Correlation between copy number variations of arm-level result and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1GB222B
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1GB222B
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 results and 10 clinical features across 885 patients, 8 significant findings detected with Q value < 0.25.

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

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

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

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

  • 9p loss cnv correlated to 'HISTOLOGICAL.TYPE'.

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

  • 20q 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 results and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 8 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Chi-square test t-test t-test Chi-square test
16q loss 0 (0%) 505 0.0199
(1.00) 		0.000184
(0.131) 		1
(1.00) 		4.53e-06
(0.00325) 		0.474
(1.00) 		0.692
(1.00) 		0.55
(1.00) 		0.0366
(1.00) 		0.958
(1.00)
8q gain 0 (0%) 516 0.833
(1.00) 		0.05
(1.00) 		0.502
(1.00) 		2.31e-06
(0.00166) 		0.0666
(1.00) 		0.243
(1.00) 		0.18
(1.00) 		0.843
(1.00) 		0.519
(1.00)
20q gain 0 (0%) 611 0.108
(1.00) 		0.762
(1.00) 		0.145
(1.00) 		6.21e-06
(0.00445) 		0.609
(1.00) 		0.148
(1.00) 		0.346
(1.00) 		0.0237
(1.00) 		0.178
(1.00)
4p loss 0 (0%) 700 0.418
(1.00) 		0.216
(1.00) 		1
(1.00) 		8.39e-05
(0.06) 		0.246
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.599
(1.00) 		0.454
(1.00)
5q loss 0 (0%) 763 0.53
(1.00) 		0.0884
(1.00) 		0.62
(1.00) 		3.71e-05
(0.0266) 		0.495
(1.00) 		0.893
(1.00) 		0.16
(1.00) 		0.101
(1.00) 		0.0719
(1.00)
9p loss 0 (0%) 699 0.0114
(1.00) 		0.667
(1.00) 		0.407
(1.00) 		0.000212
(0.151) 		0.562
(1.00) 		0.175
(1.00) 		0.165
(1.00) 		0.749
(1.00) 		0.107
(1.00)
20q loss 0 (0%) 858 0.543
(1.00) 		0.84
(1.00) 		1
(1.00) 		2.65e-06
(0.00191) 		0.649
(1.00) 		0.378
(1.00) 		0.399
(1.00) 		0.761
(1.00) 		0.835
(1.00)
1p gain 0 (0%) 791 0.318
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.371
(1.00) 		0.0401
(1.00) 		0.737
(1.00) 		0.648
(1.00) 		0.642
(1.00) 		0.219
(1.00)
1q gain 0 (0%) 412 0.088
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.0319
(1.00) 		0.478
(1.00) 		0.723
(1.00) 		0.858
(1.00) 		0.381
(1.00) 		0.387
(1.00)
2p gain 0 (0%) 839 0.85
(1.00) 		0.68
(1.00) 		1
(1.00) 		0.0317
(1.00) 		0.29
(1.00) 		0.216
(1.00) 		0.806
(1.00) 		0.356
(1.00) 		0.493
(1.00)
2q gain 0 (0%) 863 0.899
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.401
(1.00) 		0.023
(1.00) 		0.174
(1.00) 		0.499
(1.00) 		0.236
(1.00) 		0.704
(1.00)
3p gain 0 (0%) 828 0.548
(1.00) 		0.0758
(1.00) 		1
(1.00) 		0.0649
(1.00) 		1
(1.00) 		0.294
(1.00) 		0.445
(1.00) 		0.315
(1.00) 		0.0866
(1.00)
3q gain 0 (0%) 786 0.171
(1.00) 		0.609
(1.00) 		0.608
(1.00) 		0.0009
(0.637) 		0.901
(1.00) 		0.31
(1.00) 		0.42
(1.00) 		0.137
(1.00) 		0.22
(1.00)
4p gain 0 (0%) 856 0.0582
(1.00) 		0.498
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.509
(1.00) 		0.151
(1.00) 		0.782
(1.00) 		0.863
(1.00) 		0.00123
(0.867)
4q gain 0 (0%) 858 0.0211
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.302
(1.00) 		1
(1.00) 		0.166
(1.00) 		0.735
(1.00) 		0.699
(1.00) 		0.0019
(1.00)
5p gain 0 (0%) 719 0.108
(1.00) 		0.132
(1.00) 		0.679
(1.00) 		0.111
(1.00) 		0.158
(1.00) 		0.307
(1.00) 		0.153
(1.00) 		0.497
(1.00) 		0.836
(1.00)
5q gain 0 (0%) 783 0.347
(1.00) 		0.00583
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.268
(1.00) 		0.388
(1.00) 		0.701
(1.00) 		0.837
(1.00) 		0.908
(1.00)
6p gain 0 (0%) 786 0.816
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.138
(1.00) 		0.0125
(1.00) 		0.45
(1.00) 		0.878
(1.00) 		0.779
(1.00) 		0.54
(1.00)
6q gain 0 (0%) 825 0.266
(1.00) 		0.0886
(1.00) 		0.47
(1.00) 		0.212
(1.00) 		0.639
(1.00) 		0.42
(1.00) 		0.441
(1.00) 		0.796
(1.00) 		0.795
(1.00)
7p gain 0 (0%) 731 0.798
(1.00) 		0.141
(1.00) 		0.0104
(1.00) 		0.00429
(1.00) 		0.00915
(1.00) 		0.358
(1.00) 		0.344
(1.00) 		0.394
(1.00) 		0.896
(1.00)
7q gain 0 (0%) 772 0.503
(1.00) 		0.752
(1.00) 		0.0191
(1.00) 		0.0613
(1.00) 		0.0129
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.48
(1.00) 		0.961
(1.00)
8p gain 0 (0%) 720 0.547
(1.00) 		0.0767
(1.00) 		0.677
(1.00) 		0.112
(1.00) 		0.92
(1.00) 		0.4
(1.00) 		0.658
(1.00) 		0.724
(1.00) 		0.578
(1.00)
9p gain 0 (0%) 820 0.563
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.178
(1.00) 		0.598
(1.00) 		0.118
(1.00) 		0.279
(1.00) 		0.151
(1.00)
9q gain 0 (0%) 831 0.383
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.101
(1.00) 		0.816
(1.00) 		0.33
(1.00) 		0.427
(1.00) 		0.702
(1.00)
10p gain 0 (0%) 778 0.691
(1.00) 		0.758
(1.00) 		0.61
(1.00) 		0.0136
(1.00) 		0.227
(1.00) 		0.0834
(1.00) 		0.584
(1.00) 		0.122
(1.00) 		0.00447
(1.00)
10q gain 0 (0%) 839 0.92
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.693
(1.00) 		0.159
(1.00) 		0.845
(1.00) 		0.917
(1.00) 		0.526
(1.00) 		0.00857
(1.00)
11p gain 0 (0%) 821 0.663
(1.00) 		0.893
(1.00) 		0.493
(1.00) 		0.02
(1.00) 		0.648
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.278
(1.00) 		0.0313
(1.00)
11q gain 0 (0%) 840 0.0393
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.72
(1.00) 		0.841
(1.00) 		0.182
(1.00) 		0.802
(1.00) 		0.0307
(1.00)
12p gain 0 (0%) 771 0.691
(1.00) 		0.492
(1.00) 		0.0197
(1.00) 		0.561
(1.00) 		0.196
(1.00) 		0.205
(1.00) 		0.632
(1.00) 		0.81
(1.00) 		0.845
(1.00)
12q gain 0 (0%) 800 0.133
(1.00) 		0.218
(1.00) 		0.0469
(1.00) 		0.0605
(1.00) 		0.229
(1.00) 		0.024
(1.00) 		0.807
(1.00) 		0.851
(1.00) 		0.947
(1.00)
13q gain 0 (0%) 839 0.778
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.301
(1.00) 		0.724
(1.00) 		0.0491
(1.00) 		0.853
(1.00) 		0.0694
(1.00) 		0.969
(1.00)
14q gain 0 (0%) 809 0.288
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.026
(1.00) 		0.325
(1.00) 		1
(1.00) 		0.301
(1.00) 		0.0324
(1.00) 		0.0552
(1.00)
15q gain 0 (0%) 841 0.697
(1.00) 		0.6
(1.00) 		0.369
(1.00) 		0.0963
(1.00) 		0.145
(1.00) 		0.431
(1.00) 		0.928
(1.00) 		0.605
(1.00) 		0.896
(1.00)
16p gain 0 (0%) 636 0.604
(1.00) 		0.0177
(1.00) 		1
(1.00) 		0.0478
(1.00) 		0.337
(1.00) 		0.595
(1.00) 		0.122
(1.00) 		0.0918
(1.00) 		0.126
(1.00)
16q gain 0 (0%) 831 0.135
(1.00) 		0.913
(1.00) 		0.434
(1.00) 		0.0778
(1.00) 		0.623
(1.00) 		0.0836
(1.00) 		0.605
(1.00) 		0.976
(1.00) 		0.0262
(1.00)
17p gain 0 (0%) 838 0.656
(1.00) 		0.6
(1.00) 		0.00942
(1.00) 		0.000455
(0.324) 		1
(1.00) 		0.6
(1.00) 		0.865
(1.00) 		0.352
(1.00) 		0.693
(1.00)
17q gain 0 (0%) 763 0.737
(1.00) 		0.759
(1.00) 		0.0249
(1.00) 		0.123
(1.00) 		0.909
(1.00) 		0.134
(1.00) 		0.685
(1.00) 		0.597
(1.00) 		0.493
(1.00)
18p gain 0 (0%) 800 0.0703
(1.00) 		0.075
(1.00) 		0.599
(1.00) 		0.0536
(1.00) 		0.0454
(1.00) 		0.372
(1.00) 		0.613
(1.00) 		0.619
(1.00) 		0.378
(1.00)
18q gain 0 (0%) 810 0.142
(1.00) 		0.687
(1.00) 		0.551
(1.00) 		0.159
(1.00) 		0.159
(1.00) 		0.297
(1.00) 		0.869
(1.00) 		0.864
(1.00) 		0.252
(1.00)
19p gain 0 (0%) 818 0.0486
(1.00) 		0.25
(1.00) 		0.144
(1.00) 		0.872
(1.00) 		0.1
(1.00) 		0.146
(1.00) 		0.869
(1.00) 		0.396
(1.00) 		0.617
(1.00)
19q gain 0 (0%) 799 0.00573
(1.00) 		0.528
(1.00) 		0.215
(1.00) 		0.877
(1.00) 		0.355
(1.00) 		0.0118
(1.00) 		0.112
(1.00) 		0.351
(1.00) 		0.772
(1.00)
20p gain 0 (0%) 648 0.0312
(1.00) 		0.201
(1.00) 		0.0631
(1.00) 		0.000494
(0.351) 		0.722
(1.00) 		0.0683
(1.00) 		0.282
(1.00) 		0.0318
(1.00) 		0.325
(1.00)
21q gain 0 (0%) 785 0.0366
(1.00) 		0.039
(1.00) 		1
(1.00) 		0.0134
(1.00) 		0.0176
(1.00) 		0.481
(1.00) 		0.132
(1.00) 		0.0279
(1.00) 		0.195
(1.00)
22q gain 0 (0%) 844 0.772
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.578
(1.00) 		0.907
(1.00) 		0.163
(1.00) 		0.684
(1.00) 		0.0822
(1.00)
Xq gain 0 (0%) 864 0.104
(1.00) 		0.143
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.306
(1.00) 		0.0991
(1.00) 		0.0153
(1.00) 		0.697
(1.00) 		0.18
(1.00)
1p loss 0 (0%) 768 0.0598
(1.00) 		0.0227
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.416
(1.00) 		0.243
(1.00) 		0.0233
(1.00) 		0.05
(1.00) 		0.00888
(1.00)
1q loss 0 (0%) 863 0.592
(1.00) 		0.716
(1.00) 		1
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.934
(1.00) 		0.622
(1.00) 		0.99
(1.00)
2p loss 0 (0%) 813 0.734
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.572
(1.00) 		0.194
(1.00) 		0.228
(1.00) 		0.559
(1.00) 		0.387
(1.00) 		0.33
(1.00)
2q loss 0 (0%) 799 0.555
(1.00) 		0.575
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.235
(1.00) 		0.161
(1.00) 		0.493
(1.00) 		0.351
(1.00) 		0.125
(1.00)
3p loss 0 (0%) 799 0.0643
(1.00) 		0.046
(1.00) 		1
(1.00) 		0.0959
(1.00) 		0.355
(1.00) 		0.429
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.716
(1.00)
3q loss 0 (0%) 842 0.442
(1.00) 		0.08
(1.00) 		1
(1.00) 		0.116
(1.00) 		0.0439
(1.00) 		0.222
(1.00) 		0.854
(1.00) 		0.687
(1.00) 		0.765
(1.00)
4q loss 0 (0%) 730 0.44
(1.00) 		0.901
(1.00) 		0.373
(1.00) 		0.00281
(1.00) 		0.468
(1.00) 		0.938
(1.00) 		0.132
(1.00) 		0.909
(1.00) 		0.433
(1.00)
5p loss 0 (0%) 818 0.23
(1.00) 		0.0883
(1.00) 		0.509
(1.00) 		0.00267
(1.00) 		0.882
(1.00) 		0.802
(1.00) 		0.15
(1.00) 		0.661
(1.00) 		0.124
(1.00)
6p loss 0 (0%) 777 0.208
(1.00) 		0.12
(1.00) 		0.61
(1.00) 		0.527
(1.00) 		0.336
(1.00) 		0.0755
(1.00) 		0.76
(1.00) 		0.878
(1.00) 		0.982
(1.00)
6q loss 0 (0%) 718 0.985
(1.00) 		0.00357
(1.00) 		0.221
(1.00) 		0.436
(1.00) 		0.109
(1.00) 		0.434
(1.00) 		0.958
(1.00) 		0.718
(1.00) 		0.944
(1.00)
7p loss 0 (0%) 836 0.557
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.355
(1.00) 		0.3
(1.00) 		0.67
(1.00) 		0.798
(1.00) 		0.452
(1.00) 		0.152
(1.00)
7q loss 0 (0%) 822 0.114
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.543
(1.00) 		0.177
(1.00) 		0.96
(1.00) 		0.265
(1.00) 		0.19
(1.00)
8p loss 0 (0%) 619 0.00509
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.00803
(1.00) 		0.797
(1.00) 		0.45
(1.00) 		0.408
(1.00) 		0.266
(1.00) 		0.966
(1.00)
8q loss 0 (0%) 839 0.00498
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.595
(1.00) 		0.245
(1.00) 		0.559
(1.00) 		0.454
(1.00) 		0.617
(1.00)
9q loss 0 (0%) 743 0.0118
(1.00) 		0.606
(1.00) 		0.163
(1.00) 		0.0246
(1.00) 		0.831
(1.00) 		0.423
(1.00) 		0.24
(1.00) 		0.917
(1.00) 		0.355
(1.00)
10p loss 0 (0%) 810 0.0797
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.672
(1.00) 		0.0205
(1.00) 		0.701
(1.00) 		0.414
(1.00) 		0.249
(1.00)
10q loss 0 (0%) 776 0.00364
(1.00) 		0.743
(1.00) 		0.611
(1.00) 		0.041
(1.00) 		0.549
(1.00) 		0.178
(1.00) 		0.345
(1.00) 		0.656
(1.00) 		0.735
(1.00)
11p loss 0 (0%) 744 0.0262
(1.00) 		0.591
(1.00) 		0.369
(1.00) 		0.69
(1.00) 		0.592
(1.00) 		1
(1.00) 		0.222
(1.00) 		0.0431
(1.00) 		0.311
(1.00)
11q loss 0 (0%) 659 0.332
(1.00) 		0.78
(1.00) 		0.0523
(1.00) 		0.158
(1.00) 		0.472
(1.00) 		0.615
(1.00) 		0.291
(1.00) 		0.169
(1.00) 		0.123
(1.00)
12p loss 0 (0%) 818 0.108
(1.00) 		0.651
(1.00) 		0.509
(1.00) 		0.0891
(1.00) 		0.457
(1.00) 		0.717
(1.00) 		0.261
(1.00) 		0.981
(1.00) 		0.41
(1.00)
12q loss 0 (0%) 832 0.248
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.243
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.699
(1.00) 		0.17
(1.00)
13q loss 0 (0%) 621 0.086
(1.00) 		0.162
(1.00) 		0.463
(1.00) 		0.00115
(0.813) 		1
(1.00) 		0.635
(1.00) 		0.248
(1.00) 		0.703
(1.00) 		0.845
(1.00)
14q loss 0 (0%) 755 0.00782
(1.00) 		0.281
(1.00) 		0.371
(1.00) 		0.0131
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.101
(1.00) 		0.81
(1.00) 		0.709
(1.00)
15q loss 0 (0%) 725 0.14
(1.00) 		0.185
(1.00) 		0.376
(1.00) 		0.0454
(1.00) 		0.474
(1.00) 		0.389
(1.00) 		0.487
(1.00) 		0.517
(1.00) 		0.415
(1.00)
16p loss 0 (0%) 831 0.916
(1.00) 		0.586
(1.00) 		0.0999
(1.00) 		0.359
(1.00) 		0.87
(1.00) 		0.561
(1.00) 		0.712
(1.00) 		0.366
(1.00) 		0.681
(1.00)
17p loss 0 (0%) 519 0.398
(1.00) 		0.0273
(1.00) 		0.743
(1.00) 		0.11
(1.00) 		0.0934
(1.00) 		0.57
(1.00) 		0.542
(1.00) 		0.373
(1.00) 		0.227
(1.00)
17q loss 0 (0%) 743 0.679
(1.00) 		0.302
(1.00) 		0.369
(1.00) 		0.0237
(1.00) 		0.915
(1.00) 		0.952
(1.00) 		0.209
(1.00) 		0.221
(1.00) 		0.904
(1.00)
18p loss 0 (0%) 713 0.00405
(1.00) 		0.00127
(0.892) 		1
(1.00) 		0.253
(1.00) 		0.428
(1.00) 		0.71
(1.00) 		0.555
(1.00) 		0.295
(1.00) 		0.314
(1.00)
18q loss 0 (0%) 714 0.0296
(1.00) 		0.00112
(0.789) 		1
(1.00) 		0.275
(1.00) 		0.485
(1.00) 		0.36
(1.00) 		0.476
(1.00) 		0.168
(1.00) 		0.0267
(1.00)
19p loss 0 (0%) 817 0.497
(1.00) 		0.306
(1.00) 		1
(1.00) 		0.0807
(1.00) 		0.238
(1.00) 		0.279
(1.00) 		0.126
(1.00) 		0.582
(1.00) 		0.235
(1.00)
19q loss 0 (0%) 833 0.672
(1.00) 		0.959
(1.00) 		1
(1.00) 		0.271
(1.00) 		0.739
(1.00) 		0.747
(1.00) 		0.0809
(1.00) 		0.835
(1.00) 		0.0351
(1.00)
20p loss 0 (0%) 834 0.00265
(1.00) 		0.913
(1.00) 		0.415
(1.00) 		0.000379
(0.27) 		0.739
(1.00) 		0.283
(1.00) 		0.127
(1.00) 		0.315
(1.00) 		0.419
(1.00)
21q loss 0 (0%) 799 0.914
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.211
(1.00) 		0.79
(1.00) 		0.161
(1.00) 		0.603
(1.00) 		0.329
(1.00) 		0.00643
(1.00)
22q loss 0 (0%) 590 0.0946
(1.00) 		0.788
(1.00) 		0.169
(1.00) 		0.0229
(1.00) 		0.0947
(1.00) 		0.849
(1.00) 		0.0607
(1.00) 		0.0867
(1.00) 		0.769
(1.00)
Xq loss 0 (0%) 855 0.0443
(1.00) 		0.543
(1.00) 		0.0345
(1.00) 		0.585
(1.00) 		0.513
(1.00) 		0.314
(1.00) 		0.992
(1.00) 		0.373
(1.00) 		0.000685
(0.486)
'8q gain' versus 'HISTOLOGICAL.TYPE'

P value = 2.31e-06 (Chi-square test), Q value = 0.0017

Table S1.  Gene #16: '8q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
8Q GAIN CNV 314 22 2 10 3 18
8Q GAIN WILD-TYPE 368 99 2 16 8 23

Figure S1.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'20q gain' versus 'HISTOLOGICAL.TYPE'

P value = 6.21e-06 (Chi-square test), Q value = 0.0045

Table S2.  Gene #37: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
20Q GAIN CNV 243 19 0 6 1 5
20Q GAIN WILD-TYPE 439 102 4 20 10 36

Figure S2.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'4p loss' versus 'HISTOLOGICAL.TYPE'

P value = 8.39e-05 (Chi-square test), Q value = 0.06

Table S3.  Gene #47: '4p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
4P LOSS CNV 162 7 1 3 0 12
4P LOSS WILD-TYPE 520 114 3 23 11 29

Figure S3.  Get High-res Image Gene #47: '4p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'5q loss' versus 'HISTOLOGICAL.TYPE'

P value = 3.71e-05 (Chi-square test), Q value = 0.027

Table S4.  Gene #50: '5q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
5Q LOSS CNV 114 0 1 4 0 3
5Q LOSS WILD-TYPE 568 121 3 22 11 38

Figure S4.  Get High-res Image Gene #50: '5q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'9p loss' versus 'HISTOLOGICAL.TYPE'

P value = 0.000212 (Chi-square test), Q value = 0.15

Table S5.  Gene #57: '9p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
9P LOSS CNV 167 8 0 5 1 5
9P LOSS WILD-TYPE 515 113 4 21 10 36

Figure S5.  Get High-res Image Gene #57: '9p loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'16q loss' versus 'AGE'

P value = 0.000184 (t-test), Q value = 0.13

Table S6.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 884 58.6 (13.2)
16Q LOSS CNV 380 60.5 (13.0)
16Q LOSS WILD-TYPE 504 57.1 (13.2)

Figure S6.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'HISTOLOGICAL.TYPE'

P value = 4.53e-06 (Chi-square test), Q value = 0.0033

Table S7.  Gene #69: '16q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
16Q LOSS CNV 278 77 1 12 1 11
16Q LOSS WILD-TYPE 404 44 3 14 10 30

Figure S7.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'20q loss' versus 'HISTOLOGICAL.TYPE'

P value = 2.65e-06 (Chi-square test), Q value = 0.0019

Table S8.  Gene #77: '20q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients INFILTRATING DUCTAL CARCINOMA INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY) MUCINOUS CARCINOMA OTHER SPECIFY
ALL 682 121 4 26 11 41
20Q LOSS CNV 23 1 2 1 0 0
20Q LOSS WILD-TYPE 659 120 2 25 11 41

Figure S8.  Get High-res Image Gene #77: '20q loss' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = broad_values_by_arm.mutsig.cluster.txt

  • Clinical data file = BRCA-TP.clin.merged.picked.txt

  • Number of patients = 885

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 10

  • Exclude genes 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

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

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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)
[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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)
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