Correlation between copy number variation genes (focal) and selected clinical features
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.

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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