Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1319T88
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1319T88
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 80 arm-level events and 10 clinical features across 957 patients, 21 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 8q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 1p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 5q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 6q loss cnv correlated to 'AGE'.

  • 8p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 9p loss cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.

  • 16q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 18p loss cnv correlated to 'Time to Death'.

  • 19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

  • 19q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test t-test
1p loss 221 (23%) 736 0.0204
(1.00) 		0.00302
(1.00) 		6.21e-06
(0.00493) 		1.11e-05
(0.00873) 		0.000751
(0.581) 		0.345
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.556
(1.00) 		0.00564
(1.00)
9p loss 285 (30%) 672 0.0409
(1.00) 		0.422
(1.00) 		0.00127
(0.972) 		0.000108
(0.085) 		0.0163
(1.00) 		0.0481
(1.00) 		0.174
(1.00) 		6.68e-06
(0.00529) 		0.0877
(1.00) 		0.694
(1.00)
2p gain 107 (11%) 850 0.178
(1.00) 		0.898
(1.00) 		0.588
(1.00) 		0.694
(1.00) 		0.954
(1.00) 		0.969
(1.00) 		0.614
(1.00) 		0.000156
(0.123) 		0.312
(1.00) 		0.205
(1.00)
3q gain 189 (20%) 768 0.405
(1.00) 		0.369
(1.00) 		0.779
(1.00) 		0.236
(1.00) 		0.552
(1.00) 		0.115
(1.00) 		0.696
(1.00) 		1.63e-05
(0.0128) 		0.182
(1.00) 		0.14
(1.00)
6p gain 180 (19%) 777 0.173
(1.00) 		0.885
(1.00) 		0.642
(1.00) 		0.133
(1.00) 		0.526
(1.00) 		0.806
(1.00) 		0.698
(1.00) 		0.000163
(0.127) 		0.102
(1.00) 		0.789
(1.00)
6q gain 129 (13%) 828 0.154
(1.00) 		0.676
(1.00) 		0.734
(1.00) 		0.116
(1.00) 		0.0932
(1.00) 		1
(1.00) 		1
(1.00) 		0.000229
(0.179) 		0.406
(1.00) 		0.844
(1.00)
8q gain 471 (49%) 486 0.55
(1.00) 		0.857
(1.00) 		0.319
(1.00) 		0.88
(1.00) 		0.36
(1.00) 		0.08
(1.00) 		0.541
(1.00) 		7.48e-06
(0.00592) 		0.0192
(1.00) 		0.826
(1.00)
20p gain 365 (38%) 592 0.297
(1.00) 		0.318
(1.00) 		0.292
(1.00) 		0.624
(1.00) 		0.0182
(1.00) 		0.0089
(1.00) 		0.0493
(1.00) 		1.18e-06
(0.000941) 		0.0105
(1.00) 		0.675
(1.00)
20q gain 396 (41%) 561 0.365
(1.00) 		0.95
(1.00) 		0.431
(1.00) 		0.069
(1.00) 		0.105
(1.00) 		0.01
(1.00) 		0.334
(1.00) 		8.53e-08
(6.81e-05) 		0.0976
(1.00) 		0.441
(1.00)
4p loss 309 (32%) 648 0.329
(1.00) 		0.614
(1.00) 		0.365
(1.00) 		0.0372
(1.00) 		0.488
(1.00) 		0.448
(1.00) 		1
(1.00) 		5.68e-06
(0.00452) 		0.544
(1.00) 		0.918
(1.00)
4q loss 276 (29%) 681 0.872
(1.00) 		0.911
(1.00) 		0.648
(1.00) 		0.0683
(1.00) 		0.548
(1.00) 		0.361
(1.00) 		0.297
(1.00) 		8.36e-05
(0.0656) 		0.349
(1.00) 		0.923
(1.00)
5p loss 129 (13%) 828 0.155
(1.00) 		0.00978
(1.00) 		0.227
(1.00) 		0.0444
(1.00) 		0.849
(1.00) 		0.881
(1.00) 		1
(1.00) 		4.18e-06
(0.00333) 		0.213
(1.00) 		0.73
(1.00)
5q loss 203 (21%) 754 0.356
(1.00) 		0.00215
(1.00) 		0.269
(1.00) 		0.0118
(1.00) 		0.314
(1.00) 		0.586
(1.00) 		0.132
(1.00) 		2.62e-10
(2.09e-07) 		0.385
(1.00) 		0.228
(1.00)
6q loss 244 (25%) 713 0.465
(1.00) 		0.000292
(0.228) 		0.905
(1.00) 		0.421
(1.00) 		0.444
(1.00) 		0.251
(1.00) 		0.466
(1.00) 		0.794
(1.00) 		0.00912
(1.00) 		0.168
(1.00)
8p loss 356 (37%) 601 0.0387
(1.00) 		0.251
(1.00) 		0.941
(1.00) 		0.163
(1.00) 		0.48
(1.00) 		0.369
(1.00) 		0.752
(1.00) 		4.19e-05
(0.033) 		0.608
(1.00) 		0.428
(1.00)
16q loss 527 (55%) 430 0.0436
(1.00) 		0.000995
(0.767) 		0.702
(1.00) 		0.689
(1.00) 		0.367
(1.00) 		0.207
(1.00) 		0.358
(1.00) 		4.45e-11
(3.56e-08) 		0.134
(1.00) 		0.291
(1.00)
18p loss 286 (30%) 671 8.24e-06
(0.00651) 		0.013
(1.00) 		0.0397
(1.00) 		0.0146
(1.00) 		0.377
(1.00) 		0.837
(1.00) 		0.732
(1.00) 		0.0311
(1.00) 		0.938
(1.00) 		0.152
(1.00)
19p loss 169 (18%) 788 0.175
(1.00) 		0.0383
(1.00) 		0.918
(1.00) 		0.571
(1.00) 		0.489
(1.00) 		0.274
(1.00) 		1
(1.00) 		7.1e-06
(0.00562) 		0.457
(1.00) 		0.284
(1.00)
19q loss 144 (15%) 813 0.438
(1.00) 		0.713
(1.00) 		0.697
(1.00) 		0.472
(1.00) 		0.237
(1.00) 		0.383
(1.00) 		1
(1.00) 		5.12e-05
(0.0403) 		0.0916
(1.00) 		0.37
(1.00)
1p gain 175 (18%) 782 0.132
(1.00) 		0.0925
(1.00) 		0.99
(1.00) 		0.336
(1.00) 		0.333
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.00756
(1.00) 		0.00995
(1.00) 		0.515
(1.00)
1q gain 613 (64%) 344 0.243
(1.00) 		0.437
(1.00) 		0.0427
(1.00) 		0.00555
(1.00) 		0.681
(1.00) 		0.858
(1.00) 		0.752
(1.00) 		0.0172
(1.00) 		0.712
(1.00) 		0.991
(1.00)
2q gain 66 (7%) 891 0.392
(1.00) 		0.571
(1.00) 		0.648
(1.00) 		0.346
(1.00) 		0.832
(1.00) 		0.898
(1.00) 		1
(1.00) 		0.096
(1.00) 		0.675
(1.00) 		0.33
(1.00)
3p gain 129 (13%) 828 0.225
(1.00) 		0.103
(1.00) 		0.125
(1.00) 		0.0691
(1.00) 		0.317
(1.00) 		0.00275
(1.00) 		1
(1.00) 		0.00993
(1.00) 		0.678
(1.00) 		0.77
(1.00)
4p gain 69 (7%) 888 0.0511
(1.00) 		0.733
(1.00) 		0.184
(1.00) 		0.107
(1.00) 		0.761
(1.00) 		0.234
(1.00) 		0.529
(1.00) 		0.0219
(1.00) 		0.785
(1.00) 		0.852
(1.00)
4q gain 64 (7%) 893 0.0244
(1.00) 		0.922
(1.00) 		0.17
(1.00) 		0.14
(1.00) 		0.593
(1.00) 		0.277
(1.00) 		0.501
(1.00) 		0.00233
(1.00) 		1
(1.00) 		0.885
(1.00)
5p gain 274 (29%) 683 0.101
(1.00) 		0.116
(1.00) 		0.449
(1.00) 		0.501
(1.00) 		0.00228
(1.00) 		0.0485
(1.00) 		0.484
(1.00) 		0.427
(1.00) 		0.183
(1.00) 		0.638
(1.00)
5q gain 185 (19%) 772 0.567
(1.00) 		0.0248
(1.00) 		0.512
(1.00) 		0.26
(1.00) 		0.243
(1.00) 		0.236
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.419
(1.00) 		0.637
(1.00)
7p gain 274 (29%) 683 0.656
(1.00) 		0.235
(1.00) 		0.844
(1.00) 		0.768
(1.00) 		0.778
(1.00) 		0.815
(1.00) 		0.0372
(1.00) 		0.167
(1.00) 		0.183
(1.00) 		0.581
(1.00)
7q gain 229 (24%) 728 0.765
(1.00) 		0.863
(1.00) 		0.48
(1.00) 		0.547
(1.00) 		0.504
(1.00) 		0.737
(1.00) 		0.263
(1.00) 		0.252
(1.00) 		1
(1.00) 		0.859
(1.00)
8p gain 253 (26%) 704 0.913
(1.00) 		0.622
(1.00) 		0.515
(1.00) 		0.778
(1.00) 		0.794
(1.00) 		0.333
(1.00) 		0.729
(1.00) 		0.749
(1.00) 		0.688
(1.00) 		0.897
(1.00)
9p gain 123 (13%) 834 0.718
(1.00) 		0.816
(1.00) 		0.327
(1.00) 		0.73
(1.00) 		0.106
(1.00) 		0.727
(1.00) 		0.626
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.328
(1.00)
9q gain 107 (11%) 850 0.158
(1.00) 		0.687
(1.00) 		0.676
(1.00) 		0.5
(1.00) 		0.162
(1.00) 		0.909
(1.00) 		0.614
(1.00) 		0.323
(1.00) 		0.574
(1.00) 		0.639
(1.00)
10p gain 189 (20%) 768 0.625
(1.00) 		0.828
(1.00) 		0.243
(1.00) 		0.264
(1.00) 		0.371
(1.00) 		0.239
(1.00) 		0.696
(1.00) 		0.00054
(0.42) 		0.0743
(1.00) 		0.993
(1.00)
10q gain 109 (11%) 848 0.822
(1.00) 		0.577
(1.00) 		0.309
(1.00) 		0.238
(1.00) 		0.743
(1.00) 		0.552
(1.00) 		0.615
(1.00) 		0.197
(1.00) 		0.0932
(1.00) 		0.415
(1.00)
11p gain 123 (13%) 834 0.843
(1.00) 		0.92
(1.00) 		0.959
(1.00) 		0.517
(1.00) 		0.298
(1.00) 		0.974
(1.00) 		1
(1.00) 		0.0203
(1.00) 		0.673
(1.00) 		0.161
(1.00)
11q gain 86 (9%) 871 0.327
(1.00) 		0.907
(1.00) 		0.221
(1.00) 		0.596
(1.00) 		0.303
(1.00) 		0.652
(1.00) 		1
(1.00) 		0.00286
(1.00) 		0.805
(1.00) 		0.524
(1.00)
12p gain 202 (21%) 755 0.334
(1.00) 		0.76
(1.00) 		0.682
(1.00) 		0.137
(1.00) 		0.154
(1.00) 		0.474
(1.00) 		0.0398
(1.00) 		0.0317
(1.00) 		0.192
(1.00) 		0.128
(1.00)
12q gain 168 (18%) 789 0.225
(1.00) 		0.349
(1.00) 		0.161
(1.00) 		0.0585
(1.00) 		0.0147
(1.00) 		0.134
(1.00) 		0.0186
(1.00) 		0.165
(1.00) 		0.305
(1.00) 		0.0843
(1.00)
13q gain 82 (9%) 875 0.709
(1.00) 		0.299
(1.00) 		0.625
(1.00) 		0.458
(1.00) 		0.607
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.021
(1.00) 		0.313
(1.00) 		0.368
(1.00)
14q gain 130 (14%) 827 0.571
(1.00) 		0.106
(1.00) 		0.209
(1.00) 		0.0975
(1.00) 		0.102
(1.00) 		0.762
(1.00) 		0.374
(1.00) 		0.38
(1.00) 		0.756
(1.00) 		0.155
(1.00)
15q gain 83 (9%) 874 0.41
(1.00) 		0.797
(1.00) 		0.573
(1.00) 		0.825
(1.00) 		0.884
(1.00) 		0.616
(1.00) 		0.598
(1.00) 		0.0195
(1.00) 		0.257
(1.00) 		0.437
(1.00)
16p gain 426 (45%) 531 0.888
(1.00) 		0.0118
(1.00) 		0.694
(1.00) 		0.817
(1.00) 		0.456
(1.00) 		0.892
(1.00) 		0.758
(1.00) 		0.0808
(1.00) 		0.392
(1.00) 		0.566
(1.00)
16q gain 119 (12%) 838 0.0931
(1.00) 		0.464
(1.00) 		0.174
(1.00) 		0.22
(1.00) 		0.308
(1.00) 		0.244
(1.00) 		0.117
(1.00) 		0.106
(1.00) 		0.747
(1.00) 		0.708
(1.00)
17p gain 96 (10%) 861 0.0817
(1.00) 		0.604
(1.00) 		0.171
(1.00) 		0.0111
(1.00) 		0.18
(1.00) 		0.375
(1.00) 		0.00154
(1.00) 		0.242
(1.00) 		0.0246
(1.00) 		0.626
(1.00)
17q gain 197 (21%) 760 0.0378
(1.00) 		0.576
(1.00) 		0.764
(1.00) 		0.19
(1.00) 		0.893
(1.00) 		0.237
(1.00) 		0.00097
(0.749) 		0.185
(1.00) 		0.0537
(1.00) 		0.867
(1.00)
18p gain 149 (16%) 808 0.443
(1.00) 		0.118
(1.00) 		0.0984
(1.00) 		0.465
(1.00) 		0.0353
(1.00) 		0.128
(1.00) 		0.66
(1.00) 		0.0233
(1.00) 		0.171
(1.00) 		0.559
(1.00)
18q gain 129 (13%) 828 0.931
(1.00) 		0.448
(1.00) 		0.175
(1.00) 		0.472
(1.00) 		0.197
(1.00) 		0.0233
(1.00) 		0.632
(1.00) 		0.123
(1.00) 		0.299
(1.00) 		0.912
(1.00)
19p gain 159 (17%) 798 0.681
(1.00) 		0.828
(1.00) 		0.368
(1.00) 		0.189
(1.00) 		0.291
(1.00) 		0.0872
(1.00) 		0.0148
(1.00) 		0.283
(1.00) 		0.127
(1.00) 		0.284
(1.00)
19q gain 191 (20%) 766 0.313
(1.00) 		0.0509
(1.00) 		0.397
(1.00) 		0.759
(1.00) 		0.153
(1.00) 		0.0122
(1.00) 		0.0318
(1.00) 		0.682
(1.00) 		0.329
(1.00) 		0.0617
(1.00)
21q gain 178 (19%) 779 0.00704
(1.00) 		0.0584
(1.00) 		0.597
(1.00) 		0.685
(1.00) 		0.58
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.00105
(0.811) 		0.0226
(1.00) 		0.229
(1.00)
22q gain 85 (9%) 872 0.171
(1.00) 		0.908
(1.00) 		0.245
(1.00) 		0.16
(1.00) 		0.511
(1.00) 		0.323
(1.00) 		1
(1.00) 		0.00625
(1.00) 		0.383
(1.00) 		0.469
(1.00)
xq gain 127 (13%) 830 0.211
(1.00) 		0.205
(1.00) 		0.399
(1.00) 		0.232
(1.00) 		0.845
(1.00) 		0.0823
(1.00) 		1
(1.00) 		0.000571
(0.443) 		0.174
(1.00) 		0.711
(1.00)
1q loss 50 (5%) 907 0.378
(1.00) 		0.433
(1.00) 		0.915
(1.00) 		0.343
(1.00) 		0.0544
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.44
(1.00) 		1
(1.00) 		0.785
(1.00)
2p loss 161 (17%) 796 0.851
(1.00) 		0.353
(1.00) 		0.392
(1.00) 		0.461
(1.00) 		0.0449
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.0177
(1.00) 		0.53
(1.00)
2q loss 182 (19%) 775 0.356
(1.00) 		0.579
(1.00) 		0.171
(1.00) 		0.427
(1.00) 		0.0473
(1.00) 		0.109
(1.00) 		0.697
(1.00) 		0.433
(1.00) 		0.0864
(1.00) 		0.279
(1.00)
3p loss 164 (17%) 793 0.431
(1.00) 		0.049
(1.00) 		0.9
(1.00) 		0.00309
(1.00) 		0.947
(1.00) 		0.601
(1.00) 		0.226
(1.00) 		0.0332
(1.00) 		0.0109
(1.00) 		0.818
(1.00)
3q loss 90 (9%) 867 0.108
(1.00) 		0.271
(1.00) 		0.368
(1.00) 		0.00105
(0.808) 		0.767
(1.00) 		0.741
(1.00) 		0.611
(1.00) 		0.114
(1.00) 		0.028
(1.00) 		0.199
(1.00)
6p loss 168 (18%) 789 0.832
(1.00) 		0.041
(1.00) 		0.964
(1.00) 		0.618
(1.00) 		0.796
(1.00) 		0.0155
(1.00) 		1
(1.00) 		0.737
(1.00) 		0.113
(1.00) 		0.0492
(1.00)
7p loss 98 (10%) 859 0.525
(1.00) 		0.949
(1.00) 		0.332
(1.00) 		0.559
(1.00) 		0.0151
(1.00) 		0.251
(1.00) 		0.611
(1.00) 		0.0242
(1.00) 		0.242
(1.00) 		0.0379
(1.00)
7q loss 107 (11%) 850 0.126
(1.00) 		0.285
(1.00) 		0.373
(1.00) 		0.678
(1.00) 		0.141
(1.00) 		0.0939
(1.00) 		0.614
(1.00) 		0.219
(1.00) 		0.431
(1.00) 		0.0279
(1.00)
8q loss 79 (8%) 878 0.083
(1.00) 		0.109
(1.00) 		0.753
(1.00) 		0.461
(1.00) 		0.254
(1.00) 		0.769
(1.00) 		1
(1.00) 		0.433
(1.00) 		0.199
(1.00) 		0.291
(1.00)
9q loss 258 (27%) 699 0.225
(1.00) 		0.707
(1.00) 		0.108
(1.00) 		0.00123
(0.946) 		0.0506
(1.00) 		0.571
(1.00) 		0.144
(1.00) 		0.000596
(0.462) 		0.0786
(1.00) 		0.923
(1.00)
10p loss 153 (16%) 804 0.00548
(1.00) 		0.874
(1.00) 		0.0438
(1.00) 		0.0145
(1.00) 		0.107
(1.00) 		0.0081
(1.00) 		0.379
(1.00) 		0.196
(1.00) 		1
(1.00) 		0.243
(1.00)
10q loss 203 (21%) 754 0.0121
(1.00) 		0.781
(1.00) 		0.113
(1.00) 		0.0136
(1.00) 		0.107
(1.00) 		0.031
(1.00) 		0.698
(1.00) 		0.0511
(1.00) 		0.931
(1.00) 		0.163
(1.00)
11p loss 244 (25%) 713 0.0787
(1.00) 		0.783
(1.00) 		0.0169
(1.00) 		0.0339
(1.00) 		0.0153
(1.00) 		0.596
(1.00) 		1
(1.00) 		0.0141
(1.00) 		0.515
(1.00) 		0.147
(1.00)
11q loss 331 (35%) 626 0.481
(1.00) 		0.634
(1.00) 		0.194
(1.00) 		0.196
(1.00) 		0.0152
(1.00) 		0.733
(1.00) 		0.103
(1.00) 		0.52
(1.00) 		0.709
(1.00) 		0.534
(1.00)
12p loss 137 (14%) 820 0.323
(1.00) 		0.743
(1.00) 		0.189
(1.00) 		0.0343
(1.00) 		0.634
(1.00) 		0.0877
(1.00) 		1
(1.00) 		0.0175
(1.00) 		0.265
(1.00) 		0.226
(1.00)
12q loss 116 (12%) 841 0.671
(1.00) 		0.0407
(1.00) 		0.359
(1.00) 		0.0205
(1.00) 		0.872
(1.00) 		0.44
(1.00) 		0.62
(1.00) 		0.00915
(1.00) 		0.102
(1.00) 		0.638
(1.00)
13q loss 390 (41%) 567 0.0297
(1.00) 		0.529
(1.00) 		0.712
(1.00) 		0.112
(1.00) 		0.756
(1.00) 		0.961
(1.00) 		0.54
(1.00) 		0.000551
(0.428) 		0.428
(1.00) 		0.157
(1.00)
14q loss 229 (24%) 728 0.0533
(1.00) 		0.669
(1.00) 		0.854
(1.00) 		0.0794
(1.00) 		0.078
(1.00) 		0.873
(1.00) 		0.466
(1.00) 		0.000366
(0.285) 		0.212
(1.00) 		0.529
(1.00)
15q loss 280 (29%) 677 0.0502
(1.00) 		0.652
(1.00) 		0.494
(1.00) 		0.0176
(1.00) 		0.0736
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.00305
(1.00) 		0.0352
(1.00) 		0.657
(1.00)
16p loss 145 (15%) 812 0.736
(1.00) 		0.657
(1.00) 		0.29
(1.00) 		0.955
(1.00) 		0.0699
(1.00) 		0.554
(1.00) 		0.654
(1.00) 		0.306
(1.00) 		0.553
(1.00) 		0.863
(1.00)
17p loss 514 (54%) 443 0.312
(1.00) 		0.0174
(1.00) 		0.0931
(1.00) 		0.00647
(1.00) 		0.72
(1.00) 		0.844
(1.00) 		0.527
(1.00) 		0.0226
(1.00) 		1
(1.00) 		0.959
(1.00)
17q loss 242 (25%) 715 0.883
(1.00) 		0.125
(1.00) 		0.886
(1.00) 		0.557
(1.00) 		0.304
(1.00) 		0.357
(1.00) 		0.0736
(1.00) 		0.0007
(0.542) 		0.871
(1.00) 		0.881
(1.00)
18q loss 284 (30%) 673 0.00491
(1.00) 		0.0211
(1.00) 		0.0212
(1.00) 		0.0206
(1.00) 		0.117
(1.00) 		0.68
(1.00) 		0.732
(1.00) 		0.0198
(1.00) 		0.393
(1.00) 		0.22
(1.00)
20p loss 84 (9%) 873 0.165
(1.00) 		0.204
(1.00) 		0.468
(1.00) 		0.116
(1.00) 		0.635
(1.00) 		0.407
(1.00) 		0.603
(1.00) 		0.0328
(1.00) 		0.315
(1.00) 		0.455
(1.00)
20q loss 48 (5%) 909 0.192
(1.00) 		0.117
(1.00) 		0.106
(1.00) 		0.0359
(1.00) 		1
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.0249
(1.00) 		0.334
(1.00) 		0.623
(1.00)
21q loss 160 (17%) 797 0.754
(1.00) 		0.442
(1.00) 		0.0297
(1.00) 		0.466
(1.00) 		0.0234
(1.00) 		0.354
(1.00) 		0.384
(1.00) 		0.0957
(1.00) 		0.343
(1.00) 		0.659
(1.00)
22q loss 424 (44%) 533 0.135
(1.00) 		0.638
(1.00) 		0.834
(1.00) 		0.527
(1.00) 		0.377
(1.00) 		0.67
(1.00) 		0.352
(1.00) 		0.00575
(1.00) 		0.00164
(1.00) 		0.23
(1.00)
xq loss 160 (17%) 797 0.531
(1.00) 		0.111
(1.00) 		0.391
(1.00) 		0.0426
(1.00) 		0.764
(1.00) 		0.14
(1.00) 		0.226
(1.00) 		0.109
(1.00) 		0.704
(1.00) 		0.0889
(1.00)
'2p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000156 (Chi-square test), Q value = 0.12

Table S1.  Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
2P GAIN MUTATED 1 95 5 1 0 0 5
2P GAIN WILD-TYPE 0 615 149 4 28 14 39

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'3q gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.63e-05 (Chi-square test), Q value = 0.013

Table S2.  Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
3Q GAIN MUTATED 0 163 8 3 5 1 9
3Q GAIN WILD-TYPE 1 547 146 2 23 13 35

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6p gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000163 (Chi-square test), Q value = 0.13

Table S3.  Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
6P GAIN MUTATED 0 147 15 4 2 1 10
6P GAIN WILD-TYPE 1 563 139 1 26 13 34

Figure S3.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6q gain' versus 'HISTOLOGICAL.TYPE'

P value = 0.000229 (Chi-square test), Q value = 0.18

Table S4.  Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
6Q GAIN MUTATED 0 103 11 4 3 1 7
6Q GAIN WILD-TYPE 1 607 143 1 25 13 37

Figure S4.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'8q gain' versus 'HISTOLOGICAL.TYPE'

P value = 7.48e-06 (Chi-square test), Q value = 0.0059

Table S5.  Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
8Q GAIN MUTATED 1 377 46 4 13 4 25
8Q GAIN WILD-TYPE 0 333 108 1 15 10 19

Figure S5.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20p gain' versus 'HISTOLOGICAL.TYPE'

P value = 1.18e-06 (Chi-square test), Q value = 0.00094

Table S6.  Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
20P GAIN MUTATED 0 309 32 1 8 1 13
20P GAIN WILD-TYPE 1 401 122 4 20 13 31

Figure S6.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 8.53e-08 (Chi-square test), Q value = 6.8e-05

Table S7.  Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
20Q GAIN MUTATED 0 336 35 1 8 1 15
20Q GAIN WILD-TYPE 1 374 119 4 20 13 29

Figure S7.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'1p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.21e-06 (Chi-square test), Q value = 0.0049

Table S8.  Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE TIS STAGE X
ALL 77 73 9 9 321 217 2 135 27 54 15 1 16
1P LOSS MUTATED 9 9 1 3 72 40 1 41 16 19 6 0 4
1P LOSS WILD-TYPE 68 64 8 6 249 177 1 94 11 35 9 1 12

Figure S8.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1p loss' versus 'PATHOLOGY.T.STAGE'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.0087

Table S9.  Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
1P LOSS MUTATED 40 134 27 20
1P LOSS WILD-TYPE 208 422 87 16

Figure S9.  Get High-res Image Gene #41: '1p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.68e-06 (Chi-square test), Q value = 0.0045

Table S10.  Gene #47: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
4P LOSS MUTATED 1 259 25 2 6 0 15
4P LOSS WILD-TYPE 0 451 129 3 22 14 29

Figure S10.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'4q loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.36e-05 (Chi-square test), Q value = 0.066

Table S11.  Gene #48: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
4Q LOSS MUTATED 0 231 22 1 6 0 15
4Q LOSS WILD-TYPE 1 479 132 4 22 14 29

Figure S11.  Get High-res Image Gene #48: '4q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.18e-06 (Chi-square test), Q value = 0.0033

Table S12.  Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
5P LOSS MUTATED 0 112 2 3 5 0 6
5P LOSS WILD-TYPE 1 598 152 2 23 14 38

Figure S12.  Get High-res Image Gene #49: '5p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.62e-10 (Chi-square test), Q value = 2.1e-07

Table S13.  Gene #50: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
5Q LOSS MUTATED 1 183 3 3 4 0 8
5Q LOSS WILD-TYPE 0 527 151 2 24 14 36

Figure S13.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'6q loss' versus 'AGE'

P value = 0.000292 (t-test), Q value = 0.23

Table S14.  Gene #52: '6q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 954 58.6 (13.2)
6Q LOSS MUTATED 244 55.9 (13.4)
6Q LOSS WILD-TYPE 710 59.5 (13.0)

Figure S14.  Get High-res Image Gene #52: '6q loss' versus Clinical Feature #2: 'AGE'

'8p loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.19e-05 (Chi-square test), Q value = 0.033

Table S15.  Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
8P LOSS MUTATED 1 294 32 2 7 2 17
8P LOSS WILD-TYPE 0 416 122 3 21 12 27

Figure S15.  Get High-res Image Gene #55: '8p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'PATHOLOGY.T.STAGE'

P value = 0.000108 (Fisher's exact test), Q value = 0.085

Table S16.  Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 248 556 114 36
9P LOSS MUTATED 52 186 29 18
9P LOSS WILD-TYPE 196 370 85 18

Figure S16.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 6.68e-06 (Chi-square test), Q value = 0.0053

Table S17.  Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
9P LOSS MUTATED 0 243 19 3 8 3 9
9P LOSS WILD-TYPE 1 467 135 2 20 11 35

Figure S17.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.45e-11 (Chi-square test), Q value = 3.6e-08

Table S18.  Gene #69: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
16Q LOSS MUTATED 0 371 120 2 18 1 14
16Q LOSS WILD-TYPE 1 339 34 3 10 13 30

Figure S18.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18p loss' versus 'Time to Death'

P value = 8.24e-06 (logrank test), Q value = 0.0065

Table S19.  Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 920 110 0.0 - 234.2 (21.6)
18P LOSS MUTATED 270 48 0.0 - 189.0 (20.8)
18P LOSS WILD-TYPE 650 62 0.0 - 234.2 (22.5)

Figure S19.  Get High-res Image Gene #72: '18p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'HISTOLOGICAL.TYPE'

P value = 7.1e-06 (Chi-square test), Q value = 0.0056

Table S20.  Gene #74: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
19P LOSS MUTATED 0 151 5 2 2 3 5
19P LOSS WILD-TYPE 1 559 149 3 26 11 39

Figure S20.  Get High-res Image Gene #74: '19p loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'19q loss' versus 'HISTOLOGICAL.TYPE'

P value = 5.12e-05 (Chi-square test), Q value = 0.04

Table S21.  Gene #75: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 1 710 154 5 28 14 44
19Q LOSS MUTATED 0 128 4 2 2 3 4
19Q LOSS WILD-TYPE 1 582 150 3 26 11 40

Figure S21.  Get High-res Image Gene #75: '19q loss' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = BRCA-TP.merged_data.txt

  • Number of patients = 957

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 10

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle