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 subtypes identified by 63 different clustering approaches and 9 clinical features across 846 patients, 3 significant findings detected with Q value < 0.25.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 2(1q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q44) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 4(3p26.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 5(3q26.32) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 6(4q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 7(6p23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 8(6q21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 9(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 10(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 11(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 12(10p15.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 13(10q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 14(11p13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 15(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 16(11q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 17(12p13.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 18(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 19(13q12.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 20(13q34) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 21(14q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 22(15q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 23(17p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 24(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 25(17q23.1) mutation analysis'. These subtypes correlate to 'GENDER'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 26(19q12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 27(19q13.42) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 28(20q13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 2(1p21.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 3(2q37.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 4(3p14.3) mutation analysis'. These subtypes correlate to 'AGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 5(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 6(4q35.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 7(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 8(5q21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 9(6p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 10(6q15) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 11(6q27) mutation analysis'. These subtypes correlate to 'AGE'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 12(7p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 13(7q36.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 14(8p23.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 15(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 16(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 17(9q21.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 18(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 19(10q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 20(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 21(11q23.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 22(12p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 23(12q24.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 24(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 25(14q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 26(15q13.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 27(16q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 28(17p12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 29(17q21.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 30(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 31(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 32(19q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 33(20p13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 34(21q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 35(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between subtypes identified by 63 different clustering approaches and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER RADIATIONS
RADIATION
REGIMENINDICATION 		DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
Statistical Tests logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test t-test t-test Chi-square test
Amp Peak 1(1p22 3) 0.982
(1.00) 		0.834
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.542
(1.00) 		0.429
(1.00) 		0.103
(1.00) 		0.613
(1.00)
Amp Peak 2(1q21 3) 0.807
(1.00) 		0.509
(1.00) 		0.278
(1.00) 		0.153
(1.00) 		0.447
(1.00) 		0.474
(1.00) 		0.654
(1.00) 		0.375
(1.00)
Amp Peak 3(1q44) 0.0119
(1.00) 		0.872
(1.00) 		0.717
(1.00) 		0.372
(1.00) 		0.34
(1.00) 		0.216
(1.00) 		0.671
(1.00) 		0.453
(1.00)
Amp Peak 4(3p26 1) 0.00479
(1.00) 		0.501
(1.00) 		0.217
(1.00) 		0.844
(1.00) 		0.103
(1.00) 		0.108
(1.00) 		0.569
(1.00) 		0.172
(1.00)
Amp Peak 5(3q26 32) 0.629
(1.00) 		0.304
(1.00) 		0.726
(1.00) 		0.123
(1.00) 		0.329
(1.00) 		0.864
(1.00) 		0.703
(1.00) 		0.626
(1.00)
Amp Peak 6(4q13 3) 0.00223
(1.00) 		0.382
(1.00) 		1
(1.00) 		1
(1.00) 		0.849
(1.00) 		0.281
(1.00) 		0.358
(1.00) 		0.135
(1.00)
Amp Peak 7(6p23) 0.633
(1.00) 		0.345
(1.00) 		0.458
(1.00) 		0.362
(1.00) 		0.919
(1.00) 		0.122
(1.00) 		0.258
(1.00) 		0.595
(1.00)
Amp Peak 8(6q21) 0.0119
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.956
(1.00) 		0.806
(1.00) 		0.942
(1.00) 		0.391
(1.00)
Amp Peak 9(8p11 23) 0.0277
(1.00) 		0.0884
(1.00) 		0.165
(1.00) 		0.804
(1.00) 		0.0945
(1.00) 		0.143
(1.00) 		0.0108
(1.00) 		0.015
(1.00)
Amp Peak 10(8p11 21) 0.84
(1.00) 		0.0401
(1.00) 		0.165
(1.00) 		0.0395
(1.00) 		0.868
(1.00) 		0.539
(1.00) 		0.573
(1.00) 		0.316
(1.00)
Amp Peak 11(8q24 21) 0.118
(1.00) 		0.146
(1.00) 		0.507
(1.00) 		0.613
(1.00) 		0.535
(1.00) 		0.0554
(1.00) 		0.18
(1.00) 		0.496
(1.00)
Amp Peak 12(10p15 1) 0.204
(1.00) 		0.653
(1.00) 		0.0667
(1.00) 		0.248
(1.00) 		0.902
(1.00) 		0.824
(1.00) 		0.987
(1.00) 		0.412
(1.00)
Amp Peak 13(10q22 3) 0.116
(1.00) 		0.94
(1.00) 		1
(1.00) 		0.576
(1.00) 		0.218
(1.00) 		0.692
(1.00) 		0.66
(1.00) 		0.343
(1.00)
Amp Peak 14(11p13) 0.462
(1.00) 		0.791
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.616
(1.00) 		0.544
(1.00) 		0.794
(1.00) 		0.196
(1.00)
Amp Peak 15(11q13 3) 0.241
(1.00) 		0.297
(1.00) 		0.32
(1.00) 		0.68
(1.00) 		0.692
(1.00) 		0.729
(1.00) 		0.433
(1.00) 		0.225
(1.00)
Amp Peak 16(11q14 1) 0.0937
(1.00) 		0.347
(1.00) 		0.698
(1.00) 		0.781
(1.00) 		0.466
(1.00) 		0.712
(1.00) 		0.334
(1.00) 		0.394
(1.00)
Amp Peak 17(12p13 33) 0.802
(1.00) 		0.627
(1.00) 		0.459
(1.00) 		0.0815
(1.00) 		0.71
(1.00) 		0.279
(1.00) 		0.785
(1.00) 		0.171
(1.00)
Amp Peak 18(12q15) 0.0388
(1.00) 		0.253
(1.00) 		0.0127
(1.00) 		0.927
(1.00) 		0.41
(1.00) 		0.0544
(1.00) 		0.196
(1.00) 		0.0911
(1.00)
Amp Peak 19(13q12 3) 0.0366
(1.00) 		0.28
(1.00) 		0.627
(1.00) 		0.364
(1.00) 		0.257
(1.00) 		0.185
(1.00) 		0.628
(1.00) 		0.581
(1.00)
Amp Peak 20(13q34) 0.977
(1.00) 		0.104
(1.00) 		0.372
(1.00) 		0.916
(1.00) 		0.557
(1.00) 		0.126
(1.00) 		0.818
(1.00) 		0.238
(1.00)
Amp Peak 21(14q21 1) 0.429
(1.00) 		0.0405
(1.00) 		0.694
(1.00) 		0.843
(1.00) 		0.585
(1.00) 		0.00868
(1.00) 		0.0535
(1.00) 		0.0634
(1.00)
Amp Peak 22(15q26 3) 0.214
(1.00) 		0.0404
(1.00) 		0.0654
(1.00) 		0.679
(1.00) 		0.134
(1.00) 		0.701
(1.00) 		0.633
(1.00) 		0.811
(1.00)
Amp Peak 23(17p11 2) 0.133
(1.00) 		0.135
(1.00) 		0.118
(1.00) 		0.0628
(1.00) 		0.692
(1.00) 		0.333
(1.00) 		0.488
(1.00) 		0.27
(1.00)
Amp Peak 24(17q12) 0.175
(1.00) 		0.658
(1.00) 		0.000793
(0.395) 		0.932
(1.00) 		0.724
(1.00) 		0.0306
(1.00) 		0.355
(1.00) 		0.232
(1.00)
Amp Peak 25(17q23 1) 0.0678
(1.00) 		0.871
(1.00) 		0.000343
(0.172) 		0.29
(1.00) 		0.183
(1.00) 		0.435
(1.00) 		0.753
(1.00) 		0.0669
(1.00)
Amp Peak 26(19q12) 0.4
(1.00) 		0.467
(1.00) 		0.701
(1.00) 		0.168
(1.00) 		0.176
(1.00) 		0.0905
(1.00) 		0.45
(1.00) 		0.683
(1.00)
Amp Peak 27(19q13 42) 0.643
(1.00) 		0.266
(1.00) 		0.258
(1.00) 		0.526
(1.00) 		0.179
(1.00) 		0.572
(1.00) 		0.84
(1.00) 		0.932
(1.00)
Amp Peak 28(20q13 2) 0.69
(1.00) 		0.32
(1.00) 		0.181
(1.00) 		0.0442
(1.00) 		0.554
(1.00) 		0.257
(1.00) 		0.35
(1.00) 		0.329
(1.00)
Del Peak 1(1p36 13) 0.208
(1.00) 		0.415
(1.00) 		0.18
(1.00) 		0.808
(1.00) 		0.373
(1.00) 		0.0863
(1.00) 		0.0328
(1.00) 		0.0292
(1.00)
Del Peak 2(1p21 2) 0.0629
(1.00) 		0.132
(1.00) 		1
(1.00) 		0.554
(1.00) 		0.779
(1.00) 		0.016
(1.00) 		0.0302
(1.00) 		0.0302
(1.00)
Del Peak 3(2q37 3) 0.887
(1.00) 		0.992
(1.00) 		0.294
(1.00) 		0.539
(1.00) 		0.56
(1.00) 		0.452
(1.00) 		0.495
(1.00) 		0.605
(1.00)
Del Peak 4(3p14 3) 0.0195
(1.00) 		9.72e-05
(0.049) 		1
(1.00) 		0.665
(1.00) 		0.437
(1.00) 		0.733
(1.00) 		0.946
(1.00) 		0.818
(1.00)
Del Peak 5(4p16 3) 0.833
(1.00) 		0.0841
(1.00) 		0.727
(1.00) 		0.665
(1.00) 		0.94
(1.00) 		0.86
(1.00) 		0.829
(1.00) 		0.487
(1.00)
Del Peak 6(4q35 2) 0.112
(1.00) 		0.717
(1.00) 		0.286
(1.00) 		0.863
(1.00) 		0.214
(1.00) 		0.448
(1.00) 		0.941
(1.00) 		0.932
(1.00)
Del Peak 7(5q11 2) 0.232
(1.00) 		0.00986
(1.00) 		0.459
(1.00) 		0.521
(1.00) 		0.313
(1.00) 		0.599
(1.00) 		0.269
(1.00) 		0.526
(1.00)
Del Peak 8(5q21 3) 0.349
(1.00) 		0.0173
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.273
(1.00) 		0.000681
(0.34) 		0.319
(1.00)
Del Peak 9(6p25 3) 0.566
(1.00) 		0.0621
(1.00) 		0.68
(1.00) 		0.258
(1.00) 		0.832
(1.00) 		0.397
(1.00) 		0.0282
(1.00) 		0.602
(1.00)
Del Peak 10(6q15) 0.405
(1.00) 		0.105
(1.00) 		0.725
(1.00) 		0.865
(1.00) 		0.538
(1.00) 		0.462
(1.00) 		0.132
(1.00) 		0.278
(1.00)
Del Peak 11(6q27) 0.132
(1.00) 		0.000124
(0.0623) 		0.177
(1.00) 		0.498
(1.00) 		0.254
(1.00) 		0.354
(1.00) 		0.345
(1.00) 		0.599
(1.00)
Del Peak 12(7p22 3) 0.107
(1.00) 		0.339
(1.00) 		0.617
(1.00) 		0.725
(1.00) 		0.857
(1.00) 		0.793
(1.00) 		0.0331
(1.00) 		0.0272
(1.00)
Del Peak 13(7q36 1) 0.0181
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.275
(1.00) 		0.861
(1.00) 		0.782
(1.00) 		0.923
(1.00)
Del Peak 14(8p23 2) 0.276
(1.00) 		0.646
(1.00) 		0.513
(1.00) 		0.198
(1.00) 		0.729
(1.00) 		0.12
(1.00) 		0.718
(1.00) 		0.991
(1.00)
Del Peak 15(8p11 21) 0.0141
(1.00) 		0.367
(1.00) 		0.219
(1.00) 		0.684
(1.00) 		0.501
(1.00) 		0.0254
(1.00) 		0.21
(1.00) 		0.544
(1.00)
Del Peak 16(9p21 3) 0.0298
(1.00) 		0.607
(1.00) 		0.288
(1.00) 		0.128
(1.00) 		0.16
(1.00) 		0.000571
(0.285) 		0.108
(1.00) 		0.00122
(0.606)
Del Peak 17(9q21 11) 0.506
(1.00) 		0.929
(1.00) 		0.268
(1.00) 		0.857
(1.00) 		0.333
(1.00) 		0.381
(1.00) 		0.659
(1.00) 		0.399
(1.00)
Del Peak 18(10q23 31) 0.868
(1.00) 		0.58
(1.00) 		0.0659
(1.00) 		0.48
(1.00) 		0.872
(1.00) 		0.362
(1.00) 		0.858
(1.00) 		0.601
(1.00)
Del Peak 19(10q26 3) 0.0426
(1.00) 		0.834
(1.00) 		0.46
(1.00) 		0.792
(1.00) 		0.586
(1.00) 		0.282
(1.00) 		0.548
(1.00) 		0.562
(1.00)
Del Peak 20(11p15 5) 0.271
(1.00) 		0.797
(1.00) 		0.461
(1.00) 		0.93
(1.00) 		0.979
(1.00) 		0.641
(1.00) 		0.122
(1.00) 		0.673
(1.00)
Del Peak 21(11q23 2) 0.365
(1.00) 		0.346
(1.00) 		0.177
(1.00) 		0.936
(1.00) 		0.24
(1.00) 		0.142
(1.00) 		0.517
(1.00) 		0.257
(1.00)
Del Peak 22(12p13 1) 0.573
(1.00) 		0.623
(1.00) 		0.666
(1.00) 		0.529
(1.00) 		0.0576
(1.00) 		0.395
(1.00) 		0.52
(1.00) 		0.292
(1.00)
Del Peak 23(12q24 31) 0.243
(1.00) 		0.372
(1.00) 		0.372
(1.00) 		0.597
(1.00) 		0.852
(1.00) 		0.359
(1.00) 		0.678
(1.00) 		0.783
(1.00)
Del Peak 24(13q14 2) 0.0658
(1.00) 		0.763
(1.00) 		0.74
(1.00) 		0.573
(1.00) 		0.941
(1.00) 		0.425
(1.00) 		0.154
(1.00) 		0.972
(1.00)
Del Peak 25(14q24 3) 0.174
(1.00) 		0.88
(1.00) 		1
(1.00) 		0.667
(1.00) 		0.74
(1.00) 		0.0848
(1.00) 		0.807
(1.00) 		0.874
(1.00)
Del Peak 26(15q13 1) 0.412
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.736
(1.00) 		0.225
(1.00) 		0.147
(1.00) 		0.803
(1.00) 		0.389
(1.00)
Del Peak 27(16q24 3) 0.115
(1.00) 		0.000886
(0.44) 		1
(1.00) 		0.614
(1.00) 		0.176
(1.00) 		0.268
(1.00) 		0.413
(1.00) 		0.263
(1.00)
Del Peak 28(17p12) 0.147
(1.00) 		0.00382
(1.00) 		0.495
(1.00) 		0.681
(1.00) 		0.908
(1.00) 		0.0151
(1.00) 		0.24
(1.00) 		0.546
(1.00)
Del Peak 29(17q21 31) 0.597
(1.00) 		0.00051
(0.255) 		0.17
(1.00) 		0.737
(1.00) 		0.312
(1.00) 		0.0512
(1.00) 		0.135
(1.00) 		0.232
(1.00)
Del Peak 30(18q23) 0.0228
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.199
(1.00) 		0.511
(1.00) 		0.045
(1.00) 		0.184
(1.00) 		0.206
(1.00)
Del Peak 31(19p13 3) 0.415
(1.00) 		0.0347
(1.00) 		0.726
(1.00) 		0.448
(1.00) 		0.972
(1.00) 		0.654
(1.00) 		0.181
(1.00) 		0.909
(1.00)
Del Peak 32(19q13 32) 0.857
(1.00) 		0.758
(1.00) 		0.694
(1.00) 		0.843
(1.00) 		0.149
(1.00) 		0.174
(1.00) 		0.935
(1.00) 		0.417
(1.00)
Del Peak 33(20p13) 0.0125
(1.00) 		0.469
(1.00) 		0.63
(1.00) 		0.259
(1.00) 		0.707
(1.00) 		0.972
(1.00) 		0.782
(1.00) 		0.25
(1.00)
Del Peak 34(21q11 2) 0.338
(1.00) 		0.485
(1.00) 		0.217
(1.00) 		0.323
(1.00) 		0.452
(1.00) 		0.217
(1.00) 		0.619
(1.00) 		0.0136
(1.00)
Del Peak 35(22q13 32) 0.491
(1.00) 		0.563
(1.00) 		0.525
(1.00) 		0.0524
(1.00) 		0.779
(1.00) 		0.133
(1.00) 		0.848
(1.00) 		0.82
(1.00)
Clustering Approach #1: 'Amp Peak 1(1p22.3) mutation analysis'

Table S1.  Description of clustering approach #1: 'Amp Peak 1(1p22.3) mutation analysis'

Cluster Labels AMP PEAK 1(1P22.3) MUTATED AMP PEAK 1(1P22.3) WILD-TYPE
Number of samples 186 660
Clustering Approach #2: 'Amp Peak 2(1q21.3) mutation analysis'

Table S2.  Description of clustering approach #2: 'Amp Peak 2(1q21.3) mutation analysis'

Cluster Labels AMP PEAK 2(1Q21.3) MUTATED AMP PEAK 2(1Q21.3) WILD-TYPE
Number of samples 608 238
Clustering Approach #3: 'Amp Peak 3(1q44) mutation analysis'

Table S3.  Description of clustering approach #3: 'Amp Peak 3(1q44) mutation analysis'

Cluster Labels AMP PEAK 3(1Q44) MUTATED AMP PEAK 3(1Q44) WILD-TYPE
Number of samples 608 238
Clustering Approach #4: 'Amp Peak 4(3p26.1) mutation analysis'

Table S4.  Description of clustering approach #4: 'Amp Peak 4(3p26.1) mutation analysis'

Cluster Labels AMP PEAK 4(3P26.1) MUTATED AMP PEAK 4(3P26.1) WILD-TYPE
Number of samples 178 668
Clustering Approach #5: 'Amp Peak 5(3q26.32) mutation analysis'

Table S5.  Description of clustering approach #5: 'Amp Peak 5(3q26.32) mutation analysis'

Cluster Labels AMP PEAK 5(3Q26.32) MUTATED AMP PEAK 5(3Q26.32) WILD-TYPE
Number of samples 276 570
Clustering Approach #6: 'Amp Peak 6(4q13.3) mutation analysis'

Table S6.  Description of clustering approach #6: 'Amp Peak 6(4q13.3) mutation analysis'

Cluster Labels AMP PEAK 6(4Q13.3) MUTATED AMP PEAK 6(4Q13.3) WILD-TYPE
Number of samples 138 708
Clustering Approach #7: 'Amp Peak 7(6p23) mutation analysis'

Table S7.  Description of clustering approach #7: 'Amp Peak 7(6p23) mutation analysis'

Cluster Labels AMP PEAK 7(6P23) MUTATED AMP PEAK 7(6P23) WILD-TYPE
Number of samples 223 623
Clustering Approach #8: 'Amp Peak 8(6q21) mutation analysis'

Table S8.  Description of clustering approach #8: 'Amp Peak 8(6q21) mutation analysis'

Cluster Labels AMP PEAK 8(6Q21) MUTATED AMP PEAK 8(6Q21) WILD-TYPE
Number of samples 157 689
Clustering Approach #9: 'Amp Peak 9(8p11.23) mutation analysis'

Table S9.  Description of clustering approach #9: 'Amp Peak 9(8p11.23) mutation analysis'

Cluster Labels AMP PEAK 9(8P11.23) MUTATED AMP PEAK 9(8P11.23) WILD-TYPE
Number of samples 324 522
Clustering Approach #10: 'Amp Peak 10(8p11.21) mutation analysis'

Table S10.  Description of clustering approach #10: 'Amp Peak 10(8p11.21) mutation analysis'

Cluster Labels AMP PEAK 10(8P11.21) MUTATED AMP PEAK 10(8P11.21) WILD-TYPE
Number of samples 329 517
Clustering Approach #11: 'Amp Peak 11(8q24.21) mutation analysis'

Table S11.  Description of clustering approach #11: 'Amp Peak 11(8q24.21) mutation analysis'

Cluster Labels AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE
Number of samples 550 296
Clustering Approach #12: 'Amp Peak 12(10p15.1) mutation analysis'

Table S12.  Description of clustering approach #12: 'Amp Peak 12(10p15.1) mutation analysis'

Cluster Labels AMP PEAK 12(10P15.1) MUTATED AMP PEAK 12(10P15.1) WILD-TYPE
Number of samples 242 604
Clustering Approach #13: 'Amp Peak 13(10q22.3) mutation analysis'

Table S13.  Description of clustering approach #13: 'Amp Peak 13(10q22.3) mutation analysis'

Cluster Labels AMP PEAK 13(10Q22.3) MUTATED AMP PEAK 13(10Q22.3) WILD-TYPE
Number of samples 127 719
Clustering Approach #14: 'Amp Peak 14(11p13) mutation analysis'

Table S14.  Description of clustering approach #14: 'Amp Peak 14(11p13) mutation analysis'

Cluster Labels AMP PEAK 14(11P13) MUTATED AMP PEAK 14(11P13) WILD-TYPE
Number of samples 180 666
Clustering Approach #15: 'Amp Peak 15(11q13.3) mutation analysis'

Table S15.  Description of clustering approach #15: 'Amp Peak 15(11q13.3) mutation analysis'

Cluster Labels AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
Number of samples 328 518
Clustering Approach #16: 'Amp Peak 16(11q14.1) mutation analysis'

Table S16.  Description of clustering approach #16: 'Amp Peak 16(11q14.1) mutation analysis'

Cluster Labels AMP PEAK 16(11Q14.1) MUTATED AMP PEAK 16(11Q14.1) WILD-TYPE
Number of samples 212 634
Clustering Approach #17: 'Amp Peak 17(12p13.33) mutation analysis'

Table S17.  Description of clustering approach #17: 'Amp Peak 17(12p13.33) mutation analysis'

Cluster Labels AMP PEAK 17(12P13.33) MUTATED AMP PEAK 17(12P13.33) WILD-TYPE
Number of samples 220 626
Clustering Approach #18: 'Amp Peak 18(12q15) mutation analysis'

Table S18.  Description of clustering approach #18: 'Amp Peak 18(12q15) mutation analysis'

Cluster Labels AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
Number of samples 223 623
Clustering Approach #19: 'Amp Peak 19(13q12.3) mutation analysis'

Table S19.  Description of clustering approach #19: 'Amp Peak 19(13q12.3) mutation analysis'

Cluster Labels AMP PEAK 19(13Q12.3) MUTATED AMP PEAK 19(13Q12.3) WILD-TYPE
Number of samples 124 722
Clustering Approach #20: 'Amp Peak 20(13q34) mutation analysis'

Table S20.  Description of clustering approach #20: 'Amp Peak 20(13q34) mutation analysis'

Cluster Labels AMP PEAK 20(13Q34) MUTATED AMP PEAK 20(13Q34) WILD-TYPE
Number of samples 147 699
Clustering Approach #21: 'Amp Peak 21(14q21.1) mutation analysis'

Table S21.  Description of clustering approach #21: 'Amp Peak 21(14q21.1) mutation analysis'

Cluster Labels AMP PEAK 21(14Q21.1) MUTATED AMP PEAK 21(14Q21.1) WILD-TYPE
Number of samples 175 671
Clustering Approach #22: 'Amp Peak 22(15q26.3) mutation analysis'

Table S22.  Description of clustering approach #22: 'Amp Peak 22(15q26.3) mutation analysis'

Cluster Labels AMP PEAK 22(15Q26.3) MUTATED AMP PEAK 22(15Q26.3) WILD-TYPE
Number of samples 156 690
Clustering Approach #23: 'Amp Peak 23(17p11.2) mutation analysis'

Table S23.  Description of clustering approach #23: 'Amp Peak 23(17p11.2) mutation analysis'

Cluster Labels AMP PEAK 23(17P11.2) MUTATED AMP PEAK 23(17P11.2) WILD-TYPE
Number of samples 118 728
Clustering Approach #24: 'Amp Peak 24(17q12) mutation analysis'

Table S24.  Description of clustering approach #24: 'Amp Peak 24(17q12) mutation analysis'

Cluster Labels AMP PEAK 24(17Q12) MUTATED AMP PEAK 24(17Q12) WILD-TYPE
Number of samples 277 569
Clustering Approach #25: 'Amp Peak 25(17q23.1) mutation analysis'

Table S25.  Description of clustering approach #25: 'Amp Peak 25(17q23.1) mutation analysis'

Cluster Labels AMP PEAK 25(17Q23.1) MUTATED AMP PEAK 25(17Q23.1) WILD-TYPE
Number of samples 351 495
'Amp Peak 25(17q23.1) mutation analysis' versus 'GENDER'

P value = 0.000343 (Fisher's exact test), Q value = 0.17

Table S26.  Clustering Approach #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 837 9
AMP PEAK 25(17Q23.1) MUTATED 342 9
AMP PEAK 25(17Q23.1) WILD-TYPE 495 0

Figure S1.  Get High-res Image Clustering Approach #25: 'Amp Peak 25(17q23.1) mutation analysis' versus Clinical Feature #3: 'GENDER'

Clustering Approach #26: 'Amp Peak 26(19q12) mutation analysis'

Table S27.  Description of clustering approach #26: 'Amp Peak 26(19q12) mutation analysis'

Cluster Labels AMP PEAK 26(19Q12) MUTATED AMP PEAK 26(19Q12) WILD-TYPE
Number of samples 217 629
Clustering Approach #27: 'Amp Peak 27(19q13.42) mutation analysis'

Table S28.  Description of clustering approach #27: 'Amp Peak 27(19q13.42) mutation analysis'

Cluster Labels AMP PEAK 27(19Q13.42) MUTATED AMP PEAK 27(19Q13.42) WILD-TYPE
Number of samples 226 620
Clustering Approach #28: 'Amp Peak 28(20q13.2) mutation analysis'

Table S29.  Description of clustering approach #28: 'Amp Peak 28(20q13.2) mutation analysis'

Cluster Labels AMP PEAK 28(20Q13.2) MUTATED AMP PEAK 28(20Q13.2) WILD-TYPE
Number of samples 440 406
Clustering Approach #29: 'Del Peak 1(1p36.13) mutation analysis'

Table S30.  Description of clustering approach #29: 'Del Peak 1(1p36.13) mutation analysis'

Cluster Labels DEL PEAK 1(1P36.13) MUTATED DEL PEAK 1(1P36.13) WILD-TYPE
Number of samples 359 487
Clustering Approach #30: 'Del Peak 2(1p21.2) mutation analysis'

Table S31.  Description of clustering approach #30: 'Del Peak 2(1p21.2) mutation analysis'

Cluster Labels DEL PEAK 2(1P21.2) MUTATED DEL PEAK 2(1P21.2) WILD-TYPE
Number of samples 290 556
Clustering Approach #31: 'Del Peak 3(2q37.3) mutation analysis'

Table S32.  Description of clustering approach #31: 'Del Peak 3(2q37.3) mutation analysis'

Cluster Labels DEL PEAK 3(2Q37.3) MUTATED DEL PEAK 3(2Q37.3) WILD-TYPE
Number of samples 251 595
Clustering Approach #32: 'Del Peak 4(3p14.3) mutation analysis'

Table S33.  Description of clustering approach #32: 'Del Peak 4(3p14.3) mutation analysis'

Cluster Labels DEL PEAK 4(3P14.3) MUTATED DEL PEAK 4(3P14.3) WILD-TYPE
Number of samples 266 580
'Del Peak 4(3p14.3) mutation analysis' versus 'AGE'

P value = 9.72e-05 (t-test), Q value = 0.049

Table S34.  Clustering Approach #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 845 58.5 (13.2)
DEL PEAK 4(3P14.3) MUTATED 266 55.9 (13.2)
DEL PEAK 4(3P14.3) WILD-TYPE 579 59.7 (13.1)

Figure S2.  Get High-res Image Clustering Approach #32: 'Del Peak 4(3p14.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #33: 'Del Peak 5(4p16.3) mutation analysis'

Table S35.  Description of clustering approach #33: 'Del Peak 5(4p16.3) mutation analysis'

Cluster Labels DEL PEAK 5(4P16.3) MUTATED DEL PEAK 5(4P16.3) WILD-TYPE
Number of samples 266 580
Clustering Approach #34: 'Del Peak 6(4q35.2) mutation analysis'

Table S36.  Description of clustering approach #34: 'Del Peak 6(4q35.2) mutation analysis'

Cluster Labels DEL PEAK 6(4Q35.2) MUTATED DEL PEAK 6(4Q35.2) WILD-TYPE
Number of samples 266 580
Clustering Approach #35: 'Del Peak 7(5q11.2) mutation analysis'

Table S37.  Description of clustering approach #35: 'Del Peak 7(5q11.2) mutation analysis'

Cluster Labels DEL PEAK 7(5Q11.2) MUTATED DEL PEAK 7(5Q11.2) WILD-TYPE
Number of samples 220 626
Clustering Approach #36: 'Del Peak 8(5q21.3) mutation analysis'

Table S38.  Description of clustering approach #36: 'Del Peak 8(5q21.3) mutation analysis'

Cluster Labels DEL PEAK 8(5Q21.3) MUTATED DEL PEAK 8(5Q21.3) WILD-TYPE
Number of samples 212 634
Clustering Approach #37: 'Del Peak 9(6p25.3) mutation analysis'

Table S39.  Description of clustering approach #37: 'Del Peak 9(6p25.3) mutation analysis'

Cluster Labels DEL PEAK 9(6P25.3) MUTATED DEL PEAK 9(6P25.3) WILD-TYPE
Number of samples 159 687
Clustering Approach #38: 'Del Peak 10(6q15) mutation analysis'

Table S40.  Description of clustering approach #38: 'Del Peak 10(6q15) mutation analysis'

Cluster Labels DEL PEAK 10(6Q15) MUTATED DEL PEAK 10(6Q15) WILD-TYPE
Number of samples 284 562
Clustering Approach #39: 'Del Peak 11(6q27) mutation analysis'

Table S41.  Description of clustering approach #39: 'Del Peak 11(6q27) mutation analysis'

Cluster Labels DEL PEAK 11(6Q27) MUTATED DEL PEAK 11(6Q27) WILD-TYPE
Number of samples 289 557
'Del Peak 11(6q27) mutation analysis' versus 'AGE'

P value = 0.000124 (t-test), Q value = 0.062

Table S42.  Clustering Approach #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 845 58.5 (13.2)
DEL PEAK 11(6Q27) MUTATED 289 56.1 (12.8)
DEL PEAK 11(6Q27) WILD-TYPE 556 59.8 (13.3)

Figure S3.  Get High-res Image Clustering Approach #39: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #40: 'Del Peak 12(7p22.3) mutation analysis'

Table S43.  Description of clustering approach #40: 'Del Peak 12(7p22.3) mutation analysis'

Cluster Labels DEL PEAK 12(7P22.3) MUTATED DEL PEAK 12(7P22.3) WILD-TYPE
Number of samples 114 732
Clustering Approach #41: 'Del Peak 13(7q36.1) mutation analysis'

Table S44.  Description of clustering approach #41: 'Del Peak 13(7q36.1) mutation analysis'

Cluster Labels DEL PEAK 13(7Q36.1) MUTATED DEL PEAK 13(7Q36.1) WILD-TYPE
Number of samples 172 674
Clustering Approach #42: 'Del Peak 14(8p23.2) mutation analysis'

Table S45.  Description of clustering approach #42: 'Del Peak 14(8p23.2) mutation analysis'

Cluster Labels DEL PEAK 14(8P23.2) MUTATED DEL PEAK 14(8P23.2) WILD-TYPE
Number of samples 449 397
Clustering Approach #43: 'Del Peak 15(8p11.21) mutation analysis'

Table S46.  Description of clustering approach #43: 'Del Peak 15(8p11.21) mutation analysis'

Cluster Labels DEL PEAK 15(8P11.21) MUTATED DEL PEAK 15(8P11.21) WILD-TYPE
Number of samples 163 683
Clustering Approach #44: 'Del Peak 16(9p21.3) mutation analysis'

Table S47.  Description of clustering approach #44: 'Del Peak 16(9p21.3) mutation analysis'

Cluster Labels DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
Number of samples 291 555
Clustering Approach #45: 'Del Peak 17(9q21.11) mutation analysis'

Table S48.  Description of clustering approach #45: 'Del Peak 17(9q21.11) mutation analysis'

Cluster Labels DEL PEAK 17(9Q21.11) MUTATED DEL PEAK 17(9Q21.11) WILD-TYPE
Number of samples 232 614
Clustering Approach #46: 'Del Peak 18(10q23.31) mutation analysis'

Table S49.  Description of clustering approach #46: 'Del Peak 18(10q23.31) mutation analysis'

Cluster Labels DEL PEAK 18(10Q23.31) MUTATED DEL PEAK 18(10Q23.31) WILD-TYPE
Number of samples 245 601
Clustering Approach #47: 'Del Peak 19(10q26.3) mutation analysis'

Table S50.  Description of clustering approach #47: 'Del Peak 19(10q26.3) mutation analysis'

Cluster Labels DEL PEAK 19(10Q26.3) MUTATED DEL PEAK 19(10Q26.3) WILD-TYPE
Number of samples 247 599
Clustering Approach #48: 'Del Peak 20(11p15.5) mutation analysis'

Table S51.  Description of clustering approach #48: 'Del Peak 20(11p15.5) mutation analysis'

Cluster Labels DEL PEAK 20(11P15.5) MUTATED DEL PEAK 20(11P15.5) WILD-TYPE
Number of samples 249 597
Clustering Approach #49: 'Del Peak 21(11q23.2) mutation analysis'

Table S52.  Description of clustering approach #49: 'Del Peak 21(11q23.2) mutation analysis'

Cluster Labels DEL PEAK 21(11Q23.2) MUTATED DEL PEAK 21(11Q23.2) WILD-TYPE
Number of samples 423 423
Clustering Approach #50: 'Del Peak 22(12p13.1) mutation analysis'

Table S53.  Description of clustering approach #50: 'Del Peak 22(12p13.1) mutation analysis'

Cluster Labels DEL PEAK 22(12P13.1) MUTATED DEL PEAK 22(12P13.1) WILD-TYPE
Number of samples 151 695
Clustering Approach #51: 'Del Peak 23(12q24.31) mutation analysis'

Table S54.  Description of clustering approach #51: 'Del Peak 23(12q24.31) mutation analysis'

Cluster Labels DEL PEAK 23(12Q24.31) MUTATED DEL PEAK 23(12Q24.31) WILD-TYPE
Number of samples 147 699
Clustering Approach #52: 'Del Peak 24(13q14.2) mutation analysis'

Table S55.  Description of clustering approach #52: 'Del Peak 24(13q14.2) mutation analysis'

Cluster Labels DEL PEAK 24(13Q14.2) MUTATED DEL PEAK 24(13Q14.2) WILD-TYPE
Number of samples 391 455
Clustering Approach #53: 'Del Peak 25(14q24.3) mutation analysis'

Table S56.  Description of clustering approach #53: 'Del Peak 25(14q24.3) mutation analysis'

Cluster Labels DEL PEAK 25(14Q24.3) MUTATED DEL PEAK 25(14Q24.3) WILD-TYPE
Number of samples 271 575
Clustering Approach #54: 'Del Peak 26(15q13.1) mutation analysis'

Table S57.  Description of clustering approach #54: 'Del Peak 26(15q13.1) mutation analysis'

Cluster Labels DEL PEAK 26(15Q13.1) MUTATED DEL PEAK 26(15Q13.1) WILD-TYPE
Number of samples 297 549
Clustering Approach #55: 'Del Peak 27(16q24.3) mutation analysis'

Table S58.  Description of clustering approach #55: 'Del Peak 27(16q24.3) mutation analysis'

Cluster Labels DEL PEAK 27(16Q24.3) MUTATED DEL PEAK 27(16Q24.3) WILD-TYPE
Number of samples 548 298
Clustering Approach #56: 'Del Peak 28(17p12) mutation analysis'

Table S59.  Description of clustering approach #56: 'Del Peak 28(17p12) mutation analysis'

Cluster Labels DEL PEAK 28(17P12) MUTATED DEL PEAK 28(17P12) WILD-TYPE
Number of samples 513 333
Clustering Approach #57: 'Del Peak 29(17q21.31) mutation analysis'

Table S60.  Description of clustering approach #57: 'Del Peak 29(17q21.31) mutation analysis'

Cluster Labels DEL PEAK 29(17Q21.31) MUTATED DEL PEAK 29(17Q21.31) WILD-TYPE
Number of samples 300 546
Clustering Approach #58: 'Del Peak 30(18q23) mutation analysis'

Table S61.  Description of clustering approach #58: 'Del Peak 30(18q23) mutation analysis'

Cluster Labels DEL PEAK 30(18Q23) MUTATED DEL PEAK 30(18Q23) WILD-TYPE
Number of samples 278 568
Clustering Approach #59: 'Del Peak 31(19p13.3) mutation analysis'

Table S62.  Description of clustering approach #59: 'Del Peak 31(19p13.3) mutation analysis'

Cluster Labels DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
Number of samples 293 553
Clustering Approach #60: 'Del Peak 32(19q13.32) mutation analysis'

Table S63.  Description of clustering approach #60: 'Del Peak 32(19q13.32) mutation analysis'

Cluster Labels DEL PEAK 32(19Q13.32) MUTATED DEL PEAK 32(19Q13.32) WILD-TYPE
Number of samples 174 672
Clustering Approach #61: 'Del Peak 33(20p13) mutation analysis'

Table S64.  Description of clustering approach #61: 'Del Peak 33(20p13) mutation analysis'

Cluster Labels DEL PEAK 33(20P13) MUTATED DEL PEAK 33(20P13) WILD-TYPE
Number of samples 126 720
Clustering Approach #62: 'Del Peak 34(21q11.2) mutation analysis'

Table S65.  Description of clustering approach #62: 'Del Peak 34(21q11.2) mutation analysis'

Cluster Labels DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
Number of samples 175 671
Clustering Approach #63: 'Del Peak 35(22q13.32) mutation analysis'

Table S66.  Description of clustering approach #63: 'Del Peak 35(22q13.32) mutation analysis'

Cluster Labels DEL PEAK 35(22Q13.32) MUTATED DEL PEAK 35(22Q13.32) WILD-TYPE
Number of samples 380 466
Methods & Data
Input

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

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

  • Number of patients = 846

  • Number of clustering approaches = 63

  • Number of selected clinical features = 9

  • Exclude small clusters that include fewer than K patients, 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 two tumor subtypes using 't.test' function in R

Fisher's exact test

For binary clinical features, 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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