Correlation between copy number variation genes (focal) and selected clinical features
Breast Invasive Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1BK19C2
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 variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BK19C2
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 66 arm-level results and 10 clinical features across 885 patients, 26 significant findings detected with Q value < 0.25.

  • Amp Peak 5(3q26.32) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 6(4q13.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 8(6p23) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 12(8q24.21) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 13(10p15.1) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 15(11p13) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 23(15q26.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 25(17q23.1) cnv correlated to 'GENDER'.

  • Amp Peak 27(19q12) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Amp Peak 29(20q13.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 4(3p21.31) cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • Del Peak 5(4p16.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 6(4q35.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 7(5q11.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 8(5q21.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 11(6q27) cnv correlated to 'AGE'.

  • Del Peak 14(8p23.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 16(9p21.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 26(13q14.2) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 27(14q24.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 28(15q13.1) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 29(16q24.3) cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.

  • Del Peak 33(19p13.3) cnv correlated to 'HISTOLOGICAL.TYPE'.

  • Del Peak 34(19q13.32) 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 66 arm-level results and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 26 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
Del Peak 4(3p21 31) 0 (0%) 605 0.0077
(1.00) 		6.67e-05
(0.0384) 		0.475
(1.00) 		4.84e-05
(0.028) 		0.736
(1.00) 		0.461
(1.00) 		0.729
(1.00) 		0.859
(1.00) 		0.433
(1.00)
Del Peak 29(16q24 3) 0 (0%) 316 0.106
(1.00) 		0.00038
(0.217) 		1
(1.00) 		1.68e-15
(9.98e-13) 		0.622
(1.00) 		0.186
(1.00) 		0.402
(1.00) 		0.671
(1.00) 		0.256
(1.00)
Amp Peak 5(3q26 32) 0 (0%) 605 0.533
(1.00) 		0.271
(1.00) 		0.727
(1.00) 		1.16e-10
(6.84e-08) 		0.0752
(1.00) 		0.123
(1.00) 		0.822
(1.00) 		0.737
(1.00) 		0.607
(1.00)
Amp Peak 6(4q13 3) 0 (0%) 745 0.00151
(0.845) 		0.328
(1.00) 		1
(1.00) 		5.92e-05
(0.0342) 		0.747
(1.00) 		0.717
(1.00) 		0.296
(1.00) 		0.333
(1.00) 		0.292
(1.00)
Amp Peak 8(6p23) 0 (0%) 652 0.759
(1.00) 		0.156
(1.00) 		0.459
(1.00) 		9.93e-06
(0.00577) 		0.211
(1.00) 		0.597
(1.00) 		0.197
(1.00) 		0.242
(1.00) 		0.628
(1.00)
Amp Peak 12(8q24 21) 0 (0%) 316 0.0711
(1.00) 		0.0721
(1.00) 		0.503
(1.00) 		9.59e-13
(5.69e-10) 		0.367
(1.00) 		0.21
(1.00) 		0.0959
(1.00) 		0.191
(1.00) 		0.398
(1.00)
Amp Peak 13(10p15 1) 0 (0%) 632 0.171
(1.00) 		0.888
(1.00) 		0.0668
(1.00) 		4.05e-07
(0.000236) 		0.296
(1.00) 		0.926
(1.00) 		0.88
(1.00) 		0.88
(1.00) 		0.521
(1.00)
Amp Peak 15(11p13) 0 (0%) 700 0.554
(1.00) 		0.602
(1.00) 		1
(1.00) 		0.000433
(0.247) 		0.384
(1.00) 		0.457
(1.00) 		0.465
(1.00) 		0.792
(1.00) 		0.349
(1.00)
Amp Peak 23(15q26 3) 0 (0%) 723 0.25
(1.00) 		0.0196
(1.00) 		0.0639
(1.00) 		0.00041
(0.234) 		0.761
(1.00) 		0.104
(1.00) 		0.688
(1.00) 		0.559
(1.00) 		0.716
(1.00)
Amp Peak 25(17q23 1) 0 (0%) 517 0.0563
(1.00) 		0.48
(1.00) 		0.000351
(0.201) 		0.00387
(1.00) 		0.425
(1.00) 		0.0368
(1.00) 		0.535
(1.00) 		0.602
(1.00) 		0.0717
(1.00)
Amp Peak 27(19q12) 0 (0%) 663 0.332
(1.00) 		0.362
(1.00) 		0.699
(1.00) 		0.000181
(0.104) 		0.0842
(1.00) 		0.0487
(1.00) 		0.0993
(1.00) 		0.46
(1.00) 		0.554
(1.00)
Amp Peak 29(20q13 2) 0 (0%) 429 0.576
(1.00) 		0.176
(1.00) 		0.179
(1.00) 		1.68e-11
(9.93e-09) 		0.0334
(1.00) 		0.283
(1.00) 		0.277
(1.00) 		0.435
(1.00) 		0.37
(1.00)
Del Peak 5(4p16 3) 0 (0%) 611 0.733
(1.00) 		0.0648
(1.00) 		0.729
(1.00) 		1.42e-06
(0.00083) 		0.609
(1.00) 		0.834
(1.00) 		0.839
(1.00) 		0.848
(1.00) 		0.412
(1.00)
Del Peak 6(4q35 2) 0 (0%) 608 0.0847
(1.00) 		0.933
(1.00) 		0.287
(1.00) 		1.46e-05
(0.00844) 		0.932
(1.00) 		0.0796
(1.00) 		0.475
(1.00) 		0.869
(1.00) 		0.864
(1.00)
Del Peak 7(5q11 2) 0 (0%) 657 0.198
(1.00) 		0.0038
(1.00) 		0.46
(1.00) 		2.26e-10
(1.33e-07) 		0.53
(1.00) 		0.197
(1.00) 		0.607
(1.00) 		0.231
(1.00) 		0.476
(1.00)
Del Peak 8(5q21 3) 0 (0%) 667 0.31
(1.00) 		0.0108
(1.00) 		0.123
(1.00) 		2.71e-12
(1.6e-09) 		0.927
(1.00) 		0.447
(1.00) 		0.298
(1.00) 		0.000491
(0.279) 		0.267
(1.00)
Del Peak 11(6q27) 0 (0%) 583 0.113
(1.00) 		1.6e-05
(0.00925) 		0.178
(1.00) 		0.32
(1.00) 		0.561
(1.00) 		0.0802
(1.00) 		0.305
(1.00) 		0.349
(1.00) 		0.516
(1.00)
Del Peak 14(8p23 2) 0 (0%) 418 0.235
(1.00) 		0.613
(1.00) 		0.512
(1.00) 		7.95e-08
(4.65e-05) 		0.237
(1.00) 		0.693
(1.00) 		0.178
(1.00) 		0.761
(1.00) 		0.98
(1.00)
Del Peak 16(9p21 3) 0 (0%) 583 0.0222
(1.00) 		0.968
(1.00) 		0.287
(1.00) 		3.13e-08
(1.84e-05) 		0.245
(1.00) 		0.134
(1.00) 		0.000852
(0.479) 		0.144
(1.00) 		0.00584
(1.00)
Del Peak 26(13q14 2) 0 (0%) 477 0.0668
(1.00) 		0.674
(1.00) 		0.74
(1.00) 		0.000113
(0.065) 		0.752
(1.00) 		0.976
(1.00) 		0.489
(1.00) 		0.118
(1.00) 		0.963
(1.00)
Del Peak 27(14q24 3) 0 (0%) 604 0.151
(1.00) 		0.637
(1.00) 		1
(1.00) 		6.51e-09
(3.83e-06) 		0.352
(1.00) 		0.711
(1.00) 		0.124
(1.00) 		0.682
(1.00) 		0.846
(1.00)
Del Peak 28(15q13 1) 0 (0%) 578 0.353
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.000267
(0.153) 		0.564
(1.00) 		0.204
(1.00) 		0.214
(1.00) 		0.842
(1.00) 		0.451
(1.00)
Del Peak 33(19p13 3) 0 (0%) 583 0.343
(1.00) 		0.0154
(1.00) 		0.726
(1.00) 		5.43e-08
(3.18e-05) 		0.868
(1.00) 		0.604
(1.00) 		0.762
(1.00) 		0.152
(1.00) 		0.937
(1.00)
Del Peak 34(19q13 32) 0 (0%) 708 0.745
(1.00) 		0.642
(1.00) 		0.696
(1.00) 		8.07e-06
(0.0047) 		0.491
(1.00) 		0.293
(1.00) 		0.216
(1.00) 		0.905
(1.00) 		0.392
(1.00)
Amp Peak 1(1p22 3) 0 (0%) 691 0.982
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.776
(1.00) 		0.519
(1.00) 		0.348
(1.00) 		0.119
(1.00) 		0.641
(1.00)
Amp Peak 2(1q21 3) 0 (0%) 252 0.713
(1.00) 		0.543
(1.00) 		0.284
(1.00) 		0.809
(1.00) 		0.163
(1.00) 		0.448
(1.00) 		0.567
(1.00) 		0.672
(1.00) 		0.362
(1.00)
Amp Peak 3(1q44) 0 (0%) 253 0.00866
(1.00) 		0.798
(1.00) 		0.72
(1.00) 		0.154
(1.00) 		0.339
(1.00) 		0.551
(1.00) 		0.308
(1.00) 		0.748
(1.00) 		0.522
(1.00)
Amp Peak 4(3p26 1) 0 (0%) 700 0.0038
(1.00) 		0.785
(1.00) 		0.217
(1.00) 		0.00449
(1.00) 		0.772
(1.00) 		0.0281
(1.00) 		0.121
(1.00) 		0.627
(1.00) 		0.128
(1.00)
Amp Peak 7(5p15 33) 0 (0%) 567 0.143
(1.00) 		0.237
(1.00) 		1
(1.00) 		0.0602
(1.00) 		0.163
(1.00) 		0.267
(1.00) 		0.0183
(1.00) 		0.574
(1.00) 		0.758
(1.00)
Amp Peak 9(6q21) 0 (0%) 721 0.0119
(1.00) 		0.421
(1.00) 		1
(1.00) 		0.000586
(0.332) 		0.612
(1.00) 		0.868
(1.00) 		0.726
(1.00) 		0.791
(1.00) 		0.251
(1.00)
Amp Peak 10(8p11 23) 0 (0%) 547 0.0163
(1.00) 		0.11
(1.00) 		0.165
(1.00) 		0.556
(1.00) 		0.419
(1.00) 		0.0789
(1.00) 		0.199
(1.00) 		0.0101
(1.00) 		0.0352
(1.00)
Amp Peak 11(8p11 21) 0 (0%) 543 0.696
(1.00) 		0.0617
(1.00) 		0.165
(1.00) 		0.071
(1.00) 		0.0238
(1.00) 		0.644
(1.00) 		0.634
(1.00) 		0.503
(1.00) 		0.468
(1.00)
Amp Peak 14(10q22 3) 0 (0%) 754 0.0996
(1.00) 		0.59
(1.00) 		1
(1.00) 		0.0113
(1.00) 		0.438
(1.00) 		0.104
(1.00) 		0.617
(1.00) 		0.666
(1.00) 		0.318
(1.00)
Amp Peak 16(11q13 3) 0 (0%) 549 0.248
(1.00) 		0.33
(1.00) 		0.312
(1.00) 		0.506
(1.00) 		0.571
(1.00) 		0.427
(1.00) 		0.625
(1.00) 		0.412
(1.00) 		0.378
(1.00)
Amp Peak 17(11q14 1) 0 (0%) 658 0.16
(1.00) 		0.33
(1.00) 		0.701
(1.00) 		0.0232
(1.00) 		0.857
(1.00) 		0.224
(1.00) 		0.72
(1.00) 		0.403
(1.00) 		0.246
(1.00)
Amp Peak 18(12p13 33) 0 (0%) 656 0.728
(1.00) 		0.42
(1.00) 		0.46
(1.00) 		0.00238
(1.00) 		0.0724
(1.00) 		0.635
(1.00) 		0.323
(1.00) 		0.904
(1.00) 		0.349
(1.00)
Amp Peak 19(12q15) 0 (0%) 655 0.0289
(1.00) 		0.396
(1.00) 		0.0118
(1.00) 		0.0471
(1.00) 		0.928
(1.00) 		0.266
(1.00) 		0.0769
(1.00) 		0.228
(1.00) 		0.215
(1.00)
Amp Peak 20(13q12 3) 0 (0%) 759 0.0281
(1.00) 		0.209
(1.00) 		0.624
(1.00) 		0.013
(1.00) 		0.43
(1.00) 		0.14
(1.00) 		0.13
(1.00) 		0.605
(1.00) 		0.592
(1.00)
Amp Peak 21(13q34) 0 (0%) 733 0.9
(1.00) 		0.0661
(1.00) 		0.371
(1.00) 		0.0209
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.205
(1.00) 		0.784
(1.00) 		0.179
(1.00)
Amp Peak 22(14q21 1) 0 (0%) 704 0.357
(1.00) 		0.0239
(1.00) 		0.695
(1.00) 		0.165
(1.00) 		0.697
(1.00) 		0.539
(1.00) 		0.0158
(1.00) 		0.0546
(1.00) 		0.0415
(1.00)
Amp Peak 24(17q12) 0 (0%) 597 0.146
(1.00) 		0.997
(1.00) 		0.000759
(0.428) 		0.0078
(1.00) 		1
(1.00) 		0.358
(1.00) 		0.0556
(1.00) 		0.44
(1.00) 		0.367
(1.00)
Amp Peak 26(19p13 12) 0 (0%) 701 0.704
(1.00) 		0.806
(1.00) 		0.0954
(1.00) 		0.119
(1.00) 		0.0254
(1.00) 		0.168
(1.00) 		0.351
(1.00) 		0.653
(1.00) 		0.788
(1.00)
Amp Peak 28(19q13 42) 0 (0%) 653 0.543
(1.00) 		0.148
(1.00) 		0.252
(1.00) 		0.131
(1.00) 		0.326
(1.00) 		0.0476
(1.00) 		0.585
(1.00) 		0.819
(1.00) 		0.981
(1.00)
Del Peak 1(1p36 13) 0 (0%) 512 0.179
(1.00) 		0.627
(1.00) 		0.178
(1.00) 		0.0268
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.057
(1.00) 		0.0309
(1.00) 		0.0215
(1.00)
Del Peak 2(1p22 1) 0 (0%) 584 0.00252
(1.00) 		0.284
(1.00) 		0.499
(1.00) 		0.0809
(1.00) 		0.185
(1.00) 		0.592
(1.00) 		0.0103
(1.00) 		0.0251
(1.00) 		0.0195
(1.00)
Del Peak 3(2q37 3) 0 (0%) 627 0.954
(1.00) 		0.82
(1.00) 		0.46
(1.00) 		0.00211
(1.00) 		0.387
(1.00) 		0.569
(1.00) 		0.378
(1.00) 		0.601
(1.00) 		0.533
(1.00)
Del Peak 9(6p25 3) 0 (0%) 719 0.524
(1.00) 		0.0322
(1.00) 		0.679
(1.00) 		0.543
(1.00) 		0.158
(1.00) 		0.603
(1.00) 		0.544
(1.00) 		0.0286
(1.00) 		0.683
(1.00)
Del Peak 10(6q15) 0 (0%) 593 0.348
(1.00) 		0.057
(1.00) 		0.726
(1.00) 		0.611
(1.00) 		0.933
(1.00) 		0.551
(1.00) 		0.495
(1.00) 		0.115
(1.00) 		0.258
(1.00)
Del Peak 12(7p22 3) 0 (0%) 767 0.102
(1.00) 		0.238
(1.00) 		0.616
(1.00) 		0.000723
(0.408) 		0.728
(1.00) 		0.718
(1.00) 		0.797
(1.00) 		0.0255
(1.00) 		0.0715
(1.00)
Del Peak 13(7q36 1) 0 (0%) 710 0.0125
(1.00) 		0.932
(1.00) 		0.694
(1.00) 		0.0213
(1.00) 		0.374
(1.00) 		0.357
(1.00) 		0.831
(1.00) 		0.774
(1.00) 		0.908
(1.00)
Del Peak 15(8p11 21) 0 (0%) 714 0.0139
(1.00) 		0.307
(1.00) 		0.219
(1.00) 		0.0163
(1.00) 		0.765
(1.00) 		0.47
(1.00) 		0.0738
(1.00) 		0.264
(1.00) 		0.647
(1.00)
Del Peak 17(9q21 11) 0 (0%) 643 0.456
(1.00) 		0.991
(1.00) 		0.267
(1.00) 		0.000901
(0.506) 		0.724
(1.00) 		0.331
(1.00) 		0.296
(1.00) 		0.662
(1.00) 		0.355
(1.00)
Del Peak 18(10q23 31) 0 (0%) 631 0.808
(1.00) 		0.485
(1.00) 		0.0666
(1.00) 		0.00478
(1.00) 		0.487
(1.00) 		0.712
(1.00) 		0.399
(1.00) 		0.956
(1.00) 		0.722
(1.00)
Del Peak 19(10q26 3) 0 (0%) 627 0.0341
(1.00) 		0.814
(1.00) 		0.46
(1.00) 		0.0006
(0.34) 		0.729
(1.00) 		0.569
(1.00) 		0.237
(1.00) 		0.605
(1.00) 		0.559
(1.00)
Del Peak 20(11p15 5) 0 (0%) 628 0.316
(1.00) 		0.745
(1.00) 		0.293
(1.00) 		0.0224
(1.00) 		1
(1.00) 		0.968
(1.00) 		0.686
(1.00) 		0.143
(1.00) 		0.462
(1.00)
Del Peak 21(11q13 1) 0 (0%) 694 0.469
(1.00) 		0.96
(1.00) 		0.415
(1.00) 		0.674
(1.00) 		0.504
(1.00) 		0.659
(1.00) 		0.209
(1.00) 		0.746
(1.00) 		0.488
(1.00)
Del Peak 22(11q23 2) 0 (0%) 445 0.455
(1.00) 		0.31
(1.00) 		0.106
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.124
(1.00) 		0.61
(1.00) 		0.184
(1.00)
Del Peak 23(11q25) 0 (0%) 473 0.287
(1.00) 		0.0155
(1.00) 		0.0902
(1.00) 		0.0347
(1.00) 		0.528
(1.00) 		0.63
(1.00) 		0.385
(1.00) 		0.631
(1.00) 		0.09
(1.00)
Del Peak 24(12p13 1) 0 (0%) 731 0.641
(1.00) 		0.548
(1.00) 		0.66
(1.00) 		0.0031
(1.00) 		0.468
(1.00) 		0.0293
(1.00) 		0.403
(1.00) 		0.552
(1.00) 		0.282
(1.00)
Del Peak 25(12q24 21) 0 (0%) 718 0.58
(1.00) 		0.157
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.615
(1.00) 		0.831
(1.00) 		0.165
(1.00) 		0.0754
(1.00) 		0.595
(1.00)
Del Peak 30(17p12) 0 (0%) 349 0.177
(1.00) 		0.00279
(1.00) 		0.495
(1.00) 		0.00972
(1.00) 		0.629
(1.00) 		0.95
(1.00) 		0.0287
(1.00) 		0.326
(1.00) 		0.738
(1.00)
Del Peak 31(17q21 31) 0 (0%) 577 0.483
(1.00) 		0.000759
(0.428) 		0.174
(1.00) 		0.00105
(0.586) 		0.934
(1.00) 		0.159
(1.00) 		0.0435
(1.00) 		0.137
(1.00) 		0.343
(1.00)
Del Peak 32(18q23) 0 (0%) 600 0.0143
(1.00) 		0.521
(1.00) 		1
(1.00) 		0.012
(1.00) 		0.206
(1.00) 		0.54
(1.00) 		0.0518
(1.00) 		0.179
(1.00) 		0.197
(1.00)
Del Peak 35(20p13) 0 (0%) 754 0.0111
(1.00) 		0.283
(1.00) 		0.629
(1.00) 		0.00277
(1.00) 		0.658
(1.00) 		0.549
(1.00) 		0.97
(1.00) 		0.828
(1.00) 		0.502
(1.00)
Del Peak 36(21q11 2) 0 (0%) 706 0.306
(1.00) 		0.427
(1.00) 		0.217
(1.00) 		0.013
(1.00) 		0.281
(1.00) 		0.552
(1.00) 		0.24
(1.00) 		0.811
(1.00) 		0.0188
(1.00)
Del Peak 37(22q11 1) 0 (0%) 515 0.311
(1.00) 		0.805
(1.00) 		0.318
(1.00) 		0.00696
(1.00) 		0.0253
(1.00) 		0.34
(1.00) 		0.347
(1.00) 		0.537
(1.00) 		0.841
(1.00)
'Amp Peak 5(3q26.32)' versus 'HISTOLOGICAL.TYPE'

P value = 1.16e-10 (Chi-square test), Q value = 6.8e-08

Table S1.  Gene #5: 'Amp Peak 5(3q26.32)' 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
AMP PEAK 5(3Q26.32) CNV 251 9 4 5 1 10
AMP PEAK 5(3Q26.32) WILD-TYPE 431 112 0 21 10 31

Figure S1.  Get High-res Image Gene #5: 'Amp Peak 5(3q26.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 6(4q13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 5.92e-05 (Chi-square test), Q value = 0.034

Table S2.  Gene #6: 'Amp Peak 6(4q13.3)' 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
AMP PEAK 6(4Q13.3) CNV 127 3 2 1 1 6
AMP PEAK 6(4Q13.3) WILD-TYPE 555 118 2 25 10 35

Figure S2.  Get High-res Image Gene #6: 'Amp Peak 6(4q13.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 8(6p23)' versus 'HISTOLOGICAL.TYPE'

P value = 9.93e-06 (Chi-square test), Q value = 0.0058

Table S3.  Gene #8: 'Amp Peak 8(6p23)' 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
AMP PEAK 8(6P23) CNV 203 11 3 4 1 11
AMP PEAK 8(6P23) WILD-TYPE 479 110 1 22 10 30

Figure S3.  Get High-res Image Gene #8: 'Amp Peak 8(6p23)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(8q24.21)' versus 'HISTOLOGICAL.TYPE'

P value = 9.59e-13 (Chi-square test), Q value = 5.7e-10

Table S4.  Gene #12: 'Amp Peak 12(8q24.21)' 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
AMP PEAK 12(8Q24.21) CNV 481 42 4 15 4 23
AMP PEAK 12(8Q24.21) WILD-TYPE 201 79 0 11 7 18

Figure S4.  Get High-res Image Gene #12: 'Amp Peak 12(8q24.21)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 13(10p15.1)' versus 'HISTOLOGICAL.TYPE'

P value = 4.05e-07 (Chi-square test), Q value = 0.00024

Table S5.  Gene #13: 'Amp Peak 13(10p15.1)' 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
AMP PEAK 13(10P15.1) CNV 225 13 3 4 0 8
AMP PEAK 13(10P15.1) WILD-TYPE 457 108 1 22 11 33

Figure S5.  Get High-res Image Gene #13: 'Amp Peak 13(10p15.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(11p13)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000433 (Chi-square test), Q value = 0.25

Table S6.  Gene #15: 'Amp Peak 15(11p13)' 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
AMP PEAK 15(11P13) CNV 163 10 2 1 2 7
AMP PEAK 15(11P13) WILD-TYPE 519 111 2 25 9 34

Figure S6.  Get High-res Image Gene #15: 'Amp Peak 15(11p13)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(15q26.3)' versus 'HISTOLOGICAL.TYPE'

P value = 0.00041 (Chi-square test), Q value = 0.23

Table S7.  Gene #23: 'Amp Peak 23(15q26.3)' 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
AMP PEAK 23(15Q26.3) CNV 146 5 1 4 1 5
AMP PEAK 23(15Q26.3) WILD-TYPE 536 116 3 22 10 36

Figure S7.  Get High-res Image Gene #23: 'Amp Peak 23(15q26.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(17q23.1)' versus 'GENDER'

P value = 0.000351 (Fisher's exact test), Q value = 0.2

Table S8.  Gene #25: 'Amp Peak 25(17q23.1)' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 876 9
AMP PEAK 25(17Q23.1) CNV 359 9
AMP PEAK 25(17Q23.1) WILD-TYPE 517 0

Figure S8.  Get High-res Image Gene #25: 'Amp Peak 25(17q23.1)' versus Clinical Feature #3: 'GENDER'

'Amp Peak 27(19q12)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000181 (Chi-square test), Q value = 0.1

Table S9.  Gene #27: 'Amp Peak 27(19q12)' 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
AMP PEAK 27(19Q12) CNV 187 16 4 5 2 8
AMP PEAK 27(19Q12) WILD-TYPE 495 105 0 21 9 33

Figure S9.  Get High-res Image Gene #27: 'Amp Peak 27(19q12)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 29(20q13.2)' versus 'HISTOLOGICAL.TYPE'

P value = 1.68e-11 (Chi-square test), Q value = 9.9e-09

Table S10.  Gene #29: 'Amp Peak 29(20q13.2)' 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
AMP PEAK 29(20Q13.2) CNV 397 30 1 10 1 17
AMP PEAK 29(20Q13.2) WILD-TYPE 285 91 3 16 10 24

Figure S10.  Get High-res Image Gene #29: 'Amp Peak 29(20q13.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 4(3p21.31)' versus 'AGE'

P value = 6.67e-05 (t-test), Q value = 0.038

Table S11.  Gene #33: 'Del Peak 4(3p21.31)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 884 58.6 (13.2)
DEL PEAK 4(3P21.31) CNV 280 55.9 (13.3)
DEL PEAK 4(3P21.31) WILD-TYPE 604 59.8 (13.0)

Figure S11.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Clinical Feature #2: 'AGE'

'Del Peak 4(3p21.31)' versus 'HISTOLOGICAL.TYPE'

P value = 4.84e-05 (Chi-square test), Q value = 0.028

Table S12.  Gene #33: 'Del Peak 4(3p21.31)' 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
DEL PEAK 4(3P21.31) CNV 245 20 1 5 0 9
DEL PEAK 4(3P21.31) WILD-TYPE 437 101 3 21 11 32

Figure S12.  Get High-res Image Gene #33: 'Del Peak 4(3p21.31)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 5(4p16.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.42e-06 (Chi-square test), Q value = 0.00083

Table S13.  Gene #34: 'Del Peak 5(4p16.3)' 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
DEL PEAK 5(4P16.3) CNV 239 15 3 5 0 12
DEL PEAK 5(4P16.3) WILD-TYPE 443 106 1 21 11 29

Figure S13.  Get High-res Image Gene #34: 'Del Peak 5(4p16.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 6(4q35.2)' versus 'HISTOLOGICAL.TYPE'

P value = 1.46e-05 (Chi-square test), Q value = 0.0084

Table S14.  Gene #35: 'Del Peak 6(4q35.2)' 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
DEL PEAK 6(4Q35.2) CNV 243 19 2 4 0 9
DEL PEAK 6(4Q35.2) WILD-TYPE 439 102 2 22 11 32

Figure S14.  Get High-res Image Gene #35: 'Del Peak 6(4q35.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 7(5q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 2.26e-10 (Chi-square test), Q value = 1.3e-07

Table S15.  Gene #36: 'Del Peak 7(5q11.2)' 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
DEL PEAK 7(5Q11.2) CNV 206 4 4 4 1 9
DEL PEAK 7(5Q11.2) WILD-TYPE 476 117 0 22 10 32

Figure S15.  Get High-res Image Gene #36: 'Del Peak 7(5q11.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 8(5q21.3)' versus 'HISTOLOGICAL.TYPE'

P value = 2.71e-12 (Chi-square test), Q value = 1.6e-09

Table S16.  Gene #37: 'Del Peak 8(5q21.3)' 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
DEL PEAK 8(5Q21.3) CNV 201 1 4 4 0 8
DEL PEAK 8(5Q21.3) WILD-TYPE 481 120 0 22 11 33

Figure S16.  Get High-res Image Gene #37: 'Del Peak 8(5q21.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 11(6q27)' versus 'AGE'

P value = 1.6e-05 (t-test), Q value = 0.0093

Table S17.  Gene #40: 'Del Peak 11(6q27)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 884 58.6 (13.2)
DEL PEAK 11(6Q27) CNV 302 55.9 (12.7)
DEL PEAK 11(6Q27) WILD-TYPE 582 59.9 (13.3)

Figure S17.  Get High-res Image Gene #40: 'Del Peak 11(6q27)' versus Clinical Feature #2: 'AGE'

'Del Peak 14(8p23.2)' versus 'HISTOLOGICAL.TYPE'

P value = 7.95e-08 (Chi-square test), Q value = 4.7e-05

Table S18.  Gene #43: 'Del Peak 14(8p23.2)' 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
DEL PEAK 14(8P23.2) CNV 395 35 2 9 3 23
DEL PEAK 14(8P23.2) WILD-TYPE 287 86 2 17 8 18

Figure S18.  Get High-res Image Gene #43: 'Del Peak 14(8p23.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 16(9p21.3)' versus 'HISTOLOGICAL.TYPE'

P value = 3.13e-08 (Chi-square test), Q value = 1.8e-05

Table S19.  Gene #45: 'Del Peak 16(9p21.3)' 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
DEL PEAK 16(9P21.3) CNV 265 13 3 10 2 9
DEL PEAK 16(9P21.3) WILD-TYPE 417 108 1 16 9 32

Figure S19.  Get High-res Image Gene #45: 'Del Peak 16(9p21.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 26(13q14.2)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000113 (Chi-square test), Q value = 0.065

Table S20.  Gene #55: 'Del Peak 26(13q14.2)' 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
DEL PEAK 26(13Q14.2) CNV 342 40 3 10 1 12
DEL PEAK 26(13Q14.2) WILD-TYPE 340 81 1 16 10 29

Figure S20.  Get High-res Image Gene #55: 'Del Peak 26(13q14.2)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 27(14q24.3)' versus 'HISTOLOGICAL.TYPE'

P value = 6.51e-09 (Chi-square test), Q value = 3.8e-06

Table S21.  Gene #56: 'Del Peak 27(14q24.3)' 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
DEL PEAK 27(14Q24.3) CNV 253 16 3 2 1 6
DEL PEAK 27(14Q24.3) WILD-TYPE 429 105 1 24 10 35

Figure S21.  Get High-res Image Gene #56: 'Del Peak 27(14q24.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 28(15q13.1)' versus 'HISTOLOGICAL.TYPE'

P value = 0.000267 (Chi-square test), Q value = 0.15

Table S22.  Gene #57: 'Del Peak 28(15q13.1)' 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
DEL PEAK 28(15Q13.1) CNV 261 25 3 8 1 9
DEL PEAK 28(15Q13.1) WILD-TYPE 421 96 1 18 10 32

Figure S22.  Get High-res Image Gene #57: 'Del Peak 28(15q13.1)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 29(16q24.3)' versus 'AGE'

P value = 0.00038 (t-test), Q value = 0.22

Table S23.  Gene #58: 'Del Peak 29(16q24.3)' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 884 58.6 (13.2)
DEL PEAK 29(16Q24.3) CNV 568 59.7 (13.1)
DEL PEAK 29(16Q24.3) WILD-TYPE 316 56.4 (13.2)

Figure S23.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Clinical Feature #2: 'AGE'

'Del Peak 29(16q24.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.68e-15 (Chi-square test), Q value = 1e-12

Table S24.  Gene #58: 'Del Peak 29(16q24.3)' 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
DEL PEAK 29(16Q24.3) CNV 419 114 2 18 1 15
DEL PEAK 29(16Q24.3) WILD-TYPE 263 7 2 8 10 26

Figure S24.  Get High-res Image Gene #58: 'Del Peak 29(16q24.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 33(19p13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 5.43e-08 (Chi-square test), Q value = 3.2e-05

Table S25.  Gene #62: 'Del Peak 33(19p13.3)' 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
DEL PEAK 33(19P13.3) CNV 266 13 3 7 3 10
DEL PEAK 33(19P13.3) WILD-TYPE 416 108 1 19 8 31

Figure S25.  Get High-res Image Gene #62: 'Del Peak 33(19p13.3)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 34(19q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 8.07e-06 (Chi-square test), Q value = 0.0047

Table S26.  Gene #63: 'Del Peak 34(19q13.32)' 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
DEL PEAK 34(19Q13.32) CNV 161 5 2 4 2 3
DEL PEAK 34(19Q13.32) WILD-TYPE 521 116 2 22 9 38

Figure S26.  Get High-res Image Gene #63: 'Del Peak 34(19q13.32)' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 885

  • Number of significantly arm-level cnvs = 66

  • 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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