Correlation between copy number variation genes (focal) and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
22 February 2013  |  analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C19K48DX
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/C19K48DX
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 72 different clustering approaches and 12 clinical features across 319 patients, 3 significant findings detected with Q value < 0.25.

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

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

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 3(2q31.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 4(2q32.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 5(3q26.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 6(5p15.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 7(5p12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 8(6p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 9(6q12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 10(7p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 11(7q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 12(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 13(8q11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 14(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 15(9p23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 16(9p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 17(11p13) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 18(11p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 19(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 20(12p13.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 21(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 22(13q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 23(14q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 24(15q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 25(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 26(18p11.31) mutation analysis'. These subtypes correlate to 'GENDER'.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 27(18q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 28(20q11.22) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Amp Peak 29(Xq28) 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(1p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.

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

  • 2 subtypes identified in current cancer cohort by 'Del Peak 4(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 5(2q36.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 6(3p24.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 7(3p14.2) mutation analysis'. These subtypes correlate to 'TOBACCOSMOKINGHISTORYINDICATOR'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 8(3p12.2) mutation analysis'. These subtypes correlate to 'NUMBERPACKYEARSSMOKED'.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 9(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 10(4p15.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 11(4q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 12(4q35.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 13(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 14(5q35.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 15(6p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 16(7q31.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 17(7q36.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 18(8p23.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 19(9p23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 20(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 21(9q21.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 22(9q34.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 23(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 24(10p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 25(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 26(11p15.4) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 27(11q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 28(12q24.33) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 29(13q12.11) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 30(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 31(14q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 32(14q32.32) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 33(15q15.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 34(16q12.1) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 35(16q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 36(17q25.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 37(18q21.2) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 38(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 39(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 40(19q13.43) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 41(Xp21.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 42(Xp11.3) mutation analysis'. These subtypes do not correlate to any clinical features.

  • 2 subtypes identified in current cancer cohort by 'Del Peak 43(Xq21.33) 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 72 different clustering approaches and 12 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 PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED STOPPEDSMOKINGYEAR TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET
Statistical Tests logrank test t-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test t-test
Amp Peak 1(1q21 2) 0.616
(1.00) 		0.0529
(1.00) 		0.66
(1.00) 		0.776
(1.00) 		0.262
(1.00) 		0.24
(1.00) 		0.945
(1.00) 		0.216
(1.00) 		0.588
(1.00) 		0.062
(1.00) 		0.0647
(1.00) 		0.901
(1.00)
Amp Peak 2(2q11 2) 0.515
(1.00) 		0.56
(1.00) 		0.366
(1.00) 		0.00414
(1.00) 		0.534
(1.00) 		1
(1.00) 		0.0684
(1.00) 		1
(1.00) 		0.379
(1.00) 		0.0959
(1.00) 		0.125
(1.00) 		0.663
(1.00)
Amp Peak 3(2q31 2) 0.188
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.29
(1.00) 		0.295
(1.00) 		0.573
(1.00) 		0.672
(1.00) 		0.872
(1.00) 		0.114
(1.00) 		0.526
(1.00) 		0.0034
(1.00) 		0.596
(1.00)
Amp Peak 4(2q32 2) 0.487
(1.00) 		0.86
(1.00) 		0.748
(1.00) 		0.581
(1.00) 		0.326
(1.00) 		0.522
(1.00) 		0.957
(1.00) 		0.866
(1.00) 		0.0888
(1.00) 		0.0737
(1.00) 		0.0369
(1.00) 		0.725
(1.00)
Amp Peak 5(3q26 33) 0.149
(1.00) 		0.0948
(1.00) 		0.044
(1.00) 		0.531
(1.00) 		0.182
(1.00) 		1
(1.00) 		0.0899
(1.00) 		0.448
(1.00) 		0.00258
(1.00) 		0.0124
(1.00) 		0.114
(1.00) 		0.121
(1.00)
Amp Peak 6(5p15 33) 0.578
(1.00) 		0.159
(1.00) 		0.105
(1.00) 		0.336
(1.00) 		0.0817
(1.00) 		0.388
(1.00) 		0.132
(1.00) 		0.0479
(1.00) 		0.819
(1.00) 		0.0157
(1.00) 		0.249
(1.00) 		0.2
(1.00)
Amp Peak 7(5p12) 0.666
(1.00) 		0.356
(1.00) 		0.25
(1.00) 		0.431
(1.00) 		0.239
(1.00) 		0.413
(1.00) 		0.49
(1.00) 		0.01
(1.00) 		0.52
(1.00) 		0.179
(1.00) 		0.32
(1.00) 		0.878
(1.00)
Amp Peak 8(6p12 1) 0.727
(1.00) 		0.201
(1.00) 		0.641
(1.00) 		0.543
(1.00) 		0.934
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.191
(1.00) 		0.736
(1.00) 		0.188
(1.00) 		0.623
(1.00) 		0.375
(1.00)
Amp Peak 9(6q12) 0.477
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.599
(1.00) 		0.977
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.0427
(1.00) 		0.722
(1.00) 		0.0815
(1.00) 		0.533
(1.00) 		0.0222
(1.00)
Amp Peak 10(7p11 2) 0.0562
(1.00) 		0.139
(1.00) 		0.707
(1.00) 		0.0523
(1.00) 		0.4
(1.00) 		0.684
(1.00) 		0.734
(1.00) 		0.692
(1.00) 		0.791
(1.00) 		0.0487
(1.00) 		0.232
(1.00) 		0.145
(1.00)
Amp Peak 11(7q22 1) 0.0557
(1.00) 		0.415
(1.00) 		0.363
(1.00) 		0.0203
(1.00) 		0.211
(1.00) 		0.33
(1.00) 		0.235
(1.00) 		0.274
(1.00) 		0.0588
(1.00) 		0.00957
(1.00) 		0.00127
(1.00) 		0.737
(1.00)
Amp Peak 12(8p11 23) 0.162
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.112
(1.00) 		0.468
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.78
(1.00) 		0.612
(1.00) 		0.506
(1.00) 		0.637
(1.00) 		0.819
(1.00)
Amp Peak 13(8q11 21) 0.447
(1.00) 		0.5
(1.00) 		0.9
(1.00) 		0.953
(1.00) 		0.401
(1.00) 		0.0744
(1.00) 		0.396
(1.00) 		0.353
(1.00) 		0.806
(1.00) 		0.123
(1.00) 		0.0882
(1.00) 		0.136
(1.00)
Amp Peak 14(8q24 21) 0.518
(1.00) 		0.299
(1.00) 		0.677
(1.00) 		0.667
(1.00) 		0.00106
(0.904) 		0.17
(1.00) 		0.305
(1.00) 		0.771
(1.00) 		0.786
(1.00) 		0.603
(1.00) 		0.728
(1.00) 		0.0473
(1.00)
Amp Peak 15(9p23) 0.692
(1.00) 		0.665
(1.00) 		0.11
(1.00) 		0.894
(1.00) 		0.362
(1.00) 		0.639
(1.00) 		0.63
(1.00) 		0.877
(1.00) 		0.1
(1.00) 		0.749
(1.00) 		0.56
(1.00) 		0.793
(1.00)
Amp Peak 16(9p13 3) 0.874
(1.00) 		0.992
(1.00) 		0.491
(1.00) 		0.691
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.884
(1.00) 		0.811
(1.00) 		0.507
(1.00) 		0.367
(1.00) 		0.567
(1.00)
Amp Peak 17(11p13) 0.462
(1.00) 		0.0944
(1.00) 		0.754
(1.00) 		0.465
(1.00) 		0.241
(1.00) 		0.578
(1.00) 		0.63
(1.00) 		0.74
(1.00) 		0.00261
(1.00) 		0.85
(1.00) 		0.338
(1.00) 		0.172
(1.00)
Amp Peak 18(11p11 2) 0.205
(1.00) 		0.914
(1.00) 		0.53
(1.00) 		0.713
(1.00) 		0.0419
(1.00) 		0.585
(1.00) 		0.597
(1.00) 		0.621
(1.00) 		0.0454
(1.00) 		0.593
(1.00) 		0.274
(1.00) 		0.975
(1.00)
Amp Peak 19(11q13 3) 0.00597
(1.00) 		0.279
(1.00) 		0.901
(1.00) 		0.316
(1.00) 		0.0759
(1.00) 		1
(1.00) 		0.148
(1.00) 		0.187
(1.00) 		0.12
(1.00) 		0.112
(1.00) 		0.0273
(1.00) 		0.564
(1.00)
Amp Peak 20(12p13 33) 0.964
(1.00) 		0.285
(1.00) 		0.239
(1.00) 		0.407
(1.00) 		0.474
(1.00) 		0.166
(1.00) 		0.864
(1.00) 		0.678
(1.00) 		0.424
(1.00) 		0.122
(1.00) 		0.197
(1.00) 		0.186
(1.00)
Amp Peak 21(12q15) 0.375
(1.00) 		0.364
(1.00) 		0.877
(1.00) 		0.649
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.309
(1.00) 		0.326
(1.00) 		0.139
(1.00) 		0.192
(1.00) 		0.401
(1.00) 		0.363
(1.00)
Amp Peak 22(13q22 1) 0.0878
(1.00) 		0.0672
(1.00) 		0.446
(1.00) 		0.52
(1.00) 		0.536
(1.00) 		0.578
(1.00) 		0.642
(1.00) 		0.336
(1.00) 		0.0473
(1.00) 		0.926
(1.00) 		0.334
(1.00) 		0.108
(1.00)
Amp Peak 23(14q11 2) 0.885
(1.00) 		0.927
(1.00) 		1
(1.00) 		0.933
(1.00) 		0.93
(1.00) 		1
(1.00) 		0.976
(1.00) 		0.66
(1.00) 		0.4
(1.00) 		0.112
(1.00) 		0.916
(1.00) 		0.602
(1.00)
Amp Peak 24(15q26 3) 0.0152
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.982
(1.00) 		0.622
(1.00) 		0.842
(1.00) 		0.432
(1.00) 		0.696
(1.00) 		0.919
(1.00) 		0.347
(1.00) 		0.991
(1.00)
Amp Peak 25(17q12) 0.0909
(1.00) 		0.0948
(1.00) 		0.187
(1.00) 		0.424
(1.00) 		0.6
(1.00) 		0.573
(1.00) 		0.224
(1.00) 		0.384
(1.00) 		0.509
(1.00) 		0.727
(1.00) 		0.0318
(1.00) 		0.485
(1.00)
Amp Peak 26(18p11 31) 0.116
(1.00) 		0.0979
(1.00) 		0.000276
(0.238) 		0.234
(1.00) 		0.666
(1.00) 		0.639
(1.00) 		0.0362
(1.00) 		0.672
(1.00) 		0.131
(1.00) 		0.0507
(1.00) 		0.0589
(1.00) 		0.251
(1.00)
Amp Peak 27(18q11 2) 0.94
(1.00) 		0.0274
(1.00) 		0.037
(1.00) 		0.439
(1.00) 		0.778
(1.00) 		0.33
(1.00) 		0.954
(1.00) 		0.43
(1.00) 		0.272
(1.00) 		0.213
(1.00) 		0.128
(1.00) 		0.934
(1.00)
Amp Peak 28(20q11 22) 0.84
(1.00) 		0.206
(1.00) 		0.263
(1.00) 		0.819
(1.00) 		0.478
(1.00) 		0.214
(1.00) 		0.93
(1.00) 		0.51
(1.00) 		0.718
(1.00) 		0.206
(1.00) 		0.817
(1.00) 		0.12
(1.00)
Amp Peak 29(Xq28) 0.389
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.237
(1.00) 		0.311
(1.00) 		0.607
(1.00) 		0.964
(1.00) 		0.0628
(1.00) 		0.35
(1.00) 		0.0542
(1.00) 		0.273
(1.00) 		0.381
(1.00)
Del Peak 1(1p36 13) 0.108
(1.00) 		0.063
(1.00) 		0.227
(1.00) 		0.271
(1.00) 		0.608
(1.00) 		0.595
(1.00) 		0.6
(1.00) 		0.261
(1.00) 		0.0141
(1.00) 		0.24
(1.00) 		0.0711
(1.00) 		0.387
(1.00)
Del Peak 2(1p13 2) 0.27
(1.00) 		0.164
(1.00) 		0.776
(1.00) 		0.323
(1.00) 		0.615
(1.00) 		0.118
(1.00) 		0.516
(1.00) 		0.548
(1.00) 		0.0129
(1.00) 		0.332
(1.00) 		0.116
(1.00) 		0.868
(1.00)
Del Peak 3(2q21 2) 0.477
(1.00) 		0.121
(1.00) 		0.0389
(1.00) 		0.625
(1.00) 		0.137
(1.00) 		0.578
(1.00) 		0.954
(1.00) 		0.427
(1.00) 		0.65
(1.00) 		0.441
(1.00) 		0.483
(1.00) 		0.76
(1.00)
Del Peak 4(2q22 1) 0.551
(1.00) 		0.271
(1.00) 		0.166
(1.00) 		0.157
(1.00) 		0.169
(1.00) 		0.324
(1.00) 		0.302
(1.00) 		0.418
(1.00) 		0.0965
(1.00) 		0.528
(1.00) 		0.228
(1.00) 		0.988
(1.00)
Del Peak 5(2q36 2) 0.191
(1.00) 		0.867
(1.00) 		0.498
(1.00) 		0.00484
(1.00) 		0.496
(1.00) 		0.655
(1.00) 		0.208
(1.00) 		0.886
(1.00) 		0.0363
(1.00) 		0.00893
(1.00) 		0.15
(1.00) 		0.417
(1.00)
Del Peak 6(3p24 1) 0.000772
(0.66) 		0.699
(1.00) 		0.0344
(1.00) 		0.00511
(1.00) 		0.013
(1.00) 		0.655
(1.00) 		0.0107
(1.00) 		0.882
(1.00) 		0.000474
(0.407) 		0.000503
(0.431) 		0.00106
(0.904) 		0.644
(1.00)
Del Peak 7(3p14 2) 0.000458
(0.394) 		0.564
(1.00) 		0.0613
(1.00) 		0.0624
(1.00) 		0.0504
(1.00) 		0.664
(1.00) 		0.0231
(1.00) 		0.448
(1.00) 		0.00174
(1.00) 		0.00172
(1.00) 		0.00011
(0.0947) 		0.607
(1.00)
Del Peak 8(3p12 2) 0.000374
(0.322) 		0.5
(1.00) 		0.338
(1.00) 		0.0918
(1.00) 		0.0954
(1.00) 		1
(1.00) 		0.0503
(1.00) 		0.774
(1.00) 		4.69e-05
(0.0405) 		0.00498
(1.00) 		0.00843
(1.00) 		0.793
(1.00)
Del Peak 9(4p16 3) 0.0505
(1.00) 		0.0687
(1.00) 		0.26
(1.00) 		0.398
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.491
(1.00) 		0.426
(1.00) 		0.714
(1.00) 		0.012
(1.00) 		0.014
(1.00) 		0.699
(1.00)
Del Peak 10(4p15 2) 0.116
(1.00) 		0.0856
(1.00) 		0.38
(1.00) 		0.376
(1.00) 		0.588
(1.00) 		0.674
(1.00) 		0.422
(1.00) 		0.428
(1.00) 		0.211
(1.00) 		0.00878
(1.00) 		0.00259
(1.00) 		0.613
(1.00)
Del Peak 11(4q22 1) 0.624
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.969
(1.00) 		0.341
(1.00) 		0.678
(1.00) 		0.482
(1.00) 		0.42
(1.00) 		0.0561
(1.00) 		0.0565
(1.00) 		0.209
(1.00)
Del Peak 12(4q35 2) 0.174
(1.00) 		0.698
(1.00) 		0.0442
(1.00) 		0.112
(1.00) 		0.919
(1.00) 		0.204
(1.00) 		0.328
(1.00) 		0.689
(1.00) 		0.604
(1.00) 		0.00479
(1.00) 		0.0198
(1.00) 		0.0256
(1.00)
Del Peak 13(5q11 2) 0.523
(1.00) 		0.353
(1.00) 		0.166
(1.00) 		0.0872
(1.00) 		0.287
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.289
(1.00) 		0.00427
(1.00) 		0.0175
(1.00) 		0.00954
(1.00) 		0.757
(1.00)
Del Peak 14(5q35 3) 0.512
(1.00) 		0.459
(1.00) 		0.256
(1.00) 		0.0339
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.241
(1.00) 		0.424
(1.00) 		0.127
(1.00) 		0.05
(1.00) 		0.0244
(1.00) 		0.76
(1.00)
Del Peak 15(6p25 3) 0.18
(1.00) 		0.228
(1.00) 		0.277
(1.00) 		0.011
(1.00) 		0.898
(1.00) 		0.579
(1.00) 		0.302
(1.00) 		0.87
(1.00) 		0.373
(1.00) 		0.78
(1.00) 		0.314
(1.00) 		0.114
(1.00)
Del Peak 16(7q31 1) 0.78
(1.00) 		0.00903
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.578
(1.00) 		0.62
(1.00) 		0.466
(1.00) 		0.297
(1.00) 		0.0321
(1.00) 		0.0451
(1.00) 		0.00446
(1.00)
Del Peak 17(7q36 1) 0.0154
(1.00) 		0.502
(1.00) 		0.117
(1.00) 		0.777
(1.00) 		0.102
(1.00) 		1
(1.00) 		0.29
(1.00) 		1
(1.00) 		0.44
(1.00) 		0.254
(1.00) 		0.242
(1.00) 		0.112
(1.00)
Del Peak 18(8p23 2) 0.00813
(1.00) 		0.0949
(1.00) 		0.381
(1.00) 		0.81
(1.00) 		0.534
(1.00) 		1
(1.00) 		0.926
(1.00) 		0.692
(1.00) 		0.0334
(1.00) 		0.264
(1.00) 		0.619
(1.00) 		0.997
(1.00)
Del Peak 19(9p23) 0.729
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.952
(1.00) 		0.388
(1.00) 		0.95
(1.00) 		0.429
(1.00) 		0.128
(1.00) 		0.00864
(1.00) 		0.00341
(1.00) 		0.877
(1.00)
Del Peak 20(9p21 3) 0.0228
(1.00) 		0.149
(1.00) 		0.314
(1.00) 		0.558
(1.00) 		0.978
(1.00) 		0.104
(1.00) 		0.773
(1.00) 		0.353
(1.00) 		0.309
(1.00) 		0.0089
(1.00) 		0.000788
(0.672) 		0.279
(1.00)
Del Peak 21(9q21 11) 0.875
(1.00) 		0.606
(1.00) 		0.751
(1.00) 		0.844
(1.00) 		0.749
(1.00) 		1
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.27
(1.00) 		0.49
(1.00) 		0.182
(1.00) 		0.29
(1.00)
Del Peak 22(9q34 3) 0.571
(1.00) 		0.694
(1.00) 		0.184
(1.00) 		0.63
(1.00) 		0.918
(1.00) 		0.522
(1.00) 		0.938
(1.00) 		0.48
(1.00) 		0.384
(1.00) 		0.322
(1.00) 		0.542
(1.00) 		0.711
(1.00)
Del Peak 23(10p15 3) 0.158
(1.00) 		0.465
(1.00) 		1
(1.00) 		0.332
(1.00) 		0.0669
(1.00) 		1
(1.00) 		0.551
(1.00) 		0.0957
(1.00) 		0.535
(1.00) 		0.327
(1.00) 		0.759
(1.00) 		0.554
(1.00)
Del Peak 24(10p11 21) 0.257
(1.00) 		0.398
(1.00) 		0.593
(1.00) 		0.398
(1.00) 		0.644
(1.00) 		0.664
(1.00) 		0.736
(1.00) 		0.0657
(1.00) 		0.342
(1.00) 		0.199
(1.00) 		0.306
(1.00) 		0.235
(1.00)
Del Peak 25(10q23 31) 0.271
(1.00) 		0.37
(1.00) 		0.258
(1.00) 		0.724
(1.00) 		0.983
(1.00) 		0.664
(1.00) 		0.591
(1.00) 		0.655
(1.00) 		0.233
(1.00) 		0.888
(1.00) 		0.228
(1.00) 		0.01
(1.00)
Del Peak 26(11p15 4) 0.0592
(1.00) 		0.507
(1.00) 		0.594
(1.00) 		0.859
(1.00) 		0.0546
(1.00) 		0.32
(1.00) 		0.488
(1.00) 		1
(1.00) 		0.284
(1.00) 		0.2
(1.00) 		0.0614
(1.00) 		0.821
(1.00)
Del Peak 27(11q23 1) 0.77
(1.00) 		0.257
(1.00) 		0.00405
(1.00) 		0.948
(1.00) 		0.0514
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.511
(1.00) 		0.254
(1.00) 		0.785
(1.00) 		0.124
(1.00) 		0.214
(1.00)
Del Peak 28(12q24 33) 0.565
(1.00) 		0.665
(1.00) 		0.85
(1.00) 		0.501
(1.00) 		0.683
(1.00) 		0.573
(1.00) 		0.759
(1.00) 		0.688
(1.00) 		0.595
(1.00) 		0.14
(1.00) 		0.133
(1.00) 		0.487
(1.00)
Del Peak 29(13q12 11) 0.73
(1.00) 		0.798
(1.00) 		0.317
(1.00) 		0.062
(1.00) 		0.141
(1.00) 		0.684
(1.00) 		0.0215
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.174
(1.00) 		0.126
(1.00) 		0.579
(1.00)
Del Peak 30(13q14 2) 0.0121
(1.00) 		0.482
(1.00) 		0.453
(1.00) 		0.905
(1.00) 		0.273
(1.00) 		0.684
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.279
(1.00) 		0.243
(1.00) 		0.668
(1.00) 		0.227
(1.00)
Del Peak 31(14q11 2) 0.257
(1.00) 		0.216
(1.00) 		0.597
(1.00) 		0.0971
(1.00) 		0.635
(1.00) 		1
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.0245
(1.00) 		0.313
(1.00) 		0.596
(1.00) 		0.197
(1.00)
Del Peak 32(14q32 32) 0.359
(1.00) 		0.422
(1.00) 		0.161
(1.00) 		0.0598
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.406
(1.00) 		0.353
(1.00) 		0.402
(1.00) 		0.782
(1.00) 		0.494
(1.00) 		0.371
(1.00)
Del Peak 33(15q15 1) 0.465
(1.00) 		0.739
(1.00) 		0.381
(1.00) 		0.104
(1.00) 		0.17
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.164
(1.00) 		0.762
(1.00) 		0.0715
(1.00) 		0.276
(1.00) 		0.801
(1.00)
Del Peak 34(16q12 1) 0.237
(1.00) 		0.589
(1.00) 		0.51
(1.00) 		0.877
(1.00) 		0.496
(1.00) 		0.595
(1.00) 		0.55
(1.00) 		0.22
(1.00) 		0.574
(1.00) 		0.142
(1.00) 		0.00868
(1.00) 		0.442
(1.00)
Del Peak 35(16q23 3) 0.178
(1.00) 		0.287
(1.00) 		0.641
(1.00) 		0.425
(1.00) 		0.176
(1.00) 		0.164
(1.00) 		0.356
(1.00) 		0.745
(1.00) 		0.788
(1.00) 		0.271
(1.00) 		0.0137
(1.00) 		0.138
(1.00)
Del Peak 36(17q25 3) 0.952
(1.00) 		0.995
(1.00) 		1
(1.00) 		0.469
(1.00) 		0.108
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.238
(1.00) 		0.91
(1.00) 		0.372
(1.00) 		0.206
(1.00) 		0.851
(1.00)
Del Peak 37(18q21 2) 0.132
(1.00) 		0.622
(1.00) 		0.0125
(1.00) 		0.559
(1.00) 		0.52
(1.00) 		0.412
(1.00) 		0.723
(1.00) 		0.511
(1.00) 		0.000334
(0.288) 		0.000785
(0.671) 		0.0147
(1.00) 		0.511
(1.00)
Del Peak 38(18q23) 0.108
(1.00) 		0.268
(1.00) 		0.0599
(1.00) 		0.419
(1.00) 		0.555
(1.00) 		0.199
(1.00) 		0.781
(1.00) 		0.429
(1.00) 		0.00135
(1.00) 		0.000723
(0.619) 		0.0655
(1.00) 		0.252
(1.00)
Del Peak 39(19p13 3) 0.0513
(1.00) 		0.491
(1.00) 		1
(1.00) 		0.784
(1.00) 		0.536
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.409
(1.00) 		0.271
(1.00) 		0.407
(1.00) 		0.801
(1.00) 		0.344
(1.00)
Del Peak 40(19q13 43) 0.154
(1.00) 		0.807
(1.00) 		0.755
(1.00) 		0.00454
(1.00) 		0.964
(1.00) 		0.201
(1.00) 		0.167
(1.00) 		0.512
(1.00) 		0.846
(1.00) 		0.0248
(1.00) 		0.428
(1.00) 		0.0718
(1.00)
Del Peak 41(Xp21 3) 0.055
(1.00) 		0.272
(1.00) 		0.895
(1.00) 		0.02
(1.00) 		0.0405
(1.00) 		0.341
(1.00) 		0.499
(1.00) 		0.165
(1.00) 		0.0918
(1.00) 		0.254
(1.00) 		0.304
(1.00) 		0.599
(1.00)
Del Peak 42(Xp11 3) 0.00221
(1.00) 		0.889
(1.00) 		0.6
(1.00) 		0.0786
(1.00) 		0.0773
(1.00) 		0.355
(1.00) 		0.608
(1.00) 		0.129
(1.00) 		0.0193
(1.00) 		0.0201
(1.00) 		0.017
(1.00) 		0.401
(1.00)
Del Peak 43(Xq21 33) 0.442
(1.00) 		0.523
(1.00) 		0.624
(1.00) 		0.251
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.132
(1.00) 		0.602
(1.00) 		0.854
(1.00) 		0.851
(1.00) 		0.207
(1.00) 		0.405
(1.00)
Clustering Approach #1: 'Amp Peak 1(1q21.2) mutation analysis'

Table S1.  Description of clustering approach #1: 'Amp Peak 1(1q21.2) mutation analysis'

Cluster Labels AMP PEAK 1(1Q21.2) MUTATED AMP PEAK 1(1Q21.2) WILD-TYPE
Number of samples 75 244
Clustering Approach #2: 'Amp Peak 2(2q11.2) mutation analysis'

Table S2.  Description of clustering approach #2: 'Amp Peak 2(2q11.2) mutation analysis'

Cluster Labels AMP PEAK 2(2Q11.2) MUTATED AMP PEAK 2(2Q11.2) WILD-TYPE
Number of samples 68 251
Clustering Approach #3: 'Amp Peak 3(2q31.2) mutation analysis'

Table S3.  Description of clustering approach #3: 'Amp Peak 3(2q31.2) mutation analysis'

Cluster Labels AMP PEAK 3(2Q31.2) MUTATED AMP PEAK 3(2Q31.2) WILD-TYPE
Number of samples 66 253
Clustering Approach #4: 'Amp Peak 4(2q32.2) mutation analysis'

Table S4.  Description of clustering approach #4: 'Amp Peak 4(2q32.2) mutation analysis'

Cluster Labels AMP PEAK 4(2Q32.2) MUTATED AMP PEAK 4(2Q32.2) WILD-TYPE
Number of samples 58 261
Clustering Approach #5: 'Amp Peak 5(3q26.33) mutation analysis'

Table S5.  Description of clustering approach #5: 'Amp Peak 5(3q26.33) mutation analysis'

Cluster Labels AMP PEAK 5(3Q26.33) MUTATED AMP PEAK 5(3Q26.33) WILD-TYPE
Number of samples 239 80
Clustering Approach #6: 'Amp Peak 6(5p15.33) mutation analysis'

Table S6.  Description of clustering approach #6: 'Amp Peak 6(5p15.33) mutation analysis'

Cluster Labels AMP PEAK 6(5P15.33) MUTATED AMP PEAK 6(5P15.33) WILD-TYPE
Number of samples 144 175
Clustering Approach #7: 'Amp Peak 7(5p12) mutation analysis'

Table S7.  Description of clustering approach #7: 'Amp Peak 7(5p12) mutation analysis'

Cluster Labels AMP PEAK 7(5P12) MUTATED AMP PEAK 7(5P12) WILD-TYPE
Number of samples 119 200
Clustering Approach #8: 'Amp Peak 8(6p12.1) mutation analysis'

Table S8.  Description of clustering approach #8: 'Amp Peak 8(6p12.1) mutation analysis'

Cluster Labels AMP PEAK 8(6P12.1) MUTATED AMP PEAK 8(6P12.1) WILD-TYPE
Number of samples 64 255
Clustering Approach #9: 'Amp Peak 9(6q12) mutation analysis'

Table S9.  Description of clustering approach #9: 'Amp Peak 9(6q12) mutation analysis'

Cluster Labels AMP PEAK 9(6Q12) MUTATED AMP PEAK 9(6Q12) WILD-TYPE
Number of samples 59 260
Clustering Approach #10: 'Amp Peak 10(7p11.2) mutation analysis'

Table S10.  Description of clustering approach #10: 'Amp Peak 10(7p11.2) mutation analysis'

Cluster Labels AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
Number of samples 136 183
Clustering Approach #11: 'Amp Peak 11(7q22.1) mutation analysis'

Table S11.  Description of clustering approach #11: 'Amp Peak 11(7q22.1) mutation analysis'

Cluster Labels AMP PEAK 11(7Q22.1) MUTATED AMP PEAK 11(7Q22.1) WILD-TYPE
Number of samples 113 206
Clustering Approach #12: 'Amp Peak 12(8p11.23) mutation analysis'

Table S12.  Description of clustering approach #12: 'Amp Peak 12(8p11.23) mutation analysis'

Cluster Labels AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
Number of samples 101 218
Clustering Approach #13: 'Amp Peak 13(8q11.21) mutation analysis'

Table S13.  Description of clustering approach #13: 'Amp Peak 13(8q11.21) mutation analysis'

Cluster Labels AMP PEAK 13(8Q11.21) MUTATED AMP PEAK 13(8Q11.21) WILD-TYPE
Number of samples 187 132
Clustering Approach #14: 'Amp Peak 14(8q24.21) mutation analysis'

Table S14.  Description of clustering approach #14: 'Amp Peak 14(8q24.21) mutation analysis'

Cluster Labels AMP PEAK 14(8Q24.21) MUTATED AMP PEAK 14(8Q24.21) WILD-TYPE
Number of samples 230 89
Clustering Approach #15: 'Amp Peak 15(9p23) mutation analysis'

Table S15.  Description of clustering approach #15: 'Amp Peak 15(9p23) mutation analysis'

Cluster Labels AMP PEAK 15(9P23) MUTATED AMP PEAK 15(9P23) WILD-TYPE
Number of samples 76 243
Clustering Approach #16: 'Amp Peak 16(9p13.3) mutation analysis'

Table S16.  Description of clustering approach #16: 'Amp Peak 16(9p13.3) mutation analysis'

Cluster Labels AMP PEAK 16(9P13.3) MUTATED AMP PEAK 16(9P13.3) WILD-TYPE
Number of samples 90 229
Clustering Approach #17: 'Amp Peak 17(11p13) mutation analysis'

Table S17.  Description of clustering approach #17: 'Amp Peak 17(11p13) mutation analysis'

Cluster Labels AMP PEAK 17(11P13) MUTATED AMP PEAK 17(11P13) WILD-TYPE
Number of samples 62 257
Clustering Approach #18: 'Amp Peak 18(11p11.2) mutation analysis'

Table S18.  Description of clustering approach #18: 'Amp Peak 18(11p11.2) mutation analysis'

Cluster Labels AMP PEAK 18(11P11.2) MUTATED AMP PEAK 18(11P11.2) WILD-TYPE
Number of samples 62 257
Clustering Approach #19: 'Amp Peak 19(11q13.3) mutation analysis'

Table S19.  Description of clustering approach #19: 'Amp Peak 19(11q13.3) mutation analysis'

Cluster Labels AMP PEAK 19(11Q13.3) MUTATED AMP PEAK 19(11Q13.3) WILD-TYPE
Number of samples 145 174
Clustering Approach #20: 'Amp Peak 20(12p13.33) mutation analysis'

Table S20.  Description of clustering approach #20: 'Amp Peak 20(12p13.33) mutation analysis'

Cluster Labels AMP PEAK 20(12P13.33) MUTATED AMP PEAK 20(12P13.33) WILD-TYPE
Number of samples 109 210
Clustering Approach #21: 'Amp Peak 21(12q15) mutation analysis'

Table S21.  Description of clustering approach #21: 'Amp Peak 21(12q15) mutation analysis'

Cluster Labels AMP PEAK 21(12Q15) MUTATED AMP PEAK 21(12Q15) WILD-TYPE
Number of samples 63 256
Clustering Approach #22: 'Amp Peak 22(13q22.1) mutation analysis'

Table S22.  Description of clustering approach #22: 'Amp Peak 22(13q22.1) mutation analysis'

Cluster Labels AMP PEAK 22(13Q22.1) MUTATED AMP PEAK 22(13Q22.1) WILD-TYPE
Number of samples 67 252
Clustering Approach #23: 'Amp Peak 23(14q11.2) mutation analysis'

Table S23.  Description of clustering approach #23: 'Amp Peak 23(14q11.2) mutation analysis'

Cluster Labels AMP PEAK 23(14Q11.2) MUTATED AMP PEAK 23(14Q11.2) WILD-TYPE
Number of samples 88 231
Clustering Approach #24: 'Amp Peak 24(15q26.3) mutation analysis'

Table S24.  Description of clustering approach #24: 'Amp Peak 24(15q26.3) mutation analysis'

Cluster Labels AMP PEAK 24(15Q26.3) MUTATED AMP PEAK 24(15Q26.3) WILD-TYPE
Number of samples 70 249
Clustering Approach #25: 'Amp Peak 25(17q12) mutation analysis'

Table S25.  Description of clustering approach #25: 'Amp Peak 25(17q12) mutation analysis'

Cluster Labels AMP PEAK 25(17Q12) MUTATED AMP PEAK 25(17Q12) WILD-TYPE
Number of samples 55 264
Clustering Approach #26: 'Amp Peak 26(18p11.31) mutation analysis'

Table S26.  Description of clustering approach #26: 'Amp Peak 26(18p11.31) mutation analysis'

Cluster Labels AMP PEAK 26(18P11.31) MUTATED AMP PEAK 26(18P11.31) WILD-TYPE
Number of samples 101 218
'Amp Peak 26(18p11.31) mutation analysis' versus 'GENDER'

P value = 0.000276 (Fisher's exact test), Q value = 0.24

Table S27.  Clustering Approach #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 90 229
AMP PEAK 26(18P11.31) MUTATED 15 86
AMP PEAK 26(18P11.31) WILD-TYPE 75 143

Figure S1.  Get High-res Image Clustering Approach #26: 'Amp Peak 26(18p11.31) mutation analysis' versus Clinical Feature #3: 'GENDER'

Clustering Approach #27: 'Amp Peak 27(18q11.2) mutation analysis'

Table S28.  Description of clustering approach #27: 'Amp Peak 27(18q11.2) mutation analysis'

Cluster Labels AMP PEAK 27(18Q11.2) MUTATED AMP PEAK 27(18Q11.2) WILD-TYPE
Number of samples 71 248
Clustering Approach #28: 'Amp Peak 28(20q11.22) mutation analysis'

Table S29.  Description of clustering approach #28: 'Amp Peak 28(20q11.22) mutation analysis'

Cluster Labels AMP PEAK 28(20Q11.22) MUTATED AMP PEAK 28(20Q11.22) WILD-TYPE
Number of samples 144 175
Clustering Approach #29: 'Amp Peak 29(Xq28) mutation analysis'

Table S30.  Description of clustering approach #29: 'Amp Peak 29(Xq28) mutation analysis'

Cluster Labels AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
Number of samples 97 222
Clustering Approach #30: 'Del Peak 1(1p36.13) mutation analysis'

Table S31.  Description of clustering approach #30: '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 68 251
Clustering Approach #31: 'Del Peak 2(1p13.2) mutation analysis'

Table S32.  Description of clustering approach #31: 'Del Peak 2(1p13.2) mutation analysis'

Cluster Labels DEL PEAK 2(1P13.2) MUTATED DEL PEAK 2(1P13.2) WILD-TYPE
Number of samples 81 238
Clustering Approach #32: 'Del Peak 3(2q21.2) mutation analysis'

Table S33.  Description of clustering approach #32: 'Del Peak 3(2q21.2) mutation analysis'

Cluster Labels DEL PEAK 3(2Q21.2) MUTATED DEL PEAK 3(2Q21.2) WILD-TYPE
Number of samples 40 279
Clustering Approach #33: 'Del Peak 4(2q22.1) mutation analysis'

Table S34.  Description of clustering approach #33: 'Del Peak 4(2q22.1) mutation analysis'

Cluster Labels DEL PEAK 4(2Q22.1) MUTATED DEL PEAK 4(2Q22.1) WILD-TYPE
Number of samples 65 254
Clustering Approach #34: 'Del Peak 5(2q36.2) mutation analysis'

Table S35.  Description of clustering approach #34: 'Del Peak 5(2q36.2) mutation analysis'

Cluster Labels DEL PEAK 5(2Q36.2) MUTATED DEL PEAK 5(2Q36.2) WILD-TYPE
Number of samples 96 223
Clustering Approach #35: 'Del Peak 6(3p24.1) mutation analysis'

Table S36.  Description of clustering approach #35: 'Del Peak 6(3p24.1) mutation analysis'

Cluster Labels DEL PEAK 6(3P24.1) MUTATED DEL PEAK 6(3P24.1) WILD-TYPE
Number of samples 236 83
Clustering Approach #36: 'Del Peak 7(3p14.2) mutation analysis'

Table S37.  Description of clustering approach #36: 'Del Peak 7(3p14.2) mutation analysis'

Cluster Labels DEL PEAK 7(3P14.2) MUTATED DEL PEAK 7(3P14.2) WILD-TYPE
Number of samples 240 79
'Del Peak 7(3p14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.00011 (Fisher's exact test), Q value = 0.095

Table S38.  Clustering Approach #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #11: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT SMOKER LIFELONG NON-SMOKER
ALL 83 57 102 66
DEL PEAK 7(3P14.2) MUTATED 72 35 83 40
DEL PEAK 7(3P14.2) WILD-TYPE 11 22 19 26

Figure S2.  Get High-res Image Clustering Approach #36: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #11: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #37: 'Del Peak 8(3p12.2) mutation analysis'

Table S39.  Description of clustering approach #37: 'Del Peak 8(3p12.2) mutation analysis'

Cluster Labels DEL PEAK 8(3P12.2) MUTATED DEL PEAK 8(3P12.2) WILD-TYPE
Number of samples 226 93
'Del Peak 8(3p12.2) mutation analysis' versus 'NUMBERPACKYEARSSMOKED'

P value = 4.69e-05 (t-test), Q value = 0.041

Table S40.  Clustering Approach #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #9: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 173 50.9 (41.4)
DEL PEAK 8(3P12.2) MUTATED 128 56.8 (44.4)
DEL PEAK 8(3P12.2) WILD-TYPE 45 34.2 (24.7)

Figure S3.  Get High-res Image Clustering Approach #37: 'Del Peak 8(3p12.2) mutation analysis' versus Clinical Feature #9: 'NUMBERPACKYEARSSMOKED'

Clustering Approach #38: 'Del Peak 9(4p16.3) mutation analysis'

Table S41.  Description of clustering approach #38: 'Del Peak 9(4p16.3) mutation analysis'

Cluster Labels DEL PEAK 9(4P16.3) MUTATED DEL PEAK 9(4P16.3) WILD-TYPE
Number of samples 137 182
Clustering Approach #39: 'Del Peak 10(4p15.2) mutation analysis'

Table S42.  Description of clustering approach #39: 'Del Peak 10(4p15.2) mutation analysis'

Cluster Labels DEL PEAK 10(4P15.2) MUTATED DEL PEAK 10(4P15.2) WILD-TYPE
Number of samples 138 181
Clustering Approach #40: 'Del Peak 11(4q22.1) mutation analysis'

Table S43.  Description of clustering approach #40: 'Del Peak 11(4q22.1) mutation analysis'

Cluster Labels DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
Number of samples 102 217
Clustering Approach #41: 'Del Peak 12(4q35.2) mutation analysis'

Table S44.  Description of clustering approach #41: 'Del Peak 12(4q35.2) mutation analysis'

Cluster Labels DEL PEAK 12(4Q35.2) MUTATED DEL PEAK 12(4Q35.2) WILD-TYPE
Number of samples 131 188
Clustering Approach #42: 'Del Peak 13(5q11.2) mutation analysis'

Table S45.  Description of clustering approach #42: 'Del Peak 13(5q11.2) mutation analysis'

Cluster Labels DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
Number of samples 134 185
Clustering Approach #43: 'Del Peak 14(5q35.3) mutation analysis'

Table S46.  Description of clustering approach #43: 'Del Peak 14(5q35.3) mutation analysis'

Cluster Labels DEL PEAK 14(5Q35.3) MUTATED DEL PEAK 14(5Q35.3) WILD-TYPE
Number of samples 126 193
Clustering Approach #44: 'Del Peak 15(6p25.3) mutation analysis'

Table S47.  Description of clustering approach #44: 'Del Peak 15(6p25.3) mutation analysis'

Cluster Labels DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
Number of samples 64 255
Clustering Approach #45: 'Del Peak 16(7q31.1) mutation analysis'

Table S48.  Description of clustering approach #45: 'Del Peak 16(7q31.1) mutation analysis'

Cluster Labels DEL PEAK 16(7Q31.1) MUTATED DEL PEAK 16(7Q31.1) WILD-TYPE
Number of samples 49 270
Clustering Approach #46: 'Del Peak 17(7q36.1) mutation analysis'

Table S49.  Description of clustering approach #46: 'Del Peak 17(7q36.1) mutation analysis'

Cluster Labels DEL PEAK 17(7Q36.1) MUTATED DEL PEAK 17(7Q36.1) WILD-TYPE
Number of samples 80 239
Clustering Approach #47: 'Del Peak 18(8p23.2) mutation analysis'

Table S50.  Description of clustering approach #47: 'Del Peak 18(8p23.2) mutation analysis'

Cluster Labels DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
Number of samples 182 137
Clustering Approach #48: 'Del Peak 19(9p23) mutation analysis'

Table S51.  Description of clustering approach #48: 'Del Peak 19(9p23) mutation analysis'

Cluster Labels DEL PEAK 19(9P23) MUTATED DEL PEAK 19(9P23) WILD-TYPE
Number of samples 149 170
Clustering Approach #49: 'Del Peak 20(9p21.3) mutation analysis'

Table S52.  Description of clustering approach #49: 'Del Peak 20(9p21.3) mutation analysis'

Cluster Labels DEL PEAK 20(9P21.3) MUTATED DEL PEAK 20(9P21.3) WILD-TYPE
Number of samples 187 132
Clustering Approach #50: 'Del Peak 21(9q21.11) mutation analysis'

Table S53.  Description of clustering approach #50: 'Del Peak 21(9q21.11) mutation analysis'

Cluster Labels DEL PEAK 21(9Q21.11) MUTATED DEL PEAK 21(9Q21.11) WILD-TYPE
Number of samples 60 259
Clustering Approach #51: 'Del Peak 22(9q34.3) mutation analysis'

Table S54.  Description of clustering approach #51: 'Del Peak 22(9q34.3) mutation analysis'

Cluster Labels DEL PEAK 22(9Q34.3) MUTATED DEL PEAK 22(9Q34.3) WILD-TYPE
Number of samples 53 266
Clustering Approach #52: 'Del Peak 23(10p15.3) mutation analysis'

Table S55.  Description of clustering approach #52: 'Del Peak 23(10p15.3) mutation analysis'

Cluster Labels DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
Number of samples 108 211
Clustering Approach #53: 'Del Peak 24(10p11.21) mutation analysis'

Table S56.  Description of clustering approach #53: 'Del Peak 24(10p11.21) mutation analysis'

Cluster Labels DEL PEAK 24(10P11.21) MUTATED DEL PEAK 24(10P11.21) WILD-TYPE
Number of samples 101 218
Clustering Approach #54: 'Del Peak 25(10q23.31) mutation analysis'

Table S57.  Description of clustering approach #54: 'Del Peak 25(10q23.31) mutation analysis'

Cluster Labels DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
Number of samples 82 237
Clustering Approach #55: 'Del Peak 26(11p15.4) mutation analysis'

Table S58.  Description of clustering approach #55: 'Del Peak 26(11p15.4) mutation analysis'

Cluster Labels DEL PEAK 26(11P15.4) MUTATED DEL PEAK 26(11P15.4) WILD-TYPE
Number of samples 100 219
Clustering Approach #56: 'Del Peak 27(11q23.1) mutation analysis'

Table S59.  Description of clustering approach #56: 'Del Peak 27(11q23.1) mutation analysis'

Cluster Labels DEL PEAK 27(11Q23.1) MUTATED DEL PEAK 27(11Q23.1) WILD-TYPE
Number of samples 152 167
Clustering Approach #57: 'Del Peak 28(12q24.33) mutation analysis'

Table S60.  Description of clustering approach #57: 'Del Peak 28(12q24.33) mutation analysis'

Cluster Labels DEL PEAK 28(12Q24.33) MUTATED DEL PEAK 28(12Q24.33) WILD-TYPE
Number of samples 38 281
Clustering Approach #58: 'Del Peak 29(13q12.11) mutation analysis'

Table S61.  Description of clustering approach #58: 'Del Peak 29(13q12.11) mutation analysis'

Cluster Labels DEL PEAK 29(13Q12.11) MUTATED DEL PEAK 29(13Q12.11) WILD-TYPE
Number of samples 143 176
Clustering Approach #59: 'Del Peak 30(13q14.2) mutation analysis'

Table S62.  Description of clustering approach #59: 'Del Peak 30(13q14.2) mutation analysis'

Cluster Labels DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
Number of samples 135 184
Clustering Approach #60: 'Del Peak 31(14q11.2) mutation analysis'

Table S63.  Description of clustering approach #60: 'Del Peak 31(14q11.2) mutation analysis'

Cluster Labels DEL PEAK 31(14Q11.2) MUTATED DEL PEAK 31(14Q11.2) WILD-TYPE
Number of samples 45 274
Clustering Approach #61: 'Del Peak 32(14q32.32) mutation analysis'

Table S64.  Description of clustering approach #61: 'Del Peak 32(14q32.32) mutation analysis'

Cluster Labels DEL PEAK 32(14Q32.32) MUTATED DEL PEAK 32(14Q32.32) WILD-TYPE
Number of samples 47 272
Clustering Approach #62: 'Del Peak 33(15q15.1) mutation analysis'

Table S65.  Description of clustering approach #62: 'Del Peak 33(15q15.1) mutation analysis'

Cluster Labels DEL PEAK 33(15Q15.1) MUTATED DEL PEAK 33(15Q15.1) WILD-TYPE
Number of samples 76 243
Clustering Approach #63: 'Del Peak 34(16q12.1) mutation analysis'

Table S66.  Description of clustering approach #63: 'Del Peak 34(16q12.1) mutation analysis'

Cluster Labels DEL PEAK 34(16Q12.1) MUTATED DEL PEAK 34(16Q12.1) WILD-TYPE
Number of samples 54 265
Clustering Approach #64: 'Del Peak 35(16q23.3) mutation analysis'

Table S67.  Description of clustering approach #64: 'Del Peak 35(16q23.3) mutation analysis'

Cluster Labels DEL PEAK 35(16Q23.3) MUTATED DEL PEAK 35(16Q23.3) WILD-TYPE
Number of samples 64 255
Clustering Approach #65: 'Del Peak 36(17q25.3) mutation analysis'

Table S68.  Description of clustering approach #65: 'Del Peak 36(17q25.3) mutation analysis'

Cluster Labels DEL PEAK 36(17Q25.3) MUTATED DEL PEAK 36(17Q25.3) WILD-TYPE
Number of samples 41 278
Clustering Approach #66: 'Del Peak 37(18q21.2) mutation analysis'

Table S69.  Description of clustering approach #66: 'Del Peak 37(18q21.2) mutation analysis'

Cluster Labels DEL PEAK 37(18Q21.2) MUTATED DEL PEAK 37(18Q21.2) WILD-TYPE
Number of samples 168 151
Clustering Approach #67: 'Del Peak 38(18q23) mutation analysis'

Table S70.  Description of clustering approach #67: 'Del Peak 38(18q23) mutation analysis'

Cluster Labels DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
Number of samples 180 139
Clustering Approach #68: 'Del Peak 39(19p13.3) mutation analysis'

Table S71.  Description of clustering approach #68: 'Del Peak 39(19p13.3) mutation analysis'

Cluster Labels DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
Number of samples 109 210
Clustering Approach #69: 'Del Peak 40(19q13.43) mutation analysis'

Table S72.  Description of clustering approach #69: 'Del Peak 40(19q13.43) mutation analysis'

Cluster Labels DEL PEAK 40(19Q13.43) MUTATED DEL PEAK 40(19Q13.43) WILD-TYPE
Number of samples 63 256
Clustering Approach #70: 'Del Peak 41(Xp21.3) mutation analysis'

Table S73.  Description of clustering approach #70: 'Del Peak 41(Xp21.3) mutation analysis'

Cluster Labels DEL PEAK 41(XP21.3) MUTATED DEL PEAK 41(XP21.3) WILD-TYPE
Number of samples 105 214
Clustering Approach #71: 'Del Peak 42(Xp11.3) mutation analysis'

Table S74.  Description of clustering approach #71: 'Del Peak 42(Xp11.3) mutation analysis'

Cluster Labels DEL PEAK 42(XP11.3) MUTATED DEL PEAK 42(XP11.3) WILD-TYPE
Number of samples 107 212
Clustering Approach #72: 'Del Peak 43(Xq21.33) mutation analysis'

Table S75.  Description of clustering approach #72: 'Del Peak 43(Xq21.33) mutation analysis'

Cluster Labels DEL PEAK 43(XQ21.33) MUTATED DEL PEAK 43(XQ21.33) WILD-TYPE
Number of samples 55 264
Methods & Data
Input

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

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

  • Number of patients = 319

  • Number of clustering approaches = 72

  • Number of selected clinical features = 12

  • 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

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] 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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