCGA_bM1_124_SNP_N_GenomeWideSNP_6_A05_780896.nocnv_grch38.seg.v2.txt (0.00 MB)... "
21465
+ ]
21466
+ },
21467
+ {
21468
+ "name": "stdout",
21469
+ "output_type": "stream",
21470
+ "text": [
21471
+ "OK\n",
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+ "[2609/10000] (13.87GB) Downloading: fa1b44dd-3960-4ce1-be3c-2e2e0e7ece66_noid_Grn.idat (7.72 MB)... "
21473
+ ]
21474
+ },
21475
+ {
21476
+ "name": "stdout",
21477
+ "output_type": "stream",
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+ "text": [
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+ "OK\n",
21480
+ "[2610/10000] (13.88GB) Downloading: nationwidechildrens.org_clinical.TCGA-D8-A1XU.xml (0.05 MB)... "
21481
+ ]
21482
+ },
21483
+ {
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+ "name": "stdout",
21485
+ "output_type": "stream",
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199
+ AGID00305 1745 ab124827 Set163 GCLM 0.0863799959797464
200
+ AGID00212 1263 3305 Old GCN5L2 -0.023574
201
+ AGID00270 1579 3538 Set163 Gli1 -0.196810402579844
202
+ AGID00263 1520 ab69838 Set163 Gli3 0.252678851108856
203
+ AGID00548 2530 3660 Set163 Glucocorticoid-Receptor 0.314514992903906
204
+ AGID00387 1617 12793 Set163 Glutamate-D1-2 0.933218863724128
205
+ AGID00262 1491 ab156876 Set163 Glutaminase -0.0979800632150215
206
+ AGID00319 1807 4275 Set163 Granzyme-B 1.2402749005767
207
+ AGID00368 2169 ab183737 Set163 GRB7 0.185079220417508
208
+ AGID00396 2339 3593 Set163 Grp75 -0.181705067919758
209
+ AGID00174 1163 9315 Set163 GSK-3B -0.159330877455543
210
+ AGID00502 1082 9336 Old GSK3_pS9 0.49094
211
+ AGID00033 284 sc-7291 Old GSK3ALPHABETA -0.23449
212
+ AGID00034 285 9331 Old GSK3ALPHABETA_pS21S9 0.6085
213
+ AGID00129 1035 3886 Old GYS NA
214
+ AGID00130 1036 3891 Old GYS_pS641 NA
215
+ AGID01354 1342 9718 Set163 H2AX_pS139 -0.0470600433216984
216
+ AGID00363 1409 MA1-2022 Set163 H2AX_pS140 -0.0738450647659387
217
+ AGID00131 1038 MS-325-P1 Old HER2 0.90937
218
+ AGID00142 299 06-229 Old HER2_pY1248 0.69655
219
+ AGID00110 911 sc-285 Old HER3 0.4472
220
+ AGID00080 728 4791 Old HER3_pY1289 -0.085216
221
+ AGID00103 890 2573 Old HEREGULIN -0.04633
222
+ AGID00271 1582 11988 Set163 HES1 0.412469763775454
223
+ AGID00397 2340 2024 Set163 Hexokinase-I -0.0836202479387316
224
+ AGID00442 1023 2867 Set163 Hexokinase-II -0.83820155958059
225
+ AGID00419 1402 610958 Old HIF1ALPHA NA
226
+ AGID00205 1250 ab1791 Set163 Histone-H3 -0.508480176752523
227
+ AGID00398 2341 3377 Set163 Histone-H3_pS10 0.334604867860159
228
+ AGID00332 1901 ab128959 Set163 HLA-DQA1 -0.664671373955902
229
+ AGID00333 1902 14832-1-AP Set163 HMHA1 -0.0324904978182469
230
+ AGID00035 321 2402 Set163 HSP27 0.103654941333756
231
+ AGID00036 323 2401 Set163 HSP27_pS82 -0.272620010605152
232
+ AGID00320 1808 12165 Set163 HSP60 -0.252175221971708
233
+ AGID00037 325 4872 Old HSP70 0.34813
234
+ AGID00366 2158 86630 Set163 IDO -0.4595754936507
235
+ AGID00197 1221 3024 Old IGF1R_pY1135Y1136 0.20258
236
+ AGID00038 335 3922 Old IGFBP2 -0.24643
237
+ AGID00090 793 611504 Set163 IGFBP3 0.120299675953718
238
+ AGID00039 336 3027 Set163 IGFRb 0.492360002911218
239
+ AGID00336 1949 12153 Set163 IL-6 -0.0776653274340382
240
+ AGID02221 2583 57145 Set163 IMP3 0.0199298567264825
241
+ AGID02153 2459 14543 Old INPP4B 3.002
242
+ AGID00272 1586 3025 Set163 IR-b 0.471869961738276
243
+ AGID00519 2519 4302 Set163 IRF-3 0.0523452479961035
244
+ AGID00520 2520 4947 Set163 IRF-3_pS396 -0.0671705404467879
245
+ AGID00223 1316 sc-497 Old IRF1 0.029894
246
+ AGID00092 802 06-248 Old IRS1 0.20708
247
+ AGID00040 371 4502 Set163 IRS2 0.190349535036922
248
+ AGID00250 1394 sc-13157 Old JAB1 0.0048633
249
+ AGID00256 1413 ab109536 Set163 Jagged1 0.0108855262941029
250
+ AGID00177 1166 3230 Old JAK2 -0.4133
251
+ AGID00758 377 4671 Old JNK_pT183Y185 0.78424
252
+ AGID02136 2439 PA5-28262 Old JNK2 0.54198
253
+ AGID00307 1757 ab10484 Set163 KAP1 -0.00641551042485769
254
+ AGID00528 904 2180 Old KU80 -0.058346
255
+ AGID00375 2237 HPA028732 Set163 LAD1 -0.527524995139305
256
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257
+ AGID00279 1618 4108 Set163 LC3A-B -0.195975269105711
258
+ AGID00042 397 2752 Old LCK -0.49046
259
+ AGID00119 976 3582 Old LDHA NA
260
+ AGID00533 977 ab85319 Old LDHB NA
261
+ AGID00529 1477 3050 Old LKB1 0.012445
262
+ AGID00244 1367 2568 Set163 LRP6_pS1490 -0.211055021756157
263
+ AGID00439 2424 2796 Set163 Lyn -0.118155058666244
264
+ AGID02154 2460 4370 Old MAPK_pT202Y204 1.3052
265
+ AGID00198 1222 5453 Set163 Mcl-1 0.227938950090223
266
+ AGID00288 1633 AB3314P Set163 MCT4 -0.439670134331919
267
+ AGID00175 1164 3521 Set163 MDM2_pS166 0.669575001949476
268
+ AGID00044 417 1235-1/ab32576 Old MEK1 0.24908
269
+ AGID00143 1076 9154 Old MEK1_pS217S221 0.12293
270
+ AGID00201 1243 9125 Set163 MEK2 0.0369395269271018
271
+ AGID00361 2118 ab51061 Set163 MelanA 0.0490049782438428
272
+ AGID00362 2119 ab137078 Set163 Melanoma-gp100 0.137719898661885
273
+ AGID00337 1951 12711 Set163 MERIT40 -0.000745635607205295
274
+ AGID00338 1952 12110 Set163 MERIT40_pS29 0.00737000395093928
275
+ AGID02212 2574 ab195352 Set163 METTL3 0.165439995979746
276
+ AGID00225 1323 sc-20121 Set163 MIF 0.658220001594238
277
+ AGID00137 1062 WH0054206M1 Old MIG6 0.23102
278
+ AGID00403 2117 ab20663 Set163 MITF -0.0722853883115159
279
+ AGID00503 1067 ab3298 Old MITOCHONDRIA NA
280
+ AGID00321 1809 14739 Set163 Mitofusin-1 -0.184668791676369
281
+ AGID00322 1810 11925 Set163 Mitofusin-2 1.01257987433242
282
+ AGID00389 2324 3515 Set163 MLH1 -0.0404901432735174
283
+ AGID00312 1780 14993 Set163 MLKL 0.264789847507626
284
+ AGID00402 2359 MAB3328 Set163 MMP14 -0.172500060165174
285
+ AGID00045 435 4022 Set163 MMP2 -0.00835285923022388
286
+ AGID00122 1005 2195 Set163 Mnk1 -0.0619012130072234
287
+ AGID00331 1899 sc-377312 Set163 MR1 0.0437948156315225
288
+ AGID00273 1589 ab103319 Set163 MRAP -0.0149099948013964
289
+ AGID00530 440 4847 Old MRE11 0.16883
290
+ AGID00390 905 2850 Old MSH2 -0.57689
291
+ AGID00138 1063 22030002 Old MSH6 -0.42191
292
+ AGID00299 1675 ab76148 Set163 MSI2 0.304705005276583
293
+ AGID00232 1344 ab14705 Set163 MTCO1 -1.01725167963359
294
+ AGID00046 444 2983 Old MTOR 0.20959
295
+ AGID00047 446 2971 Old MTOR_pS2448 0.37491
296
+ AGID00204 1247 H00009788-M01A Set163 MTSS1 -0.0284251742485296
297
+ AGID00401 1139 21370002 Old MYH11 -0.62737
298
+ AGID00291 1647 3403 Old MYOSINIIA 0.19347
299
+ AGID00173 1160 5026 Old MYOSINIIA_pS1943 0.1713
300
+ AGID00318 1803 4282 Set163 Myt1 -0.211140253899797
301
+ AGID00216 1274 5795-1/ab129189 Old NAPSINA NA
302
+ AGID00418 452 4061 Old NCADHERIN -0.12594
303
+ AGID00156 1126 3217 Old NDRG1_pT346 -0.18717
304
+ AGID02133 2436 PA5-45913 Set163 NDUFB4 0.022120002911218
305
+ AGID00134 1046 22710002 Old NF2 0.37479
306
+ AGID00048 457 3033 Old NFKBP65_pS536 0.038155
307
+ AGID02155 2461 3608 Old NOTCH1 -0.0066568
308
+ AGID00340 1969 4147 Set163 Notch1-cleaved -0.0328352449841924
309
+ AGID00087 767 sc-5593 Set163 Notch3 0.0134199772647725
310
+ AGID00258 1420 3187 Set163 NQO1 -0.770275184368478
311
+ AGID00162 1136 sc-31 Old NRAS 0.063095
312
+ AGID00257 1419 12721 Old NRF2 NA
313
+ AGID00297 1669 2750 Set163 Oct-4 -0.151745008447731
314
+ AGID00420 466 1712-1/ab40803 Old P16INK4A 0.29688
315
+ AGID00384 470 sc-6246 Old P21 0.066977
316
+ AGID00105 897 1591-1/ab32034 Old P27 -0.27627
317
+ AGID00096 842 AF1555 Old P27_pT157 0.19695
318
+ AGID00099 878 ab64949 Old P27_pT198 -0.19534
319
+ AGID00181 1175 9228 Set163 p38-a 0.291328888746728
320
+ AGID00098 479 9211 Old P38_pT180Y182 0.0073294
321
+ AGID00049 478 9212 Old P38MAPK 0.35405
322
+ AGID00151 1119 4695 Set163 p44-42-MAPK 0.714014990131317
323
+ AGID00050 481 9282 Old P53 -0.11785
324
+ AGID00490 1187 610833 Old P62LCKLIGAND 1.0937
325
+ AGID00545 1415 ab53039 Old P63 NA
326
+ AGID00052 494 9205 Old P70S6K_pT389 0.2113
327
+ AGID00051 493 1494-1/ab32529 Old P70S6K1 0.2547
328
+ AGID00085 759 9347 Old P90RSK 0.059104
329
+ AGID00531 770 9344 Old P90RSK_pT359S363 0.62582
330
+ AGID00182 1178 9346 Set163 p90RSK_pT573 0.00525987856061763
331
+ AGID00053 499 612024 Old PAI1 -0.14299
332
+ AGID00224 1322 HPA035895 Set163 PAICS 0.0550500034657358
333
+ AGID00323 1811 2602 Set163 PAK1 0.582759574546303
334
+ AGID02199 2517 PA5-69540 Set163 PAK4 0.309204888827859
335
+ AGID00245 1370 4336-BPC-100 Set163 PAR 0.797559543077428
336
+ AGID00374 2209 66564 Set163 PARG 0.24968972780112
337
+ AGID00370 1372 sc-7150 Old PARP1 -1.2584
338
+ AGID00468 501 9546 Old PARPCLEAVED -0.32111
339
+ AGID00274 1591 ab53715 Set163 Patched 0.0102299665209912
340
+ AGID00513 2486 60433 Set163 PAX6 -0.00652010133811534
341
+ AGID00441 1621 9857 Set163 PAX8 -0.364596380878705
342
+ AGID00054 504 2542 Old PAXILLIN -0.00082777
343
+ AGID00055 509 2130 Old PCADHERIN -0.38644
344
+ AGID00248 511 ab29 Old PCNA -0.18849
345
+ AGID00413 2095 43248 Old PDCD1 NA
346
+ AGID00094 816 600-401-965 Old PDCD4 0.52097
347
+ AGID00385 1225 3169 Set163 PDGFRB 0.210324991552269
348
+ AGID00210 1258 ab110332 Set163 PDH 0.0542038447752271
349
+ AGID00324 1817 3205 Set163 PDHA1 0.175874326131082
350
+ AGID00280 1622 3820 Set163 PDHK1 -0.00957000519860372
351
+ AGID00056 515 3062 Old PDK1 0.081483
352
+ AGID00057 516 3061 Old PDK1_pS241 0.054688
353
+ AGID00300 1234 sc-19090 Old PDL1 -0.33817
354
+ AGID00124 1017 2780 Old PEA15 0.18966
355
+ AGID00125 1018 44-836G Old PEA15_pS116 -0.057227
356
+ AGID00440 2429 3192 Set163 PERK -0.356220612256816
357
+ AGID02207 2569 ab192876 Set163 PGM1 -0.0173606498253825
358
+ AGID00281 1623 13428 Set163 PHGDH -0.199160621544986
359
+ AGID00425 2399 22789-1-AP Set163 PHLPP 0.295560002287386
360
+ AGID00226 1330 sc-376412 Set163 PI3K-p110-b -0.0274000091495425
361
+ AGID00093 808 4255 Old PI3KP110ALPHA 0.54189
362
+ AGID00058 523 06-195 Old PI3KP85 0.075016
363
+ AGID00296 1667 5675 Set163 PKA-a 0.322114858987875
364
+ AGID00259 1426 9375 Set163 PKC-a-b-II_pT638_T641 0.0262699981285019
365
+ AGID00172 529 05-154 Old PKCALPHA -0.71911
366
+ AGID00460 530 06-822 Old PKCALPHA_pS657 -0.47385
367
+ AGID00114 932 07-875 Old PKCDELTA_pS664 -0.014927
368
+ AGID00163 1137 9371 Old PKCPANBETAII_pS660 -0.13888
369
+ AGID00126 1025 4053 Old PKM2 NA
370
+ AGID00512 2489 5690 Set163 PLC-gamma1 -0.0985708321081332
371
+ AGID02138 2441 GTX133463 Set163 PLC-gamma2_pY759 0.33505483559416
372
+ AGID00084 754 4513 Set163 PLK1 -0.469010066334184
373
+ AGID00203 1246 22510002 Set163 PMS2 0.101739998128502
374
+ AGID00207 1254 ab14734 Set163 Porin -0.0780599956331726
375
+ AGID00381 549 1483-1/ab32085 Old PR 0.6067
376
+ AGID00081 738 AHO1031 Set163 PRAS40 -0.0891999948013963
377
+ AGID00082 739 44-1100G Old PRAS40_pT246 0.042953
378
+ AGID00424 2398 OAAF05458 Set163 PRC1_pT481 0.229409979205585
379
+ AGID00492 1205 HPA007730 Old PRDX1 0.27338
380
+ AGID00190 1204 ab102739 Old PREX1 1.4054
381
+ AGID00061 566 9552 Old PTEN 0.24394
382
+ AGID00364 2154 ab76942 Set163 PTPN12 -0.0913601572057745
383
+ AGID00218 1290 4976 Set163 Puma 0.628195005415212
384
+ AGID00200 1242 SAB2900066 Old PYGB NA
385
+ AGID00535 1494 ab61013 Old PYGL NA
386
+ AGID00202 1245 H00005837-M10 Old PYGM NA
387
+ AGID00275 1607 3291 Set163 Pyk2_pY402 0.404824419705924
388
+ AGID00145 1083 3539 Old RAB11 0.20557
389
+ AGID00169 1150 4314 Old RAB25 -0.21194
390
+ AGID00342 1979 24555 Set163 Rad23A -0.0597850812281836
391
+ AGID00261 987 05-525 Old RAD50 0.28065
392
+ AGID00360 579 NA71 Old RAD51 -0.13104
393
+ AGID00158 1128 2280 Old RAPTOR 0.32099
394
+ AGID00059 552 9309 Old RB 0.070501
395
+ AGID00060 557 9308 Old RB_pS807S811 0.18799
396
+ AGID00164 1138 21390002 Old RBM15 -0.42434
397
+ AGID00547 735 3221 Old RET_pY905 NA
398
+ AGID00097 847 MAB3426 Set163 Rheb -0.0300300901091315
399
+ AGID00159 1129 2114 Old RICTOR 0.12699
400
+ AGID00160 1130 3806 Old RICTOR_pT1135 0.30689
401
+ AGID00282 1624 4926 Set163 RIP 0.345674960499275
402
+ AGID00283 1625 13526 Set163 RIP3 -0.0437307485988238
403
+ AGID00416 1368 2208 Set163 RPA32 -0.400495025776411
404
+ AGID00246 1375 A300-245A Set163 RPA32_pS4_S8 -0.055351098845944
405
+ AGID00341 1978 3388 Set163 RRM1 -0.0942552163918741
406
+ AGID00344 1981 PA5-27856 Set163 RRM2 -0.202506656785746
407
+ AGID00554 2425 8408 Set163 RSK1 0.45835215072509
408
+ AGID00353 2031 13018 Set163 S100A4 -0.260955005813772
409
+ AGID00330 1874 2317 Old S6 -0.63364
410
+ AGID00062 600 2211 Old S6_pS235S236 0.12797
411
+ AGID00063 601 2215 Old S6_pS240S244 -0.029168
412
+ AGID00157 1127 sc-58420 Old SCD1 -0.63414
413
+ AGID00230 1339 11998 Set163 SDHA -0.166510002911218
414
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415
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416
+ AGID02179 2495 3534 Set163 SFRP1 -0.132116031844638
417
+ AGID00431 2411 12103 Set163 SGK1 0.0369692615904362
418
+ AGID00430 2409 8156 Set163 SGK3 0.450274957969288
419
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420
+ AGID00376 2241 3397 Set163 SHP2 0.333389746100203
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
+ AGID00388 637 9131 Old STAT3_pY705 -0.15666
438
+ AGID00069 638 1289-1/ab32043 Old STAT5ALPHA 0.3397
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
+ AGID00208 1256 MS304/ab14745 Set163 UQCRC2 0.000369975254645764
465
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466
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467
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468
+ AGID00074 688 2479 Old VEGFR2 1.4576
469
+ AGID00421 2394 68547 Set163 VHL 0.014649999098909
470
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471
+ AGID00317 1802 4936 Set163 Wee1 1.21852379348236
472
+ AGID00354 2058 4910 Set163 Wee1_pS642 0.490329752061268
473
+ AGID00285 1627 12124 Set163 WIPI1 0.373789979205584
474
+ AGID00286 1628 8567 Set163 WIPI2 -0.158854994584788
475
+ AGID02214 2576 ab195380 Set163 WTAP -0.201400708257671
476
+ AGID00133 1044 sc-32136 Old XBP1 -0.073274
477
+ AGID00076 699 2042 Set163 XIAP 0.16725946821755
478
+ AGID00241 1359 sc-56813 Set163 XPA 0.329745004167547
479
+ AGID00349 1354 ab3299 Set163 XPF 0.0584173749145965
480
+ AGID02137 2440 PA5-29359 Old XRCC1 0.20866
481
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482
+ AGID00089 782 4911 Old YAP_pS127 -0.24955
483
+ AGID00504 700 17250002 Old YB1 -0.13095
484
+ AGID00095 835 2900 Old YB1_pS102 0.027166
485
+ AGID02217 2579 ab220163 Set163 YTHDF2 -0.196405025776411
486
+ AGID02210 2572 ab220161 Set163 YTHDF3 -0.343750045955658
487
+ AGID00326 1828 2705 Set163 ZAP-70 -0.050767160668643
488
+ AGID00432 2244 sc-25388 Set163 ZEB1 0.116008274202842
data/gdc_data_organized/09765b0a-94f6-47d2-af56-93368084ac3a/TCGA-A7-A0CD-01Z-00-DX2.609CED8D-5947-4753-A75B-73A8343B47EC.svs ADDED
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177
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
178
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179
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-11D-A068-02</bio:bcr_aliquot_barcode>
180
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">95039446-24f9-4724-b9e8-6c2828dad7d5</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="">1.82</bio:quantity>
183
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
184
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">H</bio:plate_row>
185
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
186
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099036550</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
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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="">0.16</bio:concentration>
210
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.85</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-A7-A0CD-01A-11R</bio:bcr_analyte_barcode>
214
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a4c2652e-990e-47a4-8a5c-0076aee4946f</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="">A00Z</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="">16</bio:day_of_shipment>
222
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</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-A7-A0CD-01A-11R-A00Z-07</bio:bcr_aliquot_barcode>
225
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">1edf44b5-61ba-47cd-81ed-b586ae81cb32</bio:bcr_aliquot_uuid>
226
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
227
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.27</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="">G</bio:plate_row>
230
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
231
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050360</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="">A010</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="">16</bio:day_of_shipment>
240
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</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-A7-A0CD-01A-11R-A010-13</bio:bcr_aliquot_barcode>
243
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">307715ed-5283-4c89-99bd-0e92343e1851</bio:bcr_aliquot_uuid>
244
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.16</bio:concentration>
245
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.20</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="">G</bio:plate_row>
248
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
249
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99051221</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="">2.20</bio:ratio_28s_18s>
263
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.60</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-A7-A0CD-01A-11W</bio:bcr_analyte_barcode>
277
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">649A4A01-939C-45F4-85B1-A29BD64FD1DF</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="">A019</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="">29</bio:day_of_shipment>
285
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</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-A7-A0CD-01A-11W-A019-09</bio:bcr_aliquot_barcode>
288
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">d29ba065-28ca-4dfb-9588-06be857f67b2</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="">C</bio:plate_row>
293
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
294
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034661</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:aliquot>
299
+ <admin:additional_studies/>
300
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A020</bio:plate_id>
301
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
302
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
303
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
304
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
305
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-11W-A020-08</bio:bcr_aliquot_barcode>
306
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8c9cc0c4-50a6-41ad-966b-3abe035d523d</bio:bcr_aliquot_uuid>
307
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
308
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
309
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
310
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
311
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
312
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035525</bio:biospecimen_barcode_bottom>
313
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
314
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
315
+ </bio:aliquot>
316
+ </bio:aliquots>
317
+ <bio:protocols>
318
+ <bio:protocol>
319
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
320
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
321
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
322
+ </bio:protocol>
323
+ </bio:protocols>
324
+ <bio:dna>
325
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
326
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
327
+ </bio:dna>
328
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
329
+ </bio:analyte>
330
+ <bio:analyte>
331
+ <admin:additional_studies/>
332
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
333
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
334
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
335
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
336
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
337
+ <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>
338
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
339
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-11X</bio:bcr_analyte_barcode>
340
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">467CCEF3-DCA6-4029-BB45-C450DA3BDD30</bio:bcr_analyte_uuid>
341
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
342
+ <bio:aliquots>
343
+ <bio:aliquot>
344
+ <admin:additional_studies/>
345
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A023</bio:plate_id>
346
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
347
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
348
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
349
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
350
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-11X-A023-09</bio:bcr_aliquot_barcode>
351
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">40d11481-c295-41e9-a460-fdc562988170</bio:bcr_aliquot_uuid>
352
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
353
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
354
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
355
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
356
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
357
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059909</bio:biospecimen_barcode_bottom>
358
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
359
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
360
+ </bio:aliquot>
361
+ <bio:aliquot>
362
+ <admin:additional_studies/>
363
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A024</bio:plate_id>
364
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
365
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
366
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
367
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
368
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-11X-A024-08</bio:bcr_aliquot_barcode>
369
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">cf9bc6b0-a8c6-48d9-ae30-4f23581e7816</bio:bcr_aliquot_uuid>
370
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
371
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
372
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
373
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
374
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
375
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035361</bio:biospecimen_barcode_bottom>
376
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
377
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
378
+ </bio:aliquot>
379
+ </bio:aliquots>
380
+ <bio:protocols>
381
+ <bio:protocol>
382
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
383
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
384
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
385
+ </bio:protocol>
386
+ </bio:protocols>
387
+ <bio:dna>
388
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
389
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
390
+ </bio:dna>
391
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
392
+ </bio:analyte>
393
+ </bio:analytes>
394
+ <bio:slides>
395
+ <bio:slide>
396
+ <admin:additional_studies/>
397
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
398
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
399
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">50</bio:percent_tumor_cells>
400
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
401
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:percent_normal_cells>
402
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_necrosis>
403
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">33</bio:percent_stromal_cells>
404
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
405
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">9</bio:percent_lymphocyte_infiltration>
406
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
407
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
408
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
409
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
410
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-01-BSA</shared:bcr_slide_barcode>
411
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a48267de-7bf0-409f-a8b5-9712f2e06a90</shared:bcr_slide_uuid>
412
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-01-BSA.a48267de-7bf0-409f-a8b5-9712f2e06a90.svs</shared:image_file_name>
413
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
414
+ </bio:slide>
415
+ <bio:slide>
416
+ <admin:additional_studies/>
417
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
418
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
419
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">65</bio:percent_tumor_cells>
420
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">85</bio:percent_tumor_nuclei>
421
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">7</bio:percent_normal_cells>
422
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_necrosis>
423
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">26</bio:percent_stromal_cells>
424
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
425
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">7</bio:percent_lymphocyte_infiltration>
426
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
427
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
428
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
429
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
430
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-01-TSA</shared:bcr_slide_barcode>
431
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8966c3d7-c0d2-47a4-badf-df9412a1e5f0</shared:bcr_slide_uuid>
432
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A7-A0CD-01A-01-TSA.8966c3d7-c0d2-47a4-badf-df9412a1e5f0.svs</shared:image_file_name>
433
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
434
+ </bio:slide>
435
+ </bio:slides>
436
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
437
+ </bio:portion>
438
+ </bio:portions>
439
+ <bio:tumor_pathology/>
440
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
441
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
442
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
443
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">DEB67EB8-155C-4ACF-B3D4-595E4CBE2E5C</bio:pathology_report_uuid>
444
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A7-A0CD.DEB67EB8-155C-4ACF-B3D4-595E4CBE2E5C.pdf</bio:pathology_report_file_name>
445
+ <bio:diagnostic_slides>
446
+ <admin:additional_studies/>
447
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">F045B9C8-049C-41BF-8432-EF89F236D34D</bio:ffpe_slide_uuid>
448
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">609CED8D-5947-4753-A75B-73A8343B47EC</bio:ffpe_slide_uuid>
449
+ </bio:diagnostic_slides>
450
+ </bio:sample>
451
+ <bio:sample>
452
+ <admin:additional_studies/>
453
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
454
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
455
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
456
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
457
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
458
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
459
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
460
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
461
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
462
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
463
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
464
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
465
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
466
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
467
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
468
+ <bio:days_to_collection precision="day" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">157</bio:days_to_collection>
469
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
470
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
471
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A</bio:bcr_sample_barcode>
472
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">12519edf-a14b-472e-98cc-d1825f3c2d39</bio:bcr_sample_uuid>
473
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
474
+ <bio:portions>
475
+ <bio:portion>
476
+ <admin:additional_studies/>
477
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
478
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
479
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">15</bio:day_of_creation>
480
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
481
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
482
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
483
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01</bio:bcr_portion_barcode>
484
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">affe2bbb-0e12-410b-8167-812627b2353f</bio:bcr_portion_uuid>
485
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
486
+ <bio:analytes>
487
+ <bio:analyte>
488
+ <admin:additional_studies/>
489
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
490
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
491
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
492
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
493
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.97</bio:a260_a280_ratio>
494
+ <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>
495
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
496
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01D</bio:bcr_analyte_barcode>
497
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">07a31ec0-5471-4c09-9c3e-81650cb823d2</bio:bcr_analyte_uuid>
498
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
499
+ <bio:aliquots>
500
+ <bio:aliquot>
501
+ <admin:additional_studies/>
502
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A012</bio:plate_id>
503
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
504
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
505
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
506
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
507
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01D-A012-01</bio:bcr_aliquot_barcode>
508
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e048e78c-0b16-40f0-87c0-aa1e7cd3b5d5</bio:bcr_aliquot_uuid>
509
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
510
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.00</bio:quantity>
511
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
512
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">G</bio:plate_row>
513
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
514
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050165</bio:biospecimen_barcode_bottom>
515
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
516
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
517
+ </bio:aliquot>
518
+ <bio:aliquot>
519
+ <admin:additional_studies/>
520
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A017</bio:plate_id>
521
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
522
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
523
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
524
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
525
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01D-A017-09</bio:bcr_aliquot_barcode>
526
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">65bc4027-cf1d-4dcd-ac69-742bbf932204</bio:bcr_aliquot_uuid>
527
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
528
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
529
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
530
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
531
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
532
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059621</bio:biospecimen_barcode_bottom>
533
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
534
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
535
+ </bio:aliquot>
536
+ <bio:aliquot>
537
+ <admin:additional_studies/>
538
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A018</bio:plate_id>
539
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
540
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
541
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
542
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
543
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01D-A018-08</bio:bcr_aliquot_barcode>
544
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">6f16c417-bb62-4a76-9db8-b58aa726ff9c</bio:bcr_aliquot_uuid>
545
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
546
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
547
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
548
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
549
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
550
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099051173</bio:biospecimen_barcode_bottom>
551
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
552
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
553
+ </bio:aliquot>
554
+ <bio:aliquot>
555
+ <admin:additional_studies/>
556
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A069</bio:plate_id>
557
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
558
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">31</bio:day_of_shipment>
559
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
560
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
561
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01D-A069-02</bio:bcr_aliquot_barcode>
562
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">f3f5fa68-69ee-4d3c-ad70-71b391eb5f16</bio:bcr_aliquot_uuid>
563
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
564
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.95</bio:quantity>
565
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
566
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">H</bio:plate_row>
567
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">10</bio:plate_column>
568
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099018138</bio:biospecimen_barcode_bottom>
569
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
570
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
571
+ </bio:aliquot>
572
+ </bio:aliquots>
573
+ <bio:protocols>
574
+ <bio:protocol>
575
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
576
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
577
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
578
+ </bio:protocol>
579
+ </bio:protocols>
580
+ <bio:dna>
581
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
582
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
583
+ </bio:dna>
584
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
585
+ </bio:analyte>
586
+ <bio:analyte>
587
+ <admin:additional_studies/>
588
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
589
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
590
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
591
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
592
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
593
+ <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>
594
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
595
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A7-A0CD-10A-01W</bio:bcr_analyte_barcode>
596
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">EBCF0A32-89EA-4BE7-B7F6-F269B8C1B26F</bio:bcr_analyte_uuid>
597
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598
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599
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600
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601
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603
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605
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606
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607
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608
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610
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611
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612
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616
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617
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618
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619
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620
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621
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623
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624
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625
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626
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628
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629
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630
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631
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636
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+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
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642
+ </bio:protocols>
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644
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
645
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
646
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647
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648
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650
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651
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652
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653
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
654
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
655
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
656
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657
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658
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659
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660
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661
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662
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668
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669
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670
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">ebce3e9f-acb9-4714-9488-00463c489bd2</bio:bcr_aliquot_uuid>
671
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672
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673
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674
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678
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684
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687
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688
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7fdb9995-a3b6-4d63-9cdf-083c6c75d77b</bio:bcr_aliquot_uuid>
689
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
690
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
691
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692
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693
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694
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695
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696
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
697
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698
+ </bio:aliquots>
699
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700
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701
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702
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+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
704
+ </bio:protocol>
705
+ </bio:protocols>
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+ <bio:dna>
707
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
708
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
709
+ </bio:dna>
710
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711
+ </bio:analyte>
712
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713
+ <bio:slides/>
714
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
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716
+ </bio:portions>
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+ <bio:tumor_pathology/>
718
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
719
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
720
+ <shared:days_to_sample_procurement cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
721
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Not Available" owner=""/>
722
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
723
+ <bio:diagnostic_slides>
724
+ <admin:additional_studies/>
725
+ </bio:diagnostic_slides>
726
+ </bio:sample>
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+ </bio:samples>
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+ </bio:patient>
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+ </bio:tcga_bcr>
data/gdc_data_organized/09765b0a-94f6-47d2-af56-93368084ac3a/nationwidechildrens.org_omf.TCGA-A7-A0CD.xml ADDED
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1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <omf:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/omf/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/omf/2.7/TCGA_BCR.Other_Malignancies.xsd" schemaVersion="2.7" xmlns:omf="http://tcga.nci/bcr/xml/clinical/omf/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:omf_v4.0="http://tcga.nci/bcr/xml/clinical/omf/2.7/4.0" xmlns:omf_shared="http://tcga.nci/bcr/xml/clinical/shared/omf/2.7" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">A1162BFB-D0AA-4710-AB1D-046AEDAE7475</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">47.98.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
12
+ <admin:patient_withdrawal>
13
+ <admin:withdrawn>false</admin:withdrawn>
14
+ </admin:patient_withdrawal>
15
+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
16
+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
17
+ </admin:admin>
18
+ <omf:patient>
19
+ <admin:additional_studies/>
20
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A7</shared:tissue_source_site>
21
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A0CD</shared:patient_id>
22
+ <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-A7-A0CD</shared:bcr_patient_barcode>
23
+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">09765b0a-94f6-47d2-af56-93368084ac3a</shared:bcr_patient_uuid>
24
+ <omf:omfs>
25
+ <omf_v4.0:omf>
26
+ <omf_shared:bcr_omf_barcode xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A7-A0CD-O8722</omf_shared:bcr_omf_barcode>
27
+ <omf_shared:bcr_omf_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">5CBFDE48-2053-4495-8E13-1616BB984B34</omf_shared:bcr_omf_uuid>
28
+ <omf_shared:malignancy_type preferred_name="malignancy_type" display_order="4" cde="3182890" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="693691">Prior Malignancy</omf_shared:malignancy_type>
29
+ <omf_shared:other_malignancy_anatomic_site preferred_name="" display_order="9999" cde="4122351" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="693683">Uterus</omf_shared:other_malignancy_anatomic_site>
30
+ <omf_shared:other_malignancy_anatomic_site_text preferred_name="" display_order="9999" cde="4122371" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="693684" xsi:nil="true"/>
31
+ <omf_shared:other_malignancy_laterality preferred_name="" display_order="9999" cde="4122391" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693685"/>
32
+ <omf_shared:other_malignancy_histological_type preferred_name="" display_order="9999" cde="4122411" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693686"/>
33
+ <omf_shared:other_malignancy_histological_type_text preferred_name="" display_order="9999" cde="4122431" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="693687" xsi:nil="true"/>
34
+ <omf_shared:days_to_other_malignancy_dx precision="day" xsd_ver="2.6" tier="2" cde="3462301" owner="TSS" procurement_status="Not Available" preferred_name="other_malignancy_dx_days_to" display_order="13" cde_ver="1.000"/>
35
+ <omf_shared:surgery>
36
+ <shared:surgery_indicator preferred_name="surgery_indicator" display_order="14" cde="3186538" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
37
+ <omf_shared:surgery_type preferred_name="other_malignancy_surgery_type" display_order="15" cde="3462300" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
38
+ <omf_shared:days_to_surgical_resection precision="day" xsd_ver="2.6" tier="2" cde="3462302" owner="TSS" procurement_status="Not Available" preferred_name="other_malignancy_surgery_days_to" display_order="19" cde_ver="1.000"/>
39
+ </omf_shared:surgery>
40
+ <omf_shared:drug_tx>
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+ <shared:drug_tx_indicator preferred_name="pharmaceutical_therapy_indicator" display_order="20" cde="3178327" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="693692">NO</shared:drug_tx_indicator>
42
+ <omf_shared:drug_tx_extent preferred_name="pharmaceutical_therapy_extent" display_order="21" cde="3178365" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693693"/>
43
+ <rx:days_to_drug_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Not Available" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000"/>
44
+ </omf_shared:drug_tx>
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+ <omf_shared:radiation_tx>
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+ <omf_shared:radiation_tx_indicator preferred_name="radiation_therapy_indicator" display_order="27" cde="3178328" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="693698">NO</omf_shared:radiation_tx_indicator>
47
+ <omf_shared:radiation_tx_extent preferred_name="radiation_therapy_extent" display_order="28" cde="3178353" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693699"/>
48
+ <omf_shared:rad_tx_to_site_of_primary_tumor preferred_name="history_rt_tx_to_site_of_tcga_tumor" display_order="29" cde="2865132" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693700"/>
49
+ <rad:days_to_radiation_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3008313" owner="TSS" procurement_status="Not Available" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000"/>
50
+ </omf_shared:radiation_tx>
51
+ <omf_shared:omf_staging>
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+ <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"/>
53
+ <shared_stage:clinical_stage preferred_name="figo_clinical_tumor_stage" display_order="9999" cde="3225684" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
54
+ <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="693710"/>
55
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181
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182
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183
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184
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185
+ </bio:aliquots>
186
+ <bio:protocols>
187
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188
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
189
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190
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
191
+ </bio:protocol>
192
+ </bio:protocols>
193
+ <bio:dna>
194
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
195
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
196
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197
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
198
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199
+ <bio:analyte>
200
+ <admin:additional_studies/>
201
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
202
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203
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">RNA</bio:analyte_type>
204
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205
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.80</bio:a260_a280_ratio>
206
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
207
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
208
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11R</bio:bcr_analyte_barcode>
209
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a91ff01f-b1be-490c-98f7-be163c518361</bio:bcr_analyte_uuid>
210
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
211
+ <bio:aliquots>
212
+ <bio:aliquot>
213
+ <admin:additional_studies/>
214
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A00Z</bio:plate_id>
215
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216
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
217
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
218
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
219
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11R-A00Z-07</bio:bcr_aliquot_barcode>
220
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">523e45c2-4f98-4010-b48e-bdbda62865cf</bio:bcr_aliquot_uuid>
221
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
222
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">4.01</bio:quantity>
223
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">26.70</bio:volume>
224
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
225
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
226
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050363</bio:biospecimen_barcode_bottom>
227
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
228
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
229
+ </bio:aliquot>
230
+ <bio:aliquot>
231
+ <admin:additional_studies/>
232
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A010</bio:plate_id>
233
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">13</bio:center_id>
234
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
235
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
236
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
237
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11R-A010-13</bio:bcr_aliquot_barcode>
238
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">47802eac-eca4-4914-8eb6-3ed69ebb6650</bio:bcr_aliquot_uuid>
239
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
240
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">3.00</bio:quantity>
241
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">20.00</bio:volume>
242
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
243
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
244
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99051274</bio:biospecimen_barcode_bottom>
245
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
246
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
247
+ </bio:aliquot>
248
+ </bio:aliquots>
249
+ <bio:protocols>
250
+ <bio:protocol>
251
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">mirVana (Allprep DNA) RNA</bio:experimental_protocol_type>
252
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
253
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
254
+ </bio:protocol>
255
+ </bio:protocols>
256
+ <bio:rna>
257
+ <bio:ratio_28s_18s cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.70</bio:ratio_28s_18s>
258
+ <bio:rinvalue cde="" xsd_ver="1.8" procurement_status="Completed" owner="">8.90</bio:rinvalue>
259
+ </bio:rna>
260
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
261
+ </bio:analyte>
262
+ <bio:analyte>
263
+ <admin:additional_studies/>
264
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
265
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
266
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
267
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
268
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
269
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
270
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
271
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11W</bio:bcr_analyte_barcode>
272
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">22183E4A-84A1-4DE0-9A78-F01EDE26051C</bio:bcr_analyte_uuid>
273
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
274
+ <bio:aliquots>
275
+ <bio:aliquot>
276
+ <admin:additional_studies/>
277
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A019</bio:plate_id>
278
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
279
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
280
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
281
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
282
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11W-A019-09</bio:bcr_aliquot_barcode>
283
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">4975eeda-984e-4a7a-8193-43d8b6e0271c</bio:bcr_aliquot_uuid>
284
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
285
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
286
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
287
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
288
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
289
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034666</bio:biospecimen_barcode_bottom>
290
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
291
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
292
+ </bio:aliquot>
293
+ <bio:aliquot>
294
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295
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A020</bio:plate_id>
296
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
297
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
298
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
299
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
300
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11W-A020-08</bio:bcr_aliquot_barcode>
301
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">98504422-a1c9-4c72-a1c2-1a04217aae6b</bio:bcr_aliquot_uuid>
302
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
303
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
304
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
305
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
306
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
307
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099035530</bio:biospecimen_barcode_bottom>
308
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
309
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
310
+ </bio:aliquot>
311
+ </bio:aliquots>
312
+ <bio:protocols>
313
+ <bio:protocol>
314
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
315
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
316
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
317
+ </bio:protocol>
318
+ </bio:protocols>
319
+ <bio:dna>
320
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
321
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
322
+ </bio:dna>
323
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
324
+ </bio:analyte>
325
+ <bio:analyte>
326
+ <admin:additional_studies/>
327
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1</bio:subportion_sequence>
328
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">X</bio:analyte_type_id>
329
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G X (Qiagen) DNA</bio:analyte_type>
330
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
331
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
332
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
333
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
334
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11X</bio:bcr_analyte_barcode>
335
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">9074B4CA-E8DB-46A9-BAA0-35C43A215330</bio:bcr_analyte_uuid>
336
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
337
+ <bio:aliquots>
338
+ <bio:aliquot>
339
+ <admin:additional_studies/>
340
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A023</bio:plate_id>
341
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
342
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
343
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
344
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
345
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11X-A023-09</bio:bcr_aliquot_barcode>
346
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0f993ea4-65c5-479c-8af0-6107c4c1f538</bio:bcr_aliquot_uuid>
347
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
348
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
349
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
350
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
351
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
352
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059795</bio:biospecimen_barcode_bottom>
353
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
354
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
355
+ </bio:aliquot>
356
+ <bio:aliquot>
357
+ <admin:additional_studies/>
358
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A024</bio:plate_id>
359
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
360
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
361
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
362
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
363
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-11X-A024-08</bio:bcr_aliquot_barcode>
364
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">333249c1-9fcf-48b9-a82e-3311920b3dce</bio:bcr_aliquot_uuid>
365
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.50</bio:concentration>
366
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">40.00</bio:quantity>
367
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">80.00</bio:volume>
368
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
369
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
370
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099034378</bio:biospecimen_barcode_bottom>
371
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
372
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
373
+ </bio:aliquot>
374
+ </bio:aliquots>
375
+ <bio:protocols>
376
+ <bio:protocol>
377
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
378
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
379
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
380
+ </bio:protocol>
381
+ </bio:protocols>
382
+ <bio:dna>
383
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
384
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
385
+ </bio:dna>
386
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
387
+ </bio:analyte>
388
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389
+ <bio:slides>
390
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391
+ <admin:additional_studies/>
392
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">BOTTOM</bio:section_location>
393
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
394
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
395
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
396
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_normal_cells>
397
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_necrosis>
398
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">18</bio:percent_stromal_cells>
399
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
400
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">3</bio:percent_lymphocyte_infiltration>
401
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
402
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
403
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
404
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
405
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-01-BS1</shared:bcr_slide_barcode>
406
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">efa980a8-9019-4413-94a1-72f68fe860e9</shared:bcr_slide_uuid>
407
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-01-BS1.efa980a8-9019-4413-94a1-72f68fe860e9.svs</shared:image_file_name>
408
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
409
+ </bio:slide>
410
+ <bio:slide>
411
+ <admin:additional_studies/>
412
+ <bio:section_location cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TOP</bio:section_location>
413
+ <bio:number_proliferating_cells cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
414
+ <bio:percent_tumor_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_cells>
415
+ <bio:percent_tumor_nuclei cde="2841225" xsd_ver="1.8" procurement_status="Completed" owner="">80</bio:percent_tumor_nuclei>
416
+ <bio:percent_normal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1</bio:percent_normal_cells>
417
+ <bio:percent_necrosis cde="2841237" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_necrosis>
418
+ <bio:percent_stromal_cells cde="" xsd_ver="1.8" procurement_status="Completed" owner="">19</bio:percent_stromal_cells>
419
+ <bio:percent_inflam_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
420
+ <bio:percent_lymphocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2</bio:percent_lymphocyte_infiltration>
421
+ <bio:percent_monocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_monocyte_infiltration>
422
+ <bio:percent_granulocyte_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
423
+ <bio:percent_neutrophil_infiltration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0</bio:percent_neutrophil_infiltration>
424
+ <bio:percent_eosinophil_infiltration cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
425
+ <shared:bcr_slide_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-01-TS1</shared:bcr_slide_barcode>
426
+ <shared:bcr_slide_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">e2b24767-1df7-431b-bba2-45d1b4e767d8</shared:bcr_slide_uuid>
427
+ <shared:image_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A08F-01A-01-TS1.e2b24767-1df7-431b-bba2-45d1b4e767d8.svs</shared:image_file_name>
428
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
429
+ </bio:slide>
430
+ </bio:slides>
431
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
432
+ </bio:portion>
433
+ </bio:portions>
434
+ <bio:tumor_pathology/>
435
+ <bio:method_of_sample_procurement cde="3103514" xsd_ver="2.3" procurement_status="Not Available" owner=""/>
436
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
437
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
438
+ <bio:pathology_report_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">683AAF99-3B91-4501-B701-C3A4E8439647</bio:pathology_report_uuid>
439
+ <bio:pathology_report_file_name cde="" xsd_ver="2.6" procurement_status="Completed" owner="">TCGA-A8-A08F.683AAF99-3B91-4501-B701-C3A4E8439647.pdf</bio:pathology_report_file_name>
440
+ <bio:diagnostic_slides>
441
+ <admin:additional_studies/>
442
+ <bio:ffpe_slide_uuid cde="" xsd_ver="2.4" procurement_status="Completed" owner="">9D2222F6-1425-46FD-BC94-728EF835FAC2</bio:ffpe_slide_uuid>
443
+ </bio:diagnostic_slides>
444
+ </bio:sample>
445
+ <bio:sample>
446
+ <admin:additional_studies/>
447
+ <bio:specimen_fraction_ordinal cde="" xsd_ver="2.7" procurement_status="Not Available" owner=""/>
448
+ <bio:sample_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">10</bio:sample_type_id>
449
+ <bio:vial_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A</bio:vial_number>
450
+ <bio:biospecimen_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
451
+ <bio:sample_type cde="" xsd_ver="2.4" procurement_status="Completed" owner="">Blood Derived Normal</bio:sample_type>
452
+ <bio:longest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
453
+ <bio:intermediate_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
454
+ <bio:shortest_dimension cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
455
+ <bio:initial_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
456
+ <bio:current_weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
457
+ <bio:freezing_method cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
458
+ <bio:oct_embedded cde="" xsd_ver="1.8" procurement_status="Completed" owner="">false</bio:oct_embedded>
459
+ <bio:preservation_method cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
460
+ <bio:tissue_type cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
461
+ <bio:composition cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
462
+ <bio:tumor_descriptor cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
463
+ <bio:days_to_collection precision="month" procurement_status="Completed" cde="" xsd_ver="2.6" owner="">637</bio:days_to_collection>
464
+ <bio:time_between_clamping_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
465
+ <bio:time_between_excision_and_freezing cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
466
+ <bio:bcr_sample_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A</bio:bcr_sample_barcode>
467
+ <bio:bcr_sample_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">25067aad-c602-4e7e-99d5-f4bc327c6fd9</bio:bcr_sample_uuid>
468
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
469
+ <bio:portions>
470
+ <bio:portion>
471
+ <admin:additional_studies/>
472
+ <bio:portion_number cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:portion_number>
473
+ <bio:portion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
474
+ <bio:day_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">12</bio:day_of_creation>
475
+ <bio:month_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">04</bio:month_of_creation>
476
+ <bio:year_of_creation cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_creation>
477
+ <bio:weight cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
478
+ <bio:bcr_portion_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01</bio:bcr_portion_barcode>
479
+ <bio:bcr_portion_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">36bf0b0f-53b4-416b-b8fb-0ae86e74bd4b</bio:bcr_portion_uuid>
480
+ <bio:is_ffpe cde="4170557" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_ffpe>
481
+ <bio:analytes>
482
+ <bio:analyte>
483
+ <admin:additional_studies/>
484
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
485
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">D</bio:analyte_type_id>
486
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">DNA</bio:analyte_type>
487
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
488
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Completed" owner="">1.90</bio:a260_a280_ratio>
489
+ <bio:gel_image_file cde="" xsd_ver="1.8" procurement_status="Completed" owner="">https://sharedoc.nchri.org/tcga-bcr/default.aspx</bio:gel_image_file>
490
+ <bio:well_number cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
491
+ <bio:bcr_analyte_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D</bio:bcr_analyte_barcode>
492
+ <bio:bcr_analyte_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">05b9eeec-9f05-4500-bdcc-8af7cc9278c0</bio:bcr_analyte_uuid>
493
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
494
+ <bio:aliquots>
495
+ <bio:aliquot>
496
+ <admin:additional_studies/>
497
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A012</bio:plate_id>
498
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">01</bio:center_id>
499
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">16</bio:day_of_shipment>
500
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
501
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
502
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D-A012-01</bio:bcr_aliquot_barcode>
503
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">8bf21eab-3541-42cd-bca0-fd2176e96f13</bio:bcr_aliquot_uuid>
504
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
505
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.00</bio:quantity>
506
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">6.67</bio:volume>
507
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
508
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
509
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">99050218</bio:biospecimen_barcode_bottom>
510
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
511
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
512
+ </bio:aliquot>
513
+ <bio:aliquot>
514
+ <admin:additional_studies/>
515
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A017</bio:plate_id>
516
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">09</bio:center_id>
517
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
518
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
519
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
520
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D-A017-09</bio:bcr_aliquot_barcode>
521
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5f895b5a-88c6-4691-b419-b634ecdae9ca</bio:bcr_aliquot_uuid>
522
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
523
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
524
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
525
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
526
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
527
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099059782</bio:biospecimen_barcode_bottom>
528
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
529
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
530
+ </bio:aliquot>
531
+ <bio:aliquot>
532
+ <admin:additional_studies/>
533
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A018</bio:plate_id>
534
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">08</bio:center_id>
535
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">29</bio:day_of_shipment>
536
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">06</bio:month_of_shipment>
537
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
538
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D-A018-08</bio:bcr_aliquot_barcode>
539
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">a72c8aad-49f2-4dc2-9a0a-ecdfd55415ba</bio:bcr_aliquot_uuid>
540
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.07</bio:concentration>
541
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">0.93</bio:quantity>
542
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.34</bio:volume>
543
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
544
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
545
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099051178</bio:biospecimen_barcode_bottom>
546
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
547
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
548
+ </bio:aliquot>
549
+ <bio:aliquot>
550
+ <admin:additional_studies/>
551
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A069</bio:plate_id>
552
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">02</bio:center_id>
553
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">31</bio:day_of_shipment>
554
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">08</bio:month_of_shipment>
555
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2010</bio:year_of_shipment>
556
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D-A069-02</bio:bcr_aliquot_barcode>
557
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2e038e9c-df9d-4020-90f3-ead18a7a9168</bio:bcr_aliquot_uuid>
558
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
559
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">1.95</bio:quantity>
560
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">13.00</bio:volume>
561
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">C</bio:plate_row>
562
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">5</bio:plate_column>
563
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">0099029256</bio:biospecimen_barcode_bottom>
564
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
565
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
566
+ </bio:aliquot>
567
+ <bio:aliquot>
568
+ <admin:additional_studies/>
569
+ <bio:plate_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">A88Z</bio:plate_id>
570
+ <bio:center_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">36</bio:center_id>
571
+ <bio:day_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">23</bio:day_of_shipment>
572
+ <bio:month_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">02</bio:month_of_shipment>
573
+ <bio:year_of_shipment cde="" xsd_ver="1.8" procurement_status="Completed" owner="">2022</bio:year_of_shipment>
574
+ <bio:bcr_aliquot_barcode cde="" xsd_ver="1.8" procurement_status="Completed" owner="">TCGA-A8-A08F-10A-01D-A88Z-36</bio:bcr_aliquot_barcode>
575
+ <bio:bcr_aliquot_uuid cde="" xsd_ver="2.3" procurement_status="Completed" owner="">7E1E263E-4676-42CB-87CB-7A05EB47ED48</bio:bcr_aliquot_uuid>
576
+ <bio:concentration cde="" xsd_ver="1.8" procurement_status="Completed" owner="">0.15</bio:concentration>
577
+ <bio:quantity units="ug" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">7.50</bio:quantity>
578
+ <bio:volume units="ul" cde="" xsd_ver="2.6" procurement_status="Completed" owner="">50.00</bio:volume>
579
+ <bio:plate_row cde="" xsd_ver="2.3" procurement_status="Completed" owner="">H</bio:plate_row>
580
+ <bio:plate_column cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2</bio:plate_column>
581
+ <bio:biospecimen_barcode_bottom cde="" xsd_ver="2.3" procurement_status="Completed" owner="">2112369310</bio:biospecimen_barcode_bottom>
582
+ <bio:source_center cde="" xsd_ver="2.4" procurement_status="Completed" owner="">23</bio:source_center>
583
+ <bio:is_derived_from_ffpe cde="4170571" xsd_ver="2.6" procurement_status="Completed" owner="">NO</bio:is_derived_from_ffpe>
584
+ </bio:aliquot>
585
+ </bio:aliquots>
586
+ <bio:protocols>
587
+ <bio:protocol>
588
+ <bio:experimental_protocol_type cde="" xsd_ver="1.8" procurement_status="Completed" owner="">aDNA Preparation Type</bio:experimental_protocol_type>
589
+ <bio:protocol_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
590
+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
591
+ </bio:protocol>
592
+ </bio:protocols>
593
+ <bio:dna>
594
+ <bio:normal_tumor_genotype_match cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:normal_tumor_genotype_match>
595
+ <bio:pcr_amplification_successful cde="" xsd_ver="1.8" procurement_status="Completed" owner="">YES</bio:pcr_amplification_successful>
596
+ </bio:dna>
597
+ <bio:spectrophotometer_method cde="" xsd_ver="2.3" procurement_status="Completed" owner="">UV Spec</bio:spectrophotometer_method>
598
+ </bio:analyte>
599
+ <bio:analyte>
600
+ <admin:additional_studies/>
601
+ <bio:subportion_sequence cde="" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
602
+ <bio:analyte_type_id cde="" xsd_ver="2.4" procurement_status="Completed" owner="">W</bio:analyte_type_id>
603
+ <bio:analyte_type cde="" xsd_ver="1.10" procurement_status="Completed" owner="">Repli-G (Qiagen) DNA</bio:analyte_type>
604
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623
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649
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+ </bio:protocols>
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657
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658
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664
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666
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667
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668
+ <bio:a260_a280_ratio cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
669
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670
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671
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672
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673
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675
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676
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677
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683
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684
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692
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695
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701
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702
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703
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704
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705
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706
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710
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711
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712
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713
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714
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+ <bio:protocol_file_name cde="" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
717
+ </bio:protocol>
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720
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721
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722
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723
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724
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725
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726
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727
+ <bio:LCE cde="3251491" xsd_ver="1.8" procurement_status="Not Available" owner=""/>
728
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729
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730
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731
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732
+ <bio_shared:other_method_of_sample_procurement cde="2006730" xsd_ver="2.5" procurement_status="Not Available" owner=""/>
733
+ <shared:days_to_sample_procurement cde="3288495" xsd_ver="2.6" procurement_status="Not Available" owner=""/>
734
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735
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736
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737
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738
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data/gdc_data_organized/0a017f15-1c6b-45e7-8d55-e0a71df1b2e8/nationwidechildrens.org_clinical.TCGA-A8-A08F.xml ADDED
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1
+ <?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_v4.0="http://tcga.nci/bcr/xml/clinical/brca/followup/2.7/4.0" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7">
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+ <admin:file_uuid xsd_ver="2.6">1783EE8C-16AC-4E74-9F7C-E3B0C9FF2F0C</admin:file_uuid>
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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:withdrawn>false</admin:withdrawn>
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+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
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+ </admin:admin>
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+ <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="157413">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="157414" 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="157204">Yes</shared:other_dx>
23
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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="157200">Alive</clin_shared:vital_status>
25
+ <clin_shared:days_to_birth precision="month" xsd_ver="1.12" tier="1" cde="3008233" owner="TSS" procurement_status="Completed" preferred_name="birth_days_to" display_order="9" cde_ver="1.000">-21641</clin_shared:days_to_birth>
26
+ <clin_shared:days_to_last_known_alive precision="day" xsd_ver="2.1" tier="2" cde="" owner="TSS" procurement_status="Not Available" preferred_name="" display_order="9999" cde_ver=""/>
27
+ <clin_shared:days_to_death precision="day" xsd_ver="1.12" tier="1" cde="3165475" owner="TSS" procurement_status="Not Applicable" preferred_name="death_days_to" display_order="25" cde_ver="1.000"/>
28
+ <clin_shared:days_to_last_followup precision="month" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">549</clin_shared:days_to_last_followup>
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+ <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="Not Available" restricted="false" source_system_identifier="157202"/>
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+ </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-A8-A08F</shared:bcr_patient_barcode>
33
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A8</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">A08F</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">0a017f15-1c6b-45e7-8d55-e0a71df1b2e8</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="157205">Yes</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>
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+ <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="month" xsd_ver="1.12" tier="1" cde="3131740" owner="TSS" procurement_status="Completed" preferred_name="initial_pathologic_dx_days_to" display_order="9999" cde_ver="1.000">0</clin_shared:days_to_initial_pathologic_diagnosis>
42
+ <clin_shared:age_at_initial_pathologic_diagnosis precision="month" xsd_ver="1.12" tier="1" cde="2006657" owner="TSS" procurement_status="Completed">59</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="157420">2008</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="157203"/>
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="157201">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="Not Available" restricted="false" source_system_identifier="157432"/>
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="157445"/>
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="157450"/>
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="157415">Right Upper Inner Quadrant</clin_shared:anatomic_neoplasm_subdivision>
52
+ </brca:anatomic_neoplasm_subdivisions>
53
+ <brca_shared:her2_neu_chromosone_17_signal_ratio_value preferred_name="her2_cent17_ratio" display_order="79" cde="2497552" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157460"/>
54
+ <brca:axillary_lymph_node_stage_method_type preferred_name="axillary_staging_method" display_order="44" cde="2516112" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157429"/>
55
+ <brca:axillary_lymph_node_stage_other_method_descriptive_text preferred_name="axillary_staging_method_other" display_order="45" cde="3124496" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157430"/>
56
+ <brca:breast_carcinoma_surgical_procedure_name preferred_name="surgical_procedure_first" display_order="38" cde="2739580" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157423">Other</brca:breast_carcinoma_surgical_procedure_name>
57
+ <brca:breast_neoplasm_other_surgical_procedure_descriptive_text preferred_name="surgery_for_positive_margins_other" display_order="42" cde="3124493" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="157427" xsi:nil="true"/>
58
+ <brca:breast_carcinoma_primary_surgical_procedure_name preferred_name="surgery_for_positive_margins" display_order="41" cde="1218" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157426"/>
59
+ <brca:surgical_procedure_purpose_other_text preferred_name="first_surgical_procedure_other" display_order="39" cde="3020338" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157424">Surgical Resection</brca:surgical_procedure_purpose_other_text>
60
+ <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157416">Infiltrating Ductal Carcinoma</shared:histological_type>
61
+ <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="157417" xsi:nil="true"/>
62
+ <clin_shared:menopause_status preferred_name="menopause_status" display_order="11" cde="2957270" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157199">Post (prior bilateral ovariectomy OR >12 mo since LMP with no prior hysterectomy)</clin_shared:menopause_status>
63
+ <brca_shared:breast_carcinoma_progesterone_receptor_status preferred_name="pr_status_by_ihc" display_order="64" cde="2957357" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157446">Positive</brca_shared:breast_carcinoma_progesterone_receptor_status>
64
+ <brca:cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator preferred_name="micromet_detection_by_ihc" display_order="46" cde="3086152" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157431"/>
65
+ <brca:breast_carcinoma_immunohistochemistry_er_pos_finding_scale preferred_name="er_positivity_scale_used" display_order="60" cde="3203081" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
66
+ <brca_shared:immunohistochemistry_positive_cell_score preferred_name="er_ihc_score" display_order="61" cde="2230166" cde_ver="3.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157443"/>
67
+ <brca_shared:her2_immunohistochemistry_level_result preferred_name="her2_ihc_score" display_order="72" cde="2178402" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157453">1+</brca_shared:her2_immunohistochemistry_level_result>
68
+ <brca:breast_cancer_surgery_margin_status preferred_name="margin_status_reexcision" display_order="43" cde="2241252" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157428"/>
69
+ <clin_shared:margin_status preferred_name="margin_status" display_order="40" cde="3114007" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157425">Negative</clin_shared:margin_status>
70
+ <clin_shared:initial_pathologic_diagnosis_method preferred_name="method_initial_path_dx" display_order="36" cde="2757941" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157421"/>
71
+ <clin_shared:init_pathology_dx_method_other preferred_name="method_initial_path_dx_other" display_order="37" cde="2757948" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="157422" xsi:nil="true"/>
72
+ <brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type preferred_name="her2_fish_status" display_order="75" cde="2854089" cde_ver="1.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157456">Negative</brca_shared:lab_procedure_her2_neu_in_situ_hybrid_outcome_type>
73
+ <brca_shared:breast_carcinoma_estrogen_receptor_status preferred_name="er_status_by_ihc" display_order="58" cde="2957359" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157441">Positive</brca_shared:breast_carcinoma_estrogen_receptor_status>
74
+ <brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="her2_status_by_ihc" display_order="70" cde="2957563" cde_ver="2.000" xsd_ver="2.2" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157451">Negative</brca_shared:lab_proc_her2_neu_immunohistochemistry_receptor_status>
75
+ <clin_shared:number_of_lymphnodes_positive_by_ihc preferred_name="lymph_nodes_examined_ihc_count" display_order="50" cde="3086383" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157434"/>
76
+ <clin_shared:number_of_lymphnodes_positive_by_he preferred_name="lymph_nodes_examined_he_count" display_order="49" cde="3086388" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157433"/>
77
+ <brca_shared:pos_finding_progesterone_receptor_other_measurement_scale_text preferred_name="pr_positivity_scale_other" display_order="68" cde="3086857" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157449"/>
78
+ <brca_shared:positive_finding_estrogen_receptor_other_measurement_scale_text preferred_name="er_positivity_scale_other" display_order="62" cde="3086851" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157444"/>
79
+ <brca_shared:her2_erbb_pos_finding_cell_percent_category preferred_name="her2_ihc_percent_positive" display_order="71" cde="3086980" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157452"/>
80
+ <brca_shared:pos_finding_her2_erbb2_other_measurement_scale_text preferred_name="her2_positivity_scale_other" display_order="73" cde="3087479" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157454"/>
81
+ <brca_shared:her2_erbb_method_calculation_method_text preferred_name="her2_positivity_method_text" display_order="74" cde="3087487" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157455"/>
82
+ <brca_shared:her2_neu_and_centromere_17_copy_number_analysis_input_total_number_count preferred_name="her2_and_cent17_cells_count" display_order="78" cde="3087902" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157459"/>
83
+ <brca_shared:her2_and_centromere_17_positive_finding_other_measurement_scale_text preferred_name="her2_and_cent17_scale_other" display_order="80" cde="3087923" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157461"/>
84
+ <brca_shared:her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="her2_fish_method" display_order="81" cde="3087929" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157462"/>
85
+ <clin_shared:tissue_prospective_collection_indicator preferred_name="prospective_collection" display_order="4" cde="3088492" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157079">NO</clin_shared:tissue_prospective_collection_indicator>
86
+ <clin_shared:tissue_retrospective_collection_indicator preferred_name="retrospective_collection" display_order="5" cde="3088528" cde_ver="1.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157080">YES</clin_shared:tissue_retrospective_collection_indicator>
87
+ <brca_shared:fluorescence_in_situ_hybridization_diagnostic_procedure_chromosome_17_signal_result_range preferred_name="cent17_copy_number" display_order="77" cde="3104295" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157458"/>
88
+ <brca:first_nonlymph_node_metastasis_anatomic_sites>
89
+ <clin_shared:metastatic_site_at_diagnosis preferred_name="metastasis_site" display_order="56" cde="3124499" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157439"/>
90
+ <clin_shared:metastatic_site_at_diagnosis_other preferred_name="metastasis_site_other" display_order="57" cde="3124503" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157440"/>
91
+ </brca:first_nonlymph_node_metastasis_anatomic_sites>
92
+ <brca_shared:er_level_cell_percentage_category preferred_name="er_status_ihc_Percent_Positive" display_order="59" cde="3128341" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157442"/>
93
+ <brca_shared:progesterone_receptor_level_cell_percent_category preferred_name="pr_status_ihc_percent_positive" display_order="65" cde="3128342" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157447"/>
94
+ <brca:distant_metastasis_present_ind2 preferred_name="metastatic_tumor_indicator" display_order="999" cde="2194698" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
95
+ <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_status preferred_name="nte_er_status" display_order="97" cde="3131865" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157463"/>
96
+ <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_level_cell_percent_category preferred_name="nte_er_status_ihc__positive" display_order="98" cde="3131869" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157464"/>
97
+ <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_er_pos_cell_score preferred_name="nte_er_ihc_intensity_score" display_order="100" cde="3131873" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157465"/>
98
+ <brca_shared:pos_finding_metastatic_breast_carcinoma_estrogen_receptor_other_measuremenet_scale_text preferred_name="nte_er_positivity_other_scale" display_order="101" cde="3131877" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157466"/>
99
+ <brca_shared:metastatic_breast_carcinoma_estrogen_receptor_detection_method_text preferred_name="nte_er_positivity_define_method" display_order="102" cde="3131881" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157467"/>
100
+ <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_status preferred_name="nte_pr_status_by_ihc" display_order="103" cde="3131884" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157468"/>
101
+ <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_immunohistochemistry_receptor_status preferred_name="nte_her2_status" display_order="109" cde="3131997" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157473"/>
102
+ <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_level_cell_percent_category preferred_name="nte_pr_status_ihc__positive" display_order="104" cde="3131891" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157469"/>
103
+ <brca_shared:metastatic_breast_carcinoma_immunohistochemistry_pr_pos_cell_score preferred_name="nte_pr_ihc_intensity_score" display_order="106" cde="3131988" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157470"/>
104
+ <brca_shared:metastatic_breast_carcinoma_pos_finding_progesterone_receptor_other_measure_scale_text preferred_name="nte_pr_positivity_other_scale" display_order="107" cde="3131992" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157471"/>
105
+ <brca_shared:metastatic_breast_carcinoma_progesterone_receptor_detection_method_text preferred_name="nte_pr_positivity_define_method" display_order="108" cde="3131993" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157472"/>
106
+ <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_cell_percent_category preferred_name="nte_her2_status_ihc__positive" display_order="110" cde="3132322" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157474"/>
107
+ <brca_shared:metastatic_breast_carcinoma_erbb2_immunohistochemistry_level_result preferred_name="nte_her2_positivity_ihc_score" display_order="111" cde="3132444" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157475"/>
108
+ <brca_shared:metastatic_breast_carcinoma_pos_finding_her2_erbb2_other_measure_scale_text preferred_name="nte_her2_positivity_other_scale" display_order="112" cde="3132448" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157476"/>
109
+ <brca_shared:metastatic_breast_carcinoma_her2_erbb_method_calculation_method_text preferred_name="nte_her2_positivity_method" display_order="113" cde="3132452" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157477"/>
110
+ <brca_shared:metastatic_breast_carcinoma_lab_proc_her2_neu_in_situ_hybridization_outcome_type preferred_name="nte_her2_fish_status" display_order="114" cde="3132455" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157478"/>
111
+ <brca_shared:metastatic_breast_carcinoma_fluorescence_in_situ_hybridization_diagnostic_proc_centromere_17_signal_result_range preferred_name="nte_cent_17_signal_number" display_order="116" cde="3132887" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157480"/>
112
+ <brca_shared:her2_neu_and_centromere_17_copy_number_metastatic_breast_carcinoma_analysis_input_total_number_count preferred_name="her2_cent17_counted_cells_count" display_order="117" cde="3132899" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157481"/>
113
+ <brca_shared:metastatic_breast_carcinoma_her2_neu_chromosone_17_signal_ratio_value preferred_name="nte_cent_17_her2_ratio" display_order="118" cde="3132903" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157482"/>
114
+ <brca_shared:metastatic_breast_carcinoma_pos_finding_other_scale_measurement_text preferred_name="nte_cent17_her2_other_scale" display_order="119" cde="3132907" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157483"/>
115
+ <brca_shared:metastatic_breast_carcinoma_her2_erbb_pos_finding_fluorescence_in_situ_hybridization_calculation_method_text preferred_name="nte_her2_fish_define_method" display_order="120" cde="3132910" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157484"/>
116
+ <brca_shared:her2_neu_metastatic_breast_carcinoma_copy_analysis_input_total_number preferred_name="nte_her2_signal_number" display_order="115" cde="3133734" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157479"/>
117
+ <brca_shared:her2_neu_breast_carcinoma_copy_analysis_input_total_number preferred_name="her2_copy_number" display_order="76" cde="3133738" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157457"/>
118
+ <brca:breast_carcinoma_immunohistochemistry_progesterone_receptor_pos_finding_scale preferred_name="pr_positivity_scale_used" display_order="66" cde="3203083" cde_ver="1.000" xsd_ver="2.4.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
119
+ <brca_shared:breast_carcinoma_immunohistochemistry_pos_cell_score preferred_name="pr_positivity_ihc_intensity_score" display_order="67" cde="3133874" cde_ver="2.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="157448"/>
120
+ <shared_stage:stage_event system="AJCC">
121
+ <shared_stage:system_version preferred_name="ajcc_staging_edition" display_order="51" cde="2722309" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="1079885">6th</shared_stage:system_version>
122
+ <shared_stage:clinical_stage preferred_name="ajcc_clinical_tumor_stage" display_order="9999" cde="3440332" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
123
+ <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157438">Stage IIIC</shared_stage:pathologic_stage>
124
+ <shared_stage:tnm_categories>
125
+ <shared_stage:clinical_categories>
126
+ <shared_stage:clinical_T preferred_name="ajcc_tumor_clinical_ct" display_order="9999" cde="3440328" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
127
+ <shared_stage:clinical_N preferred_name="ajcc_nodes_clinical_cn" display_order="9999" cde="3440330" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
128
+ <shared_stage:clinical_M preferred_name="ajcc_metastasis_clinical_cm" display_order="9999" cde="3440331" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
129
+ </shared_stage:clinical_categories>
130
+ <shared_stage:pathologic_categories>
131
+ <shared_stage:pathologic_T preferred_name="ajcc_tumor_pathologic_pt" display_order="52" cde="3045435" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157435">T2</shared_stage:pathologic_T>
132
+ <shared_stage:pathologic_N preferred_name="ajcc_nodes_pathologic_pn" display_order="53" cde="3203106" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157436">N3a</shared_stage:pathologic_N>
133
+ <shared_stage:pathologic_M preferred_name="ajcc_metastasis_pathologic_pm" display_order="54" cde="3045439" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157437">M0</shared_stage:pathologic_M>
134
+ </shared_stage:pathologic_categories>
135
+ </shared_stage:tnm_categories>
136
+ <shared_stage:psa>
137
+ <shared_stage:psa_value preferred_name="psa_most_recent_results" display_order="9999" cde="3351903" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
138
+ <shared_stage:days_to_psa precision="day" xsd_ver="2.6" tier="2" cde="3414608" owner="TSS" procurement_status="Not Applicable" preferred_name="days_to_psa_most_recent" display_order="9999" cde_ver="1.000"/>
139
+ </shared_stage:psa>
140
+ <shared_stage:gleason_grading>
141
+ <shared_stage:gleason_score preferred_name="gleason_score" display_order="9999" cde="2534619" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
142
+ <shared_stage:primary_pattern preferred_name="gleason_pattern_primary" display_order="9999" cde="2534617" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
143
+ <shared_stage:secondary_pattern preferred_name="gleason_pattern_secondary" display_order="9999" cde="2534618" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
144
+ <shared_stage:tertiary_pattern preferred_name="gleason_pattern_tertiary" display_order="9999" cde="2783875" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
145
+ </shared_stage:gleason_grading>
146
+ <shared_stage:ann_arbor>
147
+ <shared_stage:b_symptoms preferred_name="b_symptoms_present_indicator" display_order="9999" cde="2902402" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
148
+ <shared_stage:extranodal_involvement preferred_name="extranodal_lymphomatous_involvement" display_order="9999" cde="3364582" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
149
+ </shared_stage:ann_arbor>
150
+ <shared_stage:serum_markers preferred_name="" display_order="9999" cde="3901772" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
151
+ <shared_stage:igcccg_stage preferred_name="" display_order="9999" cde="3901822" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
152
+ <shared_stage:masaoka_stage preferred_name="" display_order="9999" cde="3952848" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
153
+ </shared_stage:stage_event>
154
+ <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
155
+ <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
156
+ <brca_nte:new_tumor_events>
157
+ <nte:new_tumor_event_after_initial_treatment preferred_name="new_tumor_event_dx_indicator" display_order="82" cde="3121376" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
158
+ </brca_nte:new_tumor_events>
159
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157077">27</clin_shared:day_of_form_completion>
160
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157076">5</clin_shared:month_of_form_completion>
161
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157078">2011</clin_shared:year_of_form_completion>
162
+ <brca:follow_ups>
163
+ <follow_up_v4.0:follow_up version="4.0" sequence="1">
164
+ <clin_shared:bcr_followup_barcode preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-F40843</clin_shared:bcr_followup_barcode>
165
+ <clin_shared:bcr_followup_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false">6303FB2D-9618-4364-8331-667962F57160</clin_shared:bcr_followup_uuid>
166
+ <clin_shared:lost_follow_up preferred_name="followup_lost_to" display_order="4" cde="61333" cde_ver="3.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2434371">NO</clin_shared:lost_follow_up>
167
+ <clin_shared:radiation_therapy preferred_name="radiation_treatment_adjuvant" display_order="26" cde="2005312" cde_ver="4.000" xsd_ver="1.9" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2434372">YES</clin_shared:radiation_therapy>
168
+ <clin_shared:postoperative_rx_tx preferred_name="pharmaceutical_tx_adjuvant" display_order="27" cde="3397567" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2434373">YES</clin_shared:postoperative_rx_tx>
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="2434374">TUMOR FREE</clin_shared:person_neoplasm_cancer_status>
170
+ <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="2434375">Alive</clin_shared:vital_status>
171
+ <clin_shared:days_to_last_followup precision="month" xsd_ver="1.12" tier="1" cde="3008273" owner="TSS" procurement_status="Completed" preferred_name="last_contact_days_to" display_order="21" cde_ver="1.000">1004</clin_shared:days_to_last_followup>
172
+ <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"/>
173
+ <brca_nte:new_tumor_events>
174
+ <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="2434384">NO</nte:new_tumor_event_after_initial_treatment>
175
+ <brca_nte:new_tumor_event>
176
+ <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"/>
177
+ <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="2434385"/>
178
+ <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="2434386"/>
179
+ <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="2434387"/>
180
+ <nte:new_tumor_event_additional_surgery_procedure preferred_name="new_tumor_event_surgery" display_order="90" cde="3427611" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="2434392"/>
181
+ <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"/>
182
+ <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="2434397"/>
183
+ <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="2434398"/>
184
+ <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="2434399"/>
185
+ <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="2434400"/>
186
+ <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="2434401"/>
187
+ <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="2434402"/>
188
+ <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="2434403"/>
189
+ <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="2434404"/>
190
+ <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="2434405"/>
191
+ <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="2434406"/>
192
+ <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="2434407"/>
193
+ <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="2434408"/>
194
+ <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="2434409"/>
195
+ <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="2434410"/>
196
+ <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="2434411"/>
197
+ <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="2434412"/>
198
+ <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="2434413"/>
199
+ <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="2434414"/>
200
+ <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="2434415"/>
201
+ <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="2434416"/>
202
+ <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="2434417"/>
203
+ <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="2434418"/>
204
+ <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="2434419"/>
205
+ <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="2434420"/>
206
+ <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="2434421"/>
207
+ <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="2434422"/>
208
+ </brca_nte:new_tumor_event>
209
+ </brca_nte:new_tumor_events>
210
+ <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">2</clin_shared:day_of_form_completion>
211
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">3</clin_shared:month_of_form_completion>
212
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2013</clin_shared:year_of_form_completion>
213
+ </follow_up_v4.0:follow_up>
214
+ </brca:follow_ups>
215
+ <rx:drugs>
216
+ <rx:drug>
217
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256717">NO</rx:tx_on_clinical_trial>
218
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
219
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-D37756</rx:bcr_drug_barcode>
220
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">A407F51A-F51F-4CCD-B64B-41D298C30F9C</rx:bcr_drug_uuid>
221
+ <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"/>
222
+ <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"/>
223
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
224
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
225
+ <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"/>
226
+ <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">31</rx:days_to_drug_therapy_start>
227
+ <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">92</rx:days_to_drug_therapy_end>
228
+ <rx:therapy_types>
229
+ <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="2256720">Chemotherapy</rx:therapy_type>
230
+ <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"/>
231
+ </rx:therapy_types>
232
+ <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="2256718">5-Fluorouracil</rx:drug_name>
233
+ <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256719">n/a</rx:clinical_trail_drug_classification>
234
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
235
+ <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"/>
236
+ <rx:route_of_administrations>
237
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
238
+ </rx:route_of_administrations>
239
+ <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="2256725">NO</rx:therapy_ongoing>
240
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256730">Complete Response</clin_shared:measure_of_response>
241
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
242
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
243
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
244
+ </rx:drug>
245
+ <rx:drug>
246
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256734">NO</rx:tx_on_clinical_trial>
247
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
248
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-D37757</rx:bcr_drug_barcode>
249
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">BD575045-6AED-4137-9E4C-2BB9C02A1E89</rx:bcr_drug_uuid>
250
+ <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"/>
251
+ <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"/>
252
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
253
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
254
+ <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"/>
255
+ <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">31</rx:days_to_drug_therapy_start>
256
+ <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">92</rx:days_to_drug_therapy_end>
257
+ <rx:therapy_types>
258
+ <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="2256737">Chemotherapy</rx:therapy_type>
259
+ <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"/>
260
+ </rx:therapy_types>
261
+ <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="2256735">Epirubicin</rx:drug_name>
262
+ <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256736">n/a</rx:clinical_trail_drug_classification>
263
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
264
+ <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"/>
265
+ <rx:route_of_administrations>
266
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
267
+ </rx:route_of_administrations>
268
+ <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="2256742">NO</rx:therapy_ongoing>
269
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256747">Complete Response</clin_shared:measure_of_response>
270
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
271
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
272
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
273
+ </rx:drug>
274
+ <rx:drug>
275
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256751">NO</rx:tx_on_clinical_trial>
276
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
277
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-D37758</rx:bcr_drug_barcode>
278
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">D0945071-31AC-4310-AF0A-4AC89DC8D74D</rx:bcr_drug_uuid>
279
+ <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"/>
280
+ <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"/>
281
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
282
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
283
+ <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"/>
284
+ <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">31</rx:days_to_drug_therapy_start>
285
+ <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">92</rx:days_to_drug_therapy_end>
286
+ <rx:therapy_types>
287
+ <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="2256754">Chemotherapy</rx:therapy_type>
288
+ <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"/>
289
+ </rx:therapy_types>
290
+ <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="2256752">Cyclophosphamide</rx:drug_name>
291
+ <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256753">n/a</rx:clinical_trail_drug_classification>
292
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
293
+ <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"/>
294
+ <rx:route_of_administrations>
295
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
296
+ </rx:route_of_administrations>
297
+ <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="2256759">NO</rx:therapy_ongoing>
298
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256764">Complete Response</clin_shared:measure_of_response>
299
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
300
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
301
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
302
+ </rx:drug>
303
+ <rx:drug>
304
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256768">NO</rx:tx_on_clinical_trial>
305
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
306
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-D37759</rx:bcr_drug_barcode>
307
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">4213A223-3502-4936-813C-875A28B2F161</rx:bcr_drug_uuid>
308
+ <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"/>
309
+ <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"/>
310
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
311
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
312
+ <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"/>
313
+ <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">92</rx:days_to_drug_therapy_start>
314
+ <rx:days_to_drug_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3392470" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_ended_days_to" display_order="16" cde_ver="1.000">123</rx:days_to_drug_therapy_end>
315
+ <rx:therapy_types>
316
+ <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="2256771">Chemotherapy</rx:therapy_type>
317
+ <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"/>
318
+ </rx:therapy_types>
319
+ <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="2256769">Docetaxel</rx:drug_name>
320
+ <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256770">n/a</rx:clinical_trail_drug_classification>
321
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
322
+ <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"/>
323
+ <rx:route_of_administrations>
324
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
325
+ </rx:route_of_administrations>
326
+ <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="2256776">NO</rx:therapy_ongoing>
327
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256781">Complete Response</clin_shared:measure_of_response>
328
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
329
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
330
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
331
+ </rx:drug>
332
+ <rx:drug>
333
+ <rx:tx_on_clinical_trial preferred_name="" display_order="9999" cde="3925111" cde_ver="" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256785">NO</rx:tx_on_clinical_trial>
334
+ <rx:regimen_number preferred_name="" display_order="9999" cde="2744948" cde_ver="" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
335
+ <rx:bcr_drug_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-D37760</rx:bcr_drug_barcode>
336
+ <rx:bcr_drug_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">4B4B76FD-2BE6-4E59-9D03-D67BFF3D823F</rx:bcr_drug_uuid>
337
+ <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"/>
338
+ <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"/>
339
+ <rx:prescribed_dose preferred_name="prescribed_dose" display_order="999" cde="2184728" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
340
+ <rx:prescribed_dose_units preferred_name="pharmaceutical_tx_dose_units" display_order="999" cde="3065815" cde_ver="1.000" xsd_ver="2.1" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
341
+ <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"/>
342
+ <rx:days_to_drug_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Completed" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000">243</rx:days_to_drug_therapy_start>
343
+ <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"/>
344
+ <rx:therapy_types>
345
+ <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="2256788">Hormone Therapy</rx:therapy_type>
346
+ <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"/>
347
+ </rx:therapy_types>
348
+ <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="2256786">Letrozole</rx:drug_name>
349
+ <rx:clinical_trail_drug_classification preferred_name="clinical_trial_drug_classification" display_order="6" cde="3378323" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2256787">n/a</rx:clinical_trail_drug_classification>
350
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
351
+ <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"/>
352
+ <rx:route_of_administrations>
353
+ <rx:route_of_administration preferred_name="route_of_administration" display_order="999" cde="2003586" cde_ver="6.000" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
354
+ </rx:route_of_administrations>
355
+ <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="2256793">YES</rx:therapy_ongoing>
356
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="2256798" xsi:nil="true"/>
357
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">6</clin_shared:day_of_form_completion>
358
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
359
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
360
+ </rx:drug>
361
+ </rx:drugs>
362
+ <rad:radiations>
363
+ <rad:radiation>
364
+ <rad:bcr_radiation_barcode xsd_ver="1.15" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-R38156</rad:bcr_radiation_barcode>
365
+ <rad:bcr_radiation_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">669B30AD-2747-4953-BAC9-E5E3AFAE9216</rad:bcr_radiation_uuid>
366
+ <rad:days_to_radiation_therapy_start precision="month" xsd_ver="1.12" tier="2" cde="3008313" owner="TSS" procurement_status="Completed" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000">184</rad:days_to_radiation_therapy_start>
367
+ <rad:days_to_radiation_therapy_end precision="month" xsd_ver="1.12" tier="2" cde="3008333" owner="TSS" procurement_status="Completed" preferred_name="radiation_therapy_ended_days_to" display_order="17" cde_ver="1.000">215</rad:days_to_radiation_therapy_end>
368
+ <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="2273201">External</rad:radiation_type>
369
+ <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"/>
370
+ <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="2273203"/>
371
+ <rad:units preferred_name="radiation_adjuvant_units" display_order="7" cde="61446" cde_ver="3.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273204">Gy</rad:units>
372
+ <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="2273205"/>
373
+ <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="2273202">Primary Tumor Field</rad:anatomic_treatment_site>
374
+ <clin_shared:regimen_indication preferred_name="therapy_regimen" display_order="999" cde="2793511" cde_ver="1.000" xsd_ver="1.12" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
375
+ <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"/>
376
+ <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="2273210">NO</rad:radiation_treatment_ongoing>
377
+ <rad:course_number preferred_name="course_number" display_order="999" cde="2732184" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
378
+ <clin_shared:measure_of_response preferred_name="treatment_best_response" display_order="17" cde="2857291" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="2273215">Complete Response</clin_shared:measure_of_response>
379
+ <clin_shared:day_of_form_completion preferred_name="form_completion_day" display_order="999" cde="2975716" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">11</clin_shared:day_of_form_completion>
380
+ <clin_shared:month_of_form_completion preferred_name="form_completion_month" display_order="999" cde="2975718" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">12</clin_shared:month_of_form_completion>
381
+ <clin_shared:year_of_form_completion preferred_name="form_completion_year" display_order="999" cde="2975720" cde_ver="1.000" xsd_ver="2.2" tier="2" owner="TSS" procurement_status="Completed" restricted="false">2012</clin_shared:year_of_form_completion>
382
+ </rad:radiation>
383
+ </rad:radiations>
384
+ </brca:patient>
385
+ </brca:tcga_bcr>
data/gdc_data_organized/0a017f15-1c6b-45e7-8d55-e0a71df1b2e8/nationwidechildrens.org_omf.TCGA-A8-A08F.xml ADDED
@@ -0,0 +1,70 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <omf:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/clinical/omf/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/clinical/omf/2.7/TCGA_BCR.Other_Malignancies.xsd" schemaVersion="2.7" xmlns:omf="http://tcga.nci/bcr/xml/clinical/omf/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:omf_v4.0="http://tcga.nci/bcr/xml/clinical/omf/2.7/4.0" xmlns:omf_shared="http://tcga.nci/bcr/xml/clinical/shared/omf/2.7" xmlns:rx="http://tcga.nci/bcr/xml/clinical/pharmaceutical/2.7" xmlns:rad="http://tcga.nci/bcr/xml/clinical/radiation/2.7" xmlns:shared_stage="http://tcga.nci/bcr/xml/clinical/shared/stage/2.7" xmlns:clin_shared="http://tcga.nci/bcr/xml/clinical/shared/2.7">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">59694F95-83D6-49E3-948D-05C4E4DBCE4C</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">47.98.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
12
+ <admin:patient_withdrawal>
13
+ <admin:withdrawn>false</admin:withdrawn>
14
+ </admin:patient_withdrawal>
15
+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
16
+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
17
+ </admin:admin>
18
+ <omf:patient>
19
+ <admin:additional_studies/>
20
+ <shared:tissue_source_site cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A8</shared:tissue_source_site>
21
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A08F</shared:patient_id>
22
+ <shared:bcr_patient_barcode preferred_name="" display_order="9999" cde="2003301" cde_ver="" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F</shared:bcr_patient_barcode>
23
+ <shared:bcr_patient_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" owner="TSS" procurement_status="Completed" restricted="false">0a017f15-1c6b-45e7-8d55-e0a71df1b2e8</shared:bcr_patient_uuid>
24
+ <omf:omfs>
25
+ <omf_v4.0:omf>
26
+ <omf_shared:bcr_omf_barcode xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F-O12210</omf_shared:bcr_omf_barcode>
27
+ <omf_shared:bcr_omf_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.6" owner="TSS" procurement_status="Completed" restricted="false">AD20A788-94F4-44FF-80BA-7CB368D0B7DD</omf_shared:bcr_omf_uuid>
28
+ <omf_shared:malignancy_type preferred_name="malignancy_type" display_order="4" cde="3182890" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961558">Prior Malignancy</omf_shared:malignancy_type>
29
+ <omf_shared:other_malignancy_anatomic_site preferred_name="" display_order="9999" cde="4122351" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961550">Uterus</omf_shared:other_malignancy_anatomic_site>
30
+ <omf_shared:other_malignancy_anatomic_site_text preferred_name="" display_order="9999" cde="4122371" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="961551" xsi:nil="true"/>
31
+ <omf_shared:other_malignancy_laterality preferred_name="" display_order="9999" cde="4122391" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961552"/>
32
+ <omf_shared:other_malignancy_histological_type preferred_name="" display_order="9999" cde="4122411" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961553">Other, specify</omf_shared:other_malignancy_histological_type>
33
+ <omf_shared:other_malignancy_histological_type_text preferred_name="" display_order="9999" cde="4122431" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961554">malignant neoplasm of uterus, part unspecified</omf_shared:other_malignancy_histological_type_text>
34
+ <omf_shared:days_to_other_malignancy_dx precision="day" xsd_ver="2.6" tier="2" cde="3462301" owner="TSS" procurement_status="Not Available" preferred_name="other_malignancy_dx_days_to" display_order="13" cde_ver="1.000"/>
35
+ <omf_shared:surgery>
36
+ <shared:surgery_indicator preferred_name="surgery_indicator" display_order="14" cde="3186538" cde_ver="2.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
37
+ <omf_shared:surgery_type preferred_name="other_malignancy_surgery_type" display_order="15" cde="3462300" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
38
+ <omf_shared:days_to_surgical_resection precision="month" xsd_ver="2.6" tier="2" cde="3462302" owner="TSS" procurement_status="Completed" preferred_name="other_malignancy_surgery_days_to" display_order="19" cde_ver="1.000">-3834</omf_shared:days_to_surgical_resection>
39
+ </omf_shared:surgery>
40
+ <omf_shared:drug_tx>
41
+ <shared:drug_tx_indicator preferred_name="pharmaceutical_therapy_indicator" display_order="20" cde="3178327" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961559">NO</shared:drug_tx_indicator>
42
+ <omf_shared:drug_tx_extent preferred_name="pharmaceutical_therapy_extent" display_order="21" cde="3178365" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961560"/>
43
+ <rx:days_to_drug_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3392465" owner="TSS" procurement_status="Not Available" preferred_name="pharmaceutical_tx_started_days_to" display_order="26" cde_ver="1.000"/>
44
+ <omf_shared:administered_drug>
45
+ <rx:drug_name preferred_name="pharmaceutical_therapy_drug_name" display_order="22" cde="2975232" cde_ver="1.000" xsd_ver="1.10" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961561"/>
46
+ </omf_shared:administered_drug>
47
+ </omf_shared:drug_tx>
48
+ <omf_shared:radiation_tx>
49
+ <omf_shared:radiation_tx_indicator preferred_name="radiation_therapy_indicator" display_order="27" cde="3178328" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="961565">YES</omf_shared:radiation_tx_indicator>
50
+ <omf_shared:radiation_tx_extent preferred_name="radiation_therapy_extent" display_order="28" cde="3178353" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961566"/>
51
+ <omf_shared:rad_tx_to_site_of_primary_tumor preferred_name="history_rt_tx_to_site_of_tcga_tumor" display_order="29" cde="2865132" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961567"/>
52
+ <rad:days_to_radiation_therapy_start precision="day" xsd_ver="1.12" tier="2" cde="3008313" owner="TSS" procurement_status="Not Available" preferred_name="radiation_therapy_started_days_to" display_order="33" cde_ver="1.000"/>
53
+ </omf_shared:radiation_tx>
54
+ <omf_shared:omf_staging>
55
+ <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"/>
56
+ <shared_stage:clinical_stage preferred_name="figo_clinical_tumor_stage" display_order="9999" cde="3225684" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
57
+ <shared_stage:pathologic_stage preferred_name="ajcc_pathologic_tumor_stage" display_order="55" cde="3203222" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961577"/>
58
+ <shared_stage:pathologic_categories>
59
+ <shared_stage:pathologic_T preferred_name="ajcc_tumor_pathologic_pt" display_order="52" cde="3045435" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961574"/>
60
+ <shared_stage:pathologic_N preferred_name="ajcc_nodes_pathologic_pn" display_order="53" cde="3203106" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961575"/>
61
+ <shared_stage:pathologic_M preferred_name="ajcc_metastasis_pathologic_pm" display_order="54" cde="3045439" cde_ver="1.000" xsd_ver="2.6" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="961576"/>
62
+ </shared_stage:pathologic_categories>
63
+ </omf_shared:omf_staging>
64
+ <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="961548">25</clin_shared:day_of_form_completion>
65
+ <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="961547">5</clin_shared:month_of_form_completion>
66
+ <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="961549">2011</clin_shared:year_of_form_completion>
67
+ </omf_v4.0:omf>
68
+ </omf:omfs>
69
+ </omf:patient>
70
+ </omf:tcga_bcr>
data/gdc_data_organized/0a017f15-1c6b-45e7-8d55-e0a71df1b2e8/nationwidechildrens.org_ssf.TCGA-A8-A08F.xml ADDED
@@ -0,0 +1,93 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <ssf:tcga_bcr xsi:schemaLocation="http://tcga.nci/bcr/xml/ssf/2.7 https://raw.githubusercontent.com/nchbcr/xsd/2.7/tcga.nci/bcr/xml/ssf/2.7/TCGA_BCR.SSF.xsd" schemaVersion="2.7" xmlns:ssf="http://tcga.nci/bcr/xml/ssf/2.7" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:admin="http://tcga.nci/bcr/xml/administration/2.7" xmlns:shared="http://tcga.nci/bcr/xml/shared/2.7" xmlns:ssf_disease="http://tcga.nci/bcr/xml/ssf_disease/2.7">
3
+ <admin:admin>
4
+ <admin:bcr xsd_ver="1.17">Nationwide Children's Hospital</admin:bcr>
5
+ <admin:file_uuid xsd_ver="2.6">A9A9D5F3-1B96-4301-BA1E-DA4B6BB24304</admin:file_uuid>
6
+ <admin:batch_number xsd_ver="1.17">47.98.0</admin:batch_number>
7
+ <admin:project_code xsd_ver="2.7">TCGA</admin:project_code>
8
+ <admin:disease_code xsd_ver="2.6">BRCA</admin:disease_code>
9
+ <admin:day_of_dcc_upload xsd_ver="1.17">22</admin:day_of_dcc_upload>
10
+ <admin:month_of_dcc_upload xsd_ver="1.17">12</admin:month_of_dcc_upload>
11
+ <admin:year_of_dcc_upload xsd_ver="1.17">2016</admin:year_of_dcc_upload>
12
+ <admin:patient_withdrawal>
13
+ <admin:withdrawn>false</admin:withdrawn>
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+ </admin:patient_withdrawal>
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+ <admin:program xsi:nil="true" xsd_ver="2.7"/>
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+ <admin:dbgap_registration_code xsi:nil="true" xsd_ver="2.7"/>
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+ </admin:admin>
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+ <ssf:patient>
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+ <admin:additional_studies/>
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+ <shared:bcr_patient_barcode preferred_name="" display_order="9999" cde="2003301" cde_ver="" xsd_ver="1.8" owner="TSS" procurement_status="Completed" restricted="false">TCGA-A8-A08F</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">0a017f15-1c6b-45e7-8d55-e0a71df1b2e8</shared:bcr_patient_uuid>
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23
+ <shared:patient_id cde="" cde_ver="" xsd_ver="2.4" owner="TSS" procurement_status="Completed" restricted="false">A08F</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">f4f60d69-6c0d-4a73-90fa-ee369de95fdd</ssf:bcr_sample_uuid>
28
+ <shared:days_to_sample_procurement precision="month" xsd_ver="2.3" tier="" cde="" owner="TSS" procurement_status="Completed" preferred_name="" display_order="9999" cde_ver="">0</shared:days_to_sample_procurement>
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+ <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="156870">Other Method, specify</shared:method_of_sample_procurement>
30
+ <shared:other_method_of_sample_procurement preferred_name="cancer_procurement_method_other" display_order="12" cde="2006730" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156871">Mastectomy</shared:other_method_of_sample_procurement>
31
+ <ssf:vessel_used preferred_name="tumor_sample_vessel_used" display_order="16" cde="3081940" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156872">Cryovial</ssf:vessel_used>
32
+ <ssf:other_vessel_used preferred_name="tumor_sample_ship_vessel_other" display_order="17" cde="3288137" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="156873"/>
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+ <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="156874">100</ssf:tumor_weight>
35
+ <ssf:sample_prescreened preferred_name="tumor_sample_prescreened_at_tss" display_order="19" cde="3081942" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156877">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="156875">70</shared:tumor_nuclei_percent>
37
+ <shared:tumor_necrosis_percent preferred_name="necrosis_percent" display_order="25" cde="2841237" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156876">20</shared:tumor_necrosis_percent>
38
+ <ssf:days_to_pathology_review floored="true" precision="month" xsd_ver="2.5" tier="2" cde="3288497" owner="TSS" procurement_status="Completed" preferred_name="tss_pathology_review_days_to" display_order="63" cde_ver="1.000">0</ssf:days_to_pathology_review>
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+ <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="157046">YES</ssf:path_confirm_tumor_nuclei_metrics>
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+ <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="157047">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="157049">YES</ssf:path_confirm_report_attached>
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+ <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="157048">YES</ssf:path_confirm_diagnosis_matching>
43
+ <ssf:reason_path_confirm_diagnosis_not_matching preferred_name="histologic_dx_inconsistent_reason" display_order="69" cde="3288315" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false"/>
44
+ <ssf:top_slide_submitted preferred_name="tumor_sample_top_slide_submitted" display_order="999" cde="3081944" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156878">NO</ssf:top_slide_submitted>
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+ <ssf:digital_image_submitted preferred_name="tumor_sample_image_submitted" display_order="999" cde="3081948" cde_ver="1.000" xsd_ver="1.8" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156880">NO</ssf:digital_image_submitted>
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+ <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>
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+ <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"/>
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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="157051">Yes, History of Prior Malignancy</shared:other_dx>
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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="157051">No</shared:history_of_neoadjuvant_treatment>
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+ <shared:consent_or_death_status preferred_name="patient_consent_status" display_order="72" cde="3288361" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="157052">Consented</shared:consent_or_death_status>
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+ <shared:days_to_consent precision="month" xsd_ver="2.5" tier="1" cde="3288498" owner="TSS" procurement_status="Completed" preferred_name="patient_consent_days_to" display_order="76" cde_ver="1.000">0</shared:days_to_consent>
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+ <shared:country preferred_name="tumor_sample_procurement_country" display_order="13" cde="3203072" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="740792">Germany</shared:country>
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+ <ssf_disease:disease_details/>
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+ <ssf:tumor_histologies>
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+ <ssf:tumor_histology>
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+ <shared:histological_type preferred_name="histologic_diagnosis" display_order="3" cde="3081934" cde_ver="3.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156863">Infiltrating Ductal Carcinoma</shared:histological_type>
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+ <shared:histological_type_other preferred_name="histologic_diagnosis_other" display_order="31" cde="3124492" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
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+ <shared:histological_percentage preferred_name="histologic_diagnosis_percent" display_order="9999" cde="3729998" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
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+ <shared:tumor_morphology_percentage preferred_name="" display_order="9999" cde="3729984" cde_ver="1.000" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false" xsi:nil="true"/>
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+ </ssf:tumor_histology>
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+ </ssf:tumor_histologies>
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+ <ssf:tumor_locations>
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+ <ssf:tumor_focality preferred_name="tumor_focality" display_order="9999" cde="3174022" cde_ver="1.000" xsd_ver="2.5" tier="2" owner="TSS" procurement_status="Not Applicable" restricted="false"/>
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+ <ssf:laterality preferred_name="" display_order="9999" cde="4742852" cde_ver="" xsd_ver="2.6" tier="" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156866">Right</ssf:laterality>
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+ <ssf:site_of_disease preferred_name="" display_order="9999" cde="4742851" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156866">Breast</ssf:site_of_disease>
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+ <ssf:site_of_disease_text preferred_name="" display_order="9999" cde="4742871" cde_ver="" xsd_ver="2.6" tier="2" owner="TSS" procurement_status="Not Available" restricted="false"/>
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+ <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="156866"/>
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+ </ssf:tumor_location>
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+ </ssf:tumor_locations>
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+ </ssf:tumor_sample>
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+ <ssf:normal_control>
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+ <ssf:bcr_sample_uuid preferred_name="" display_order="9999" cde="" cde_ver="" xsd_ver="2.3" tier="2" owner="TSS" procurement_status="Completed" restricted="false">25067aad-c602-4e7e-99d5-f4bc327c6fd9</ssf:bcr_sample_uuid>
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+ <ssf:method_of_normal_sample_procurement preferred_name="normal_control_method" display_order="50" cde="3288147" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Completed" restricted="false" source_system_identifier="156926">Blood Draw</ssf:method_of_normal_sample_procurement>
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+ <ssf:other_method_of_normal_sample_procurement preferred_name="normal_control_method_other" display_order="51" cde="3288151" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Applicable" restricted="false" source_system_identifier="156927"/>
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+ <ssf:days_to_normal_sample_procurement precision="month" xsd_ver="2.3" tier="1" cde="3288496" owner="TSS" procurement_status="Completed" preferred_name="normal_control_procurement_days_to" display_order="55" cde_ver="1.000">0</ssf:days_to_normal_sample_procurement>
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+ <ssf:normal_sample_site_proximity_to_tumor preferred_name="normal_control_proximity_to_tumor" display_order="59" cde="3088708" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="156928"/>
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+ <ssf:ncedna_dna_conc preferred_name="normal_control_DNA_concentration" display_order="48" cde="3288187" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="156919"/>
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+ <ssf:ncedna_dna_qty preferred_name="normal_control_DNA_quantity" display_order="46" cde="3288185" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="156917"/>
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+ <ssf:ncedna_dna_vol preferred_name="normal_control_DNA_volume" display_order="49" cde="3288188" cde_ver="1.000" xsd_ver="2.5" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="156920"/>
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+ <ssf:normal_tissue_anatomic_site preferred_name="" display_order="57" cde="4132152" cde_ver="1.000" xsd_ver="2.5" tier="1" owner="TSS" procurement_status="Not Available" restricted="false" source_system_identifier="156921"/>
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+ </ssf:normal_control>
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+ </ssf:normal_controls>
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+ </ssf:patient>
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+ </ssf:tcga_bcr>
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