Correlation between copy number variations of arm-level result and selected clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C14B2ZSD
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C14B2ZSD
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 57 arm-level events and 15 clinical features across 482 patients, 56 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • 3p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 4p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 4q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 5p gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 5q gain cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 7p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 7q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 8q gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 9q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 12p gain cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 12q gain cnv correlated to 'PATHOLOGY.M.STAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 13q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 16p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 16q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 17p gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 17q gain cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

  • 18p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 18q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 19p gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 19q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 20p gain cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 20q gain cnv correlated to 'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.M.STAGE', and 'NUMBER.OF.LYMPH.NODES'.

  • 21q gain cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • xq gain cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 2p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 2q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 3q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 8p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 9q loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 10p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 10q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 11p loss cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • 11q loss cnv correlated to 'AGE' and 'NEOPLASM.DISEASESTAGE'.

  • 13q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • 17q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.

  • xq loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 57 arm-level events and 15 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 56 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		RADIATIONEXPOSURE EXTRATHYROIDAL
EXTENSION 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		MULTIFOCALITY TUMOR
SIZE
nCNV (%) nWild-Type logrank test t-test Chi-square 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 Fisher's exact test Fisher's exact test Fisher's exact test t-test Fisher's exact test t-test
5q gain 15 (3%) 467 0.0205
(1.00) 		0.0105
(1.00) 		5.04e-05
(0.0405) 		0.66
(1.00) 		0.0108
(1.00) 		1.13e-05
(0.00912) 		0.557
(1.00) 		0.0277
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.0354
(1.00) 		0.539
(1.00) 		1.41e-25
(1.19e-22) 		0.608
(1.00) 		0.152
(1.00)
20p gain 12 (2%) 470 0.34
(1.00) 		0.094
(1.00) 		5.17e-05
(0.0415) 		0.57
(1.00) 		0.0678
(1.00) 		0.000161
(0.128) 		0.528
(1.00) 		0.00457
(1.00) 		1
(1.00) 		1
(1.00) 		0.0245
(1.00) 		0.854
(1.00) 		1.51e-25
(1.27e-22) 		1
(1.00) 		0.133
(1.00)
20q gain 12 (2%) 470 0.34
(1.00) 		0.094
(1.00) 		5.17e-05
(0.0415) 		0.57
(1.00) 		0.0678
(1.00) 		0.000161
(0.128) 		0.528
(1.00) 		0.00457
(1.00) 		1
(1.00) 		1
(1.00) 		0.0245
(1.00) 		0.854
(1.00) 		1.51e-25
(1.27e-22) 		1
(1.00) 		0.133
(1.00)
1q gain 23 (5%) 459 0.165
(1.00) 		0.00069
(0.542) 		7.73e-06
(0.00626) 		0.000214
(0.169) 		0.002
(1.00) 		0.692
(1.00) 		0.343
(1.00) 		0.0261
(1.00) 		0.501
(1.00) 		0.586
(1.00) 		0.000325
(0.257) 		0.0237
(1.00) 		0.549
(1.00) 		0.0545
(1.00) 		0.0539
(1.00)
7p gain 16 (3%) 466 0.362
(1.00) 		0.0441
(1.00) 		3.58e-05
(0.0289) 		0.851
(1.00) 		0.0057
(1.00) 		0.00153
(1.00) 		1
(1.00) 		0.0112
(1.00) 		1
(1.00) 		1
(1.00) 		0.0132
(1.00) 		0.539
(1.00) 		1.38e-25
(1.16e-22) 		0.803
(1.00) 		0.65
(1.00)
7q gain 18 (4%) 464 0.376
(1.00) 		0.0306
(1.00) 		0.000194
(0.154) 		0.942
(1.00) 		0.0057
(1.00) 		0.00289
(1.00) 		0.791
(1.00) 		0.00773
(1.00) 		1
(1.00) 		1
(1.00) 		0.0253
(1.00) 		0.251
(1.00) 		1.38e-25
(1.16e-22) 		0.812
(1.00) 		0.6
(1.00)
12p gain 13 (3%) 469 0.517
(1.00) 		0.16
(1.00) 		0.0308
(1.00) 		1
(1.00) 		0.00359
(1.00) 		7.1e-05
(0.0568) 		1
(1.00) 		0.00971
(1.00) 		1
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.304
(1.00) 		1.44e-25
(1.22e-22) 		0.587
(1.00) 		0.919
(1.00)
12q gain 14 (3%) 468 0.517
(1.00) 		0.136
(1.00) 		0.0535
(1.00) 		0.969
(1.00) 		0.00359
(1.00) 		2.71e-05
(0.0219) 		1
(1.00) 		0.00394
(1.00) 		1
(1.00) 		1
(1.00) 		0.244
(1.00) 		0.261
(1.00) 		1.44e-25
(1.22e-22) 		0.792
(1.00) 		0.919
(1.00)
16q gain 12 (2%) 470 0.216
(1.00) 		0.106
(1.00) 		6.71e-05
(0.0537) 		0.757
(1.00) 		0.0678
(1.00) 		0.00297
(1.00) 		1
(1.00) 		0.0233
(1.00) 		1
(1.00) 		1
(1.00) 		0.0245
(1.00) 		0.359
(1.00) 		1.51e-25
(1.27e-22) 		1
(1.00) 		0.681
(1.00)
17p gain 16 (3%) 466 0.418
(1.00) 		0.103
(1.00) 		3.58e-05
(0.0289) 		0.851
(1.00) 		0.036
(1.00) 		0.00789
(1.00) 		1
(1.00) 		0.0448
(1.00) 		1
(1.00) 		1
(1.00) 		0.767
(1.00) 		0.321
(1.00) 		1.42e-06
(0.00115) 		1
(1.00) 		0.41
(1.00)
17q gain 17 (4%) 465 0.418
(1.00) 		0.168
(1.00) 		9.64e-05
(0.0768) 		0.864
(1.00) 		0.0206
(1.00) 		0.00594
(1.00) 		1
(1.00) 		0.0711
(1.00) 		1
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.352
(1.00) 		1.97e-07
(0.000161) 		0.806
(1.00) 		0.587
(1.00)
11q loss 9 (2%) 473 0.00286
(1.00) 		9.41e-05
(0.0751) 		5.89e-06
(0.00478) 		0.207
(1.00) 		0.503
(1.00) 		0.121
(1.00) 		0.00179
(1.00) 		1
(1.00) 		0.235
(1.00) 		1
(1.00) 		0.797
(1.00) 		0.507
(1.00) 		0.251
(1.00) 		1
(1.00) 		0.0135
(1.00)
xq loss 3 (1%) 479 0.752
(1.00) 		0.181
(1.00) 		9.08e-05
(0.0725) 		0.223
(1.00) 		0.248
(1.00) 		0.135
(1.00) 		0.174
(1.00) 		0.647
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		1.69e-25
(1.39e-22) 		1
(1.00)
3p gain 3 (1%) 479 0.0123
(1.00) 		0.0169
(1.00) 		4.31e-05
(0.0347) 		0.12
(1.00) 		1
(1.00) 		0.0114
(1.00) 		0.569
(1.00) 		0.234
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		0.0229
(1.00) 		1
(1.00) 		0.628
(1.00)
4p gain 5 (1%) 477 0.0265
(1.00) 		0.0542
(1.00) 		0.36
(1.00) 		0.704
(1.00) 		0.0611
(1.00) 		0.0295
(1.00) 		1
(1.00) 		0.187
(1.00) 		0.138
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		1.62e-25
(1.35e-22) 		0.186
(1.00) 		0.304
(1.00)
4q gain 5 (1%) 477 0.0265
(1.00) 		0.0542
(1.00) 		0.36
(1.00) 		0.704
(1.00) 		0.0611
(1.00) 		0.0295
(1.00) 		1
(1.00) 		0.187
(1.00) 		0.138
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		1.62e-25
(1.35e-22) 		0.186
(1.00) 		0.304
(1.00)
5p gain 18 (4%) 464 0.0822
(1.00) 		0.000966
(0.757) 		0.00021
(0.166) 		0.509
(1.00) 		0.172
(1.00) 		0.000431
(0.34) 		0.586
(1.00) 		0.0934
(1.00) 		0.417
(1.00) 		1
(1.00) 		0.0342
(1.00) 		0.558
(1.00) 		0.012
(1.00) 		1
(1.00) 		0.106
(1.00)
8q gain 7 (1%) 475 0.109
(1.00) 		0.37
(1.00) 		2.38e-06
(0.00193) 		0.41
(1.00) 		1
(1.00) 		0.0966
(1.00) 		0.681
(1.00) 		0.823
(1.00) 		1
(1.00) 		1
(1.00) 		0.00834
(1.00) 		0.38
(1.00) 		0.00203
(1.00) 		0.13
(1.00) 		0.281
(1.00)
9q gain 4 (1%) 478 0.697
(1.00) 		0.0155
(1.00) 		0.0694
(1.00) 		0.629
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.000162
(0.129) 		0.34
(1.00) 		0.00993
(1.00)
11p gain 6 (1%) 476 0.558
(1.00) 		0.777
(1.00) 		0.938
(1.00) 		0.762
(1.00) 		0.123
(1.00) 		0.19
(1.00) 		0.194
(1.00) 		0.257
(1.00) 		1
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.455
(1.00) 		1.66e-25
(1.37e-22) 		0.224
(1.00) 		0.563
(1.00)
11q gain 5 (1%) 477 0.561
(1.00) 		0.808
(1.00) 		0.962
(1.00) 		0.892
(1.00) 		0.248
(1.00) 		0.249
(1.00) 		0.612
(1.00) 		0.571
(1.00) 		1
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.385
(1.00) 		1.69e-25
(1.39e-22) 		0.0648
(1.00) 		0.829
(1.00)
13q gain 5 (1%) 477 0.73
(1.00) 		0.166
(1.00) 		0.0178
(1.00) 		0.704
(1.00) 		0.123
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.187
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1.66e-25
(1.37e-22) 		0.666
(1.00) 		0.655
(1.00)
16p gain 14 (3%) 468 0.224
(1.00) 		0.158
(1.00) 		0.000481
(0.379) 		0.819
(1.00) 		0.0371
(1.00) 		0.00535
(1.00) 		1
(1.00) 		0.0825
(1.00) 		1
(1.00) 		1
(1.00) 		0.0366
(1.00) 		0.161
(1.00) 		1.48e-25
(1.24e-22) 		1
(1.00) 		0.69
(1.00)
18p gain 6 (1%) 476 0.616
(1.00) 		0.743
(1.00) 		0.938
(1.00) 		0.762
(1.00) 		0.0611
(1.00) 		0.476
(1.00) 		0.659
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		1.66e-25
(1.37e-22) 		0.691
(1.00) 		0.61
(1.00)
18q gain 6 (1%) 476 0.616
(1.00) 		0.743
(1.00) 		0.938
(1.00) 		0.762
(1.00) 		0.0611
(1.00) 		0.476
(1.00) 		0.659
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		1.66e-25
(1.37e-22) 		0.691
(1.00) 		0.61
(1.00)
19p gain 8 (2%) 474 0.733
(1.00) 		0.0784
(1.00) 		0.871
(1.00) 		0.613
(1.00) 		0.0302
(1.00) 		0.00251
(1.00) 		0.218
(1.00) 		0.00911
(1.00) 		1
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.448
(1.00) 		1.55e-25
(1.29e-22) 		0.152
(1.00) 		0.219
(1.00)
19q gain 10 (2%) 472 0.0339
(1.00) 		0.0278
(1.00) 		0.753
(1.00) 		0.329
(1.00) 		0.0149
(1.00) 		0.00111
(0.867) 		0.139
(1.00) 		0.00576
(1.00) 		0.257
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.681
(1.00) 		1.51e-25
(1.27e-22) 		0.524
(1.00) 		0.145
(1.00)
21q gain 5 (1%) 477 0.616
(1.00) 		0.0433
(1.00) 		0.765
(1.00) 		0.561
(1.00) 		0.248
(1.00) 		0.689
(1.00) 		0.612
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.31
(1.00) 		1.69e-25
(1.39e-22) 		0.0648
(1.00) 		0.314
(1.00)
xq gain 8 (2%) 474 0.0775
(1.00) 		0.0531
(1.00) 		7.36e-07
(0.000599) 		0.557
(1.00) 		0.449
(1.00) 		0.00251
(1.00) 		0.688
(1.00) 		0.255
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.0205
(1.00) 		0.154
(1.00) 		0.805
(1.00) 		0.152
(1.00) 		0.472
(1.00)
2p loss 10 (2%) 472 0.719
(1.00) 		0.281
(1.00) 		0.00344
(1.00) 		0.697
(1.00) 		0.00732
(1.00) 		0.0136
(1.00) 		0.73
(1.00) 		0.00576
(1.00) 		1
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.551
(1.00) 		1.48e-25
(1.24e-22) 		1
(1.00) 		0.696
(1.00)
2q loss 10 (2%) 472 0.575
(1.00) 		0.256
(1.00) 		0.00344
(1.00) 		0.823
(1.00) 		0.0149
(1.00) 		0.0136
(1.00) 		0.73
(1.00) 		0.00576
(1.00) 		1
(1.00) 		1
(1.00) 		0.142
(1.00) 		0.551
(1.00) 		1.51e-25
(1.27e-22) 		1
(1.00) 		0.48
(1.00)
3q loss 4 (1%) 478 0.597
(1.00) 		0.645
(1.00) 		0.204
(1.00) 		0.629
(1.00) 		0.248
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		1.69e-25
(1.39e-22) 		1
(1.00) 		0.101
(1.00)
8p loss 4 (1%) 478 0.871
(1.00) 		0.983
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.374
(1.00) 		0.0592
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		1.66e-25
(1.37e-22) 		1
(1.00) 		0.89
(1.00)
8q loss 4 (1%) 478 0.871
(1.00) 		0.983
(1.00) 		0.191
(1.00) 		1
(1.00) 		0.248
(1.00) 		0.374
(1.00) 		0.0592
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		1.66e-25
(1.37e-22) 		1
(1.00) 		0.89
(1.00)
9q loss 22 (5%) 460 0.0297
(1.00) 		0.0219
(1.00) 		1.38e-09
(1.13e-06) 		0.19
(1.00) 		0.64
(1.00) 		0.0152
(1.00) 		0.323
(1.00) 		0.712
(1.00) 		0.485
(1.00) 		0.586
(1.00) 		0.0674
(1.00) 		0.568
(1.00) 		0.235
(1.00) 		0.666
(1.00) 		0.112
(1.00)
10p loss 7 (1%) 475 0.587
(1.00) 		0.332
(1.00) 		0.106
(1.00) 		0.261
(1.00) 		0.0302
(1.00) 		0.0966
(1.00) 		0.389
(1.00) 		0.396
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		1.62e-25
(1.35e-22) 		0.709
(1.00) 		0.051
(1.00)
10q loss 6 (1%) 476 0.648
(1.00) 		0.337
(1.00) 		0.46
(1.00) 		0.329
(1.00) 		0.0611
(1.00) 		0.19
(1.00) 		0.194
(1.00) 		0.786
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1.66e-25
(1.37e-22) 		0.422
(1.00) 		0.0462
(1.00)
11p loss 7 (1%) 475 0.00137
(1.00) 		0.000519
(0.408) 		1.61e-07
(0.000131) 		0.229
(1.00) 		0.449
(1.00) 		0.0966
(1.00) 		0.0162
(1.00) 		0.823
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.544
(1.00) 		0.52
(1.00) 		0.0801
(1.00) 		0.709
(1.00) 		0.0355
(1.00)
13q loss 14 (3%) 468 0.383
(1.00) 		0.0466
(1.00) 		0.607
(1.00) 		0.592
(1.00) 		0.0108
(1.00) 		0.366
(1.00) 		0.538
(1.00) 		0.471
(1.00) 		0.342
(1.00) 		0.000726
(0.57) 		0.627
(1.00) 		0.671
(1.00) 		9.97e-15
(8.16e-12) 		0.792
(1.00) 		0.153
(1.00)
17q loss 4 (1%) 478 0.805
(1.00) 		0.369
(1.00) 		0.795
(1.00) 		0.629
(1.00) 		0.123
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.465
(1.00) 		0.112
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1.69e-25
(1.39e-22) 		1
(1.00) 		0.485
(1.00)
1p gain 3 (1%) 479 0.919
(1.00) 		0.304
(1.00) 		0.0193
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.0787
(1.00) 		1
(1.00) 		0.232
(1.00) 		0.15
(1.00) 		1
(1.00)
8p gain 6 (1%) 476 0.627
(1.00) 		0.634
(1.00) 		0.938
(1.00) 		0.906
(1.00) 		0.623
(1.00) 		0.19
(1.00) 		1
(1.00) 		0.786
(1.00) 		1
(1.00) 		1
(1.00) 		0.354
(1.00) 		0.455
(1.00) 		0.00203
(1.00) 		0.224
(1.00) 		0.425
(1.00)
9p gain 3 (1%) 479 0.702
(1.00) 		0.0789
(1.00) 		0.0443
(1.00) 		0.806
(1.00) 		0.248
(1.00) 		0.608
(1.00) 		1
(1.00) 		0.234
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.598
(1.00) 		0.0613
(1.00)
14q gain 11 (2%) 471 0.535
(1.00) 		0.029
(1.00) 		0.00241
(1.00) 		0.38
(1.00) 		0.0678
(1.00) 		0.0348
(1.00) 		0.302
(1.00) 		0.0638
(1.00) 		1
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.49
(1.00) 		0.0173
(1.00) 		0.123
(1.00) 		0.312
(1.00)
1p loss 4 (1%) 478 0.601
(1.00) 		0.604
(1.00) 		0.204
(1.00) 		0.629
(1.00) 		0.248
(1.00) 		0.374
(1.00) 		0.578
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.177
(1.00)
1q loss 3 (1%) 479 0.604
(1.00) 		0.871
(1.00) 		0.805
(1.00) 		0.806
(1.00) 		0.499
(1.00) 		0.135
(1.00) 		0.569
(1.00) 		0.234
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		1
(1.00) 		0.177
(1.00)
3p loss 3 (1%) 479 0.661
(1.00) 		0.67
(1.00) 		0.805
(1.00) 		0.806
(1.00) 		0.499
(1.00) 		0.135
(1.00) 		1
(1.00) 		0.647
(1.00) 		1
(1.00) 		1
(1.00) 		0.609
(1.00) 		1
(1.00) 		0.598
(1.00) 		0.0828
(1.00)
6p loss 4 (1%) 478 0.633
(1.00) 		0.42
(1.00) 		0.805
(1.00) 		1
(1.00) 		1
(1.00) 		0.107
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.0252
(1.00)
6q loss 7 (1%) 475 0.00836
(1.00) 		0.123
(1.00) 		0.37
(1.00) 		0.79
(1.00) 		0.372
(1.00) 		0.00974
(1.00) 		0.389
(1.00) 		0.823
(1.00) 		0.188
(1.00) 		0.219
(1.00) 		0.384
(1.00) 		0.748
(1.00) 		0.00203
(1.00) 		0.459
(1.00) 		0.0166
(1.00)
9p loss 18 (4%) 464 0.419
(1.00) 		0.203
(1.00) 		0.00279
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.0259
(1.00) 		0.275
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.65
(1.00) 		0.007
(1.00) 		0.633
(1.00) 		0.186
(1.00)
15q loss 8 (2%) 474 0.559
(1.00) 		0.707
(1.00) 		0.221
(1.00) 		0.724
(1.00) 		0.122
(1.00) 		0.0622
(1.00) 		0.688
(1.00) 		0.054
(1.00) 		1
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.786
(1.00) 		0.386
(1.00) 		0.731
(1.00) 		0.0858
(1.00)
17p loss 7 (1%) 475 0.588
(1.00) 		0.682
(1.00) 		0.527
(1.00) 		0.14
(1.00) 		0.449
(1.00) 		0.343
(1.00) 		0.681
(1.00) 		0.155
(1.00) 		0.0152
(1.00) 		0.251
(1.00) 		0.246
(1.00) 		0.748
(1.00) 		0.929
(1.00) 		1
(1.00) 		0.0925
(1.00)
18p loss 4 (1%) 478 0.758
(1.00) 		0.544
(1.00) 		0.191
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.00203
(1.00) 		0.628
(1.00) 		0.233
(1.00)
18q loss 4 (1%) 478 0.758
(1.00) 		0.544
(1.00) 		0.191
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.374
(1.00) 		1
(1.00) 		0.465
(1.00) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		1
(1.00) 		0.00203
(1.00) 		0.628
(1.00) 		0.233
(1.00)
19p loss 5 (1%) 477 0.13
(1.00) 		0.52
(1.00) 		0.315
(1.00) 		1
(1.00) 		1
(1.00) 		0.689
(1.00) 		0.612
(1.00) 		1
(1.00) 		1
(1.00) 		0.0141
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.38
(1.00) 		0.0195
(1.00)
21q loss 8 (2%) 474 0.847
(1.00) 		0.0972
(1.00) 		0.00902
(1.00) 		0.176
(1.00) 		0.724
(1.00) 		0.773
(1.00) 		0.443
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.98
(1.00) 		0.152
(1.00) 		0.671
(1.00)
22q loss 84 (17%) 398 0.492
(1.00) 		0.898
(1.00) 		0.696
(1.00) 		0.526
(1.00) 		0.315
(1.00) 		0.578
(1.00) 		0.497
(1.00) 		0.273
(1.00) 		0.481
(1.00) 		0.333
(1.00) 		0.306
(1.00) 		0.492
(1.00) 		0.306
(1.00) 		0.225
(1.00) 		0.861
(1.00)
'1q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.73e-06 (Chi-square test), Q value = 0.0063

Table S1.  Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
1Q GAIN MUTATED 6 0 9 1 7 0
1Q GAIN WILD-TYPE 267 50 97 1 36 6

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'1q gain' versus 'PATHOLOGY.T.STAGE'

P value = 0.000214 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3 T4
ALL 139 160 160 21
1Q GAIN MUTATED 2 3 14 4
1Q GAIN WILD-TYPE 137 157 146 17

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'3p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.31e-05 (Chi-square test), Q value = 0.035

Table S3.  Gene #3: '3p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
3P GAIN MUTATED 1 1 0 0 0 1
3P GAIN WILD-TYPE 272 49 106 2 43 5

Figure S3.  Get High-res Image Gene #3: '3p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'4p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S4.  Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
4P GAIN MUTATED 5 0.0 (0.0)
4P GAIN WILD-TYPE 378 3.6 (6.2)

Figure S4.  Get High-res Image Gene #4: '4p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'4q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S5.  Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
4Q GAIN MUTATED 5 0.0 (0.0)
4Q GAIN WILD-TYPE 378 3.6 (6.2)

Figure S5.  Get High-res Image Gene #5: '4q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'5p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00021 (Chi-square test), Q value = 0.17

Table S6.  Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
5P GAIN MUTATED 4 5 7 1 1 0
5P GAIN WILD-TYPE 269 45 99 1 42 6

Figure S6.  Get High-res Image Gene #6: '5p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.04e-05 (Chi-square test), Q value = 0.041

Table S7.  Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
5Q GAIN MUTATED 4 5 5 1 0 0
5Q GAIN WILD-TYPE 269 45 101 1 43 6

Figure S7.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'5q gain' versus 'PATHOLOGY.M.STAGE'

P value = 1.13e-05 (Fisher's exact test), Q value = 0.0091

Table S8.  Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 264 9 208
5Q GAIN MUTATED 0 0 15
5Q GAIN WILD-TYPE 264 9 193

Figure S8.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'5q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.41e-25 (t-test), Q value = 1.2e-22

Table S9.  Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
5Q GAIN MUTATED 11 0.0 (0.0)
5Q GAIN WILD-TYPE 372 3.7 (6.3)

Figure S9.  Get High-res Image Gene #7: '5q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.58e-05 (Chi-square test), Q value = 0.029

Table S10.  Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
7P GAIN MUTATED 6 6 3 1 0 0
7P GAIN WILD-TYPE 267 44 103 1 43 6

Figure S10.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.38e-25 (t-test), Q value = 1.2e-22

Table S11.  Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
7P GAIN MUTATED 12 0.0 (0.0)
7P GAIN WILD-TYPE 371 3.7 (6.3)

Figure S11.  Get High-res Image Gene #8: '7p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'7q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.000194 (Chi-square test), Q value = 0.15

Table S12.  Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
7Q GAIN MUTATED 7 6 4 1 0 0
7Q GAIN WILD-TYPE 266 44 102 1 43 6

Figure S12.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'7q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.38e-25 (t-test), Q value = 1.2e-22

Table S13.  Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
7Q GAIN MUTATED 12 0.0 (0.0)
7Q GAIN WILD-TYPE 371 3.7 (6.3)

Figure S13.  Get High-res Image Gene #9: '7q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.38e-06 (Chi-square test), Q value = 0.0019

Table S14.  Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
8Q GAIN MUTATED 3 1 2 1 0 0
8Q GAIN WILD-TYPE 270 49 104 1 43 6

Figure S14.  Get High-res Image Gene #11: '8q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'9q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000162 (t-test), Q value = 0.13

Table S15.  Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
9Q GAIN MUTATED 3 0.3 (0.6)
9Q GAIN WILD-TYPE 380 3.6 (6.2)

Figure S15.  Get High-res Image Gene #13: '9q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S16.  Gene #14: '11p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
11P GAIN MUTATED 4 0.0 (0.0)
11P GAIN WILD-TYPE 379 3.6 (6.2)

Figure S16.  Get High-res Image Gene #14: '11p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S17.  Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
11Q GAIN MUTATED 3 0.0 (0.0)
11Q GAIN WILD-TYPE 380 3.6 (6.2)

Figure S17.  Get High-res Image Gene #15: '11q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12p gain' versus 'PATHOLOGY.M.STAGE'

P value = 7.1e-05 (Fisher's exact test), Q value = 0.057

Table S18.  Gene #16: '12p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 264 9 208
12P GAIN MUTATED 0 0 13
12P GAIN WILD-TYPE 264 9 195

Figure S18.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'12p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.44e-25 (t-test), Q value = 1.2e-22

Table S19.  Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
12P GAIN MUTATED 10 0.0 (0.0)
12P GAIN WILD-TYPE 373 3.7 (6.3)

Figure S19.  Get High-res Image Gene #16: '12p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'12q gain' versus 'PATHOLOGY.M.STAGE'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.022

Table S20.  Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 264 9 208
12Q GAIN MUTATED 0 0 14
12Q GAIN WILD-TYPE 264 9 194

Figure S20.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'12q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.44e-25 (t-test), Q value = 1.2e-22

Table S21.  Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
12Q GAIN MUTATED 10 0.0 (0.0)
12Q GAIN WILD-TYPE 373 3.7 (6.3)

Figure S21.  Get High-res Image Gene #17: '12q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'13q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S22.  Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
13Q GAIN MUTATED 4 0.0 (0.0)
13Q GAIN WILD-TYPE 379 3.6 (6.2)

Figure S22.  Get High-res Image Gene #18: '13q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.48e-25 (t-test), Q value = 1.2e-22

Table S23.  Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
16P GAIN MUTATED 9 0.0 (0.0)
16P GAIN WILD-TYPE 374 3.6 (6.3)

Figure S23.  Get High-res Image Gene #20: '16p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'16q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.71e-05 (Chi-square test), Q value = 0.054

Table S24.  Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
16Q GAIN MUTATED 5 4 2 1 0 0
16Q GAIN WILD-TYPE 268 46 104 1 43 6

Figure S24.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'16q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S25.  Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
16Q GAIN MUTATED 8 0.0 (0.0)
16Q GAIN WILD-TYPE 375 3.6 (6.3)

Figure S25.  Get High-res Image Gene #21: '16q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.58e-05 (Chi-square test), Q value = 0.029

Table S26.  Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
17P GAIN MUTATED 6 6 3 1 0 0
17P GAIN WILD-TYPE 267 44 103 1 43 6

Figure S26.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.42e-06 (t-test), Q value = 0.0012

Table S27.  Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
17P GAIN MUTATED 12 0.6 (1.4)
17P GAIN WILD-TYPE 371 3.7 (6.3)

Figure S27.  Get High-res Image Gene #22: '17p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.64e-05 (Chi-square test), Q value = 0.077

Table S28.  Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
17Q GAIN MUTATED 7 6 3 1 0 0
17Q GAIN WILD-TYPE 266 44 103 1 43 6

Figure S28.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'17q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.97e-07 (t-test), Q value = 0.00016

Table S29.  Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
17Q GAIN MUTATED 13 0.5 (1.3)
17Q GAIN WILD-TYPE 370 3.7 (6.3)

Figure S29.  Get High-res Image Gene #23: '17q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S30.  Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
18P GAIN MUTATED 4 0.0 (0.0)
18P GAIN WILD-TYPE 379 3.6 (6.2)

Figure S30.  Get High-res Image Gene #24: '18p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'18q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S31.  Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
18Q GAIN MUTATED 4 0.0 (0.0)
18Q GAIN WILD-TYPE 379 3.6 (6.2)

Figure S31.  Get High-res Image Gene #25: '18q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'19p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.55e-25 (t-test), Q value = 1.3e-22

Table S32.  Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
19P GAIN MUTATED 7 0.0 (0.0)
19P GAIN WILD-TYPE 376 3.6 (6.3)

Figure S32.  Get High-res Image Gene #26: '19p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'19q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S33.  Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
19Q GAIN MUTATED 8 0.0 (0.0)
19Q GAIN WILD-TYPE 375 3.6 (6.3)

Figure S33.  Get High-res Image Gene #27: '19q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20p gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.17e-05 (Chi-square test), Q value = 0.041

Table S34.  Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
20P GAIN MUTATED 4 4 3 1 0 0
20P GAIN WILD-TYPE 269 46 103 1 43 6

Figure S34.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20p gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S35.  Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 264 9 208
20P GAIN MUTATED 0 0 12
20P GAIN WILD-TYPE 264 9 196

Figure S35.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20p gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S36.  Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
20P GAIN MUTATED 8 0.0 (0.0)
20P GAIN WILD-TYPE 375 3.6 (6.3)

Figure S36.  Get High-res Image Gene #28: '20p gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'20q gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.17e-05 (Chi-square test), Q value = 0.041

Table S37.  Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
20Q GAIN MUTATED 4 4 3 1 0 0
20Q GAIN WILD-TYPE 269 46 103 1 43 6

Figure S37.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'20q gain' versus 'PATHOLOGY.M.STAGE'

P value = 0.000161 (Fisher's exact test), Q value = 0.13

Table S38.  Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients M0 M1 MX
ALL 264 9 208
20Q GAIN MUTATED 0 0 12
20Q GAIN WILD-TYPE 264 9 196

Figure S38.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S39.  Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
20Q GAIN MUTATED 8 0.0 (0.0)
20Q GAIN WILD-TYPE 375 3.6 (6.3)

Figure S39.  Get High-res Image Gene #29: '20q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'21q gain' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S40.  Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
21Q GAIN MUTATED 3 0.0 (0.0)
21Q GAIN WILD-TYPE 380 3.6 (6.2)

Figure S40.  Get High-res Image Gene #30: '21q gain' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq gain' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.36e-07 (Chi-square test), Q value = 6e-04

Table S41.  Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
XQ GAIN MUTATED 2 3 2 1 0 0
XQ GAIN WILD-TYPE 271 47 104 1 43 6

Figure S41.  Get High-res Image Gene #31: 'xq gain' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'2p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.48e-25 (t-test), Q value = 1.2e-22

Table S42.  Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
2P LOSS MUTATED 9 0.0 (0.0)
2P LOSS WILD-TYPE 374 3.6 (6.3)

Figure S42.  Get High-res Image Gene #34: '2p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'2q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.51e-25 (t-test), Q value = 1.3e-22

Table S43.  Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
2Q LOSS MUTATED 8 0.0 (0.0)
2Q LOSS WILD-TYPE 375 3.6 (6.3)

Figure S43.  Get High-res Image Gene #35: '2q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'3q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S44.  Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
3Q LOSS MUTATED 3 0.0 (0.0)
3Q LOSS WILD-TYPE 380 3.6 (6.2)

Figure S44.  Get High-res Image Gene #37: '3q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S45.  Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
8P LOSS MUTATED 4 0.0 (0.0)
8P LOSS WILD-TYPE 379 3.6 (6.2)

Figure S45.  Get High-res Image Gene #40: '8p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'8q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S46.  Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
8Q LOSS MUTATED 4 0.0 (0.0)
8Q LOSS WILD-TYPE 379 3.6 (6.2)

Figure S46.  Get High-res Image Gene #41: '8q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'9q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.38e-09 (Chi-square test), Q value = 1.1e-06

Table S47.  Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
9Q LOSS MUTATED 8 5 3 2 3 1
9Q LOSS WILD-TYPE 265 45 103 0 40 5

Figure S47.  Get High-res Image Gene #43: '9q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'10p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.62e-25 (t-test), Q value = 1.3e-22

Table S48.  Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
10P LOSS MUTATED 5 0.0 (0.0)
10P LOSS WILD-TYPE 378 3.6 (6.2)

Figure S48.  Get High-res Image Gene #44: '10p loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'10q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.66e-25 (t-test), Q value = 1.4e-22

Table S49.  Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
10Q LOSS MUTATED 4 0.0 (0.0)
10Q LOSS WILD-TYPE 379 3.6 (6.2)

Figure S49.  Get High-res Image Gene #45: '10q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'11p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.61e-07 (Chi-square test), Q value = 0.00013

Table S50.  Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
11P LOSS MUTATED 1 1 4 1 0 0
11P LOSS WILD-TYPE 272 49 102 1 43 6

Figure S50.  Get High-res Image Gene #46: '11p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'11q loss' versus 'AGE'

P value = 9.41e-05 (t-test), Q value = 0.075

Table S51.  Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 482 47.1 (15.6)
11Q LOSS MUTATED 9 67.0 (8.9)
11Q LOSS WILD-TYPE 473 46.7 (15.5)

Figure S51.  Get High-res Image Gene #47: '11q loss' versus Clinical Feature #2: 'AGE'

'11q loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.89e-06 (Chi-square test), Q value = 0.0048

Table S52.  Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
11Q LOSS MUTATED 1 2 4 1 1 0
11Q LOSS WILD-TYPE 272 48 102 1 42 6

Figure S52.  Get High-res Image Gene #47: '11q loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'13q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 9.97e-15 (t-test), Q value = 8.2e-12

Table S53.  Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
13Q LOSS MUTATED 10 0.2 (0.6)
13Q LOSS WILD-TYPE 373 3.7 (6.3)

Figure S53.  Get High-res Image Gene #48: '13q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'17q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S54.  Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
17Q LOSS MUTATED 3 0.0 (0.0)
17Q LOSS WILD-TYPE 380 3.6 (6.2)

Figure S54.  Get High-res Image Gene #51: '17q loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

'xq loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.08e-05 (Chi-square test), Q value = 0.073

Table S55.  Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVC
ALL 273 50 106 2 43 6
XQ LOSS MUTATED 0 3 0 0 0 0
XQ LOSS WILD-TYPE 273 47 106 2 43 6

Figure S55.  Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'xq loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 1.69e-25 (t-test), Q value = 1.4e-22

Table S56.  Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 383 3.6 (6.2)
XQ LOSS MUTATED 3 0.0 (0.0)
XQ LOSS WILD-TYPE 380 3.6 (6.2)

Figure S56.  Get High-res Image Gene #57: 'xq loss' versus Clinical Feature #13: 'NUMBER.OF.LYMPH.NODES'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = THCA-TP.merged_data.txt

  • Number of patients = 482

  • Number of significantly arm-level cnvs = 57

  • Number of selected clinical features = 15

  • Exclude regions 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

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

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

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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