Correlation between copy number variations of arm-level result and selected clinical features
Thymoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C17S7N9Q
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 51 arm-level events and 8 clinical features across 123 patients, 62 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'Time to Death',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 3q gain cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 5p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 5q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 7q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 8p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 8q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 9p gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'RACE'.

  • 9q gain cnv correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'RACE'.

  • 12p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 12q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 14q gain cnv correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • 15q gain cnv correlated to 'TUMOR_TISSUE_SITE',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • 17q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 19q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20p gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 20q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 21q gain cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 1p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 3p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 3q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 6p loss cnv correlated to 'Time to Death',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 6q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 9p loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 11p loss cnv correlated to 'TUMOR_TISSUE_SITE' and 'ETHNICITY'.

  • 11q loss cnv correlated to 'YEARS_TO_BIRTH',  'HISTOLOGICAL_TYPE', and 'ETHNICITY'.

  • 12q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 16q loss cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 17p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 17q loss cnv correlated to 'ETHNICITY'.

  • 18p loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 18q loss cnv correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

  • 19p loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 19q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.

  • 21q loss cnv correlated to 'ETHNICITY'.

  • 22q loss cnv correlated to 'ETHNICITY'.

  • xq loss cnv correlated to 'ETHNICITY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 51 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 62 significant findings detected.

Clinical
Features
Time
to
Death
YEARS
TO
BIRTH
TUMOR
TISSUE
SITE
GENDER RADIATION
THERAPY
HISTOLOGICAL
TYPE
RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-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
1q gain 23 (19%) 100 2.8e-05
(0.00408)
0.358
(0.712)
0.585
(0.938)
0.247
(0.622)
0.0157
(0.139)
3e-05
(0.00408)
0.319
(0.681)
0.371
(0.724)
9p gain 11 (9%) 112 0.351
(0.711)
0.00243
(0.0472)
1
(1.00)
1
(1.00)
0.00755
(0.088)
0.106
(0.433)
0.0323
(0.216)
1
(1.00)
9q gain 11 (9%) 112 0.351
(0.711)
0.00243
(0.0472)
1
(1.00)
1
(1.00)
0.00755
(0.088)
0.107
(0.433)
0.0313
(0.213)
1
(1.00)
15q gain 12 (10%) 111 0.333
(0.697)
0.88
(1.00)
0.0234
(0.175)
1
(1.00)
0.0216
(0.166)
0.0144
(0.134)
1
(1.00)
1
(1.00)
6p loss 21 (17%) 102 0.00414
(0.0704)
0.0898
(0.412)
0.779
(1.00)
0.64
(0.95)
0.449
(0.807)
0.00041
(0.0147)
0.777
(1.00)
0.00777
(0.088)
11q loss 7 (6%) 116 0.437
(0.803)
0.014
(0.133)
0.178
(0.533)
0.442
(0.803)
0.229
(0.59)
0.00584
(0.0781)
0.705
(0.971)
0.0118
(0.117)
3q gain 5 (4%) 118 0.000347
(0.0147)
0.093
(0.416)
0.585
(0.938)
0.67
(0.97)
1
(1.00)
0.00036
(0.0147)
1
(1.00)
1
(1.00)
14q gain 13 (11%) 110 0.411
(0.765)
0.0188
(0.149)
1
(1.00)
0.772
(1.00)
0.13
(0.442)
0.0046
(0.0751)
0.803
(1.00)
1
(1.00)
3p loss 12 (10%) 111 0.141
(0.471)
0.232
(0.591)
0.296
(0.661)
0.765
(1.00)
0.336
(0.697)
0.0114
(0.116)
1
(1.00)
0.00566
(0.0781)
3q loss 7 (6%) 116 0.448
(0.807)
0.205
(0.574)
0.178
(0.533)
0.116
(0.433)
0.229
(0.59)
0.0281
(0.195)
0.705
(0.971)
0.00702
(0.0868)
6q loss 20 (16%) 103 0.049
(0.29)
0.124
(0.439)
0.769
(1.00)
1
(1.00)
0.609
(0.938)
0.00013
(0.00758)
0.503
(0.874)
0.00593
(0.0781)
11p loss 9 (7%) 114 0.397
(0.753)
0.155
(0.491)
0.0239
(0.175)
1
(1.00)
0.489
(0.857)
0.0508
(0.296)
1
(1.00)
0.00234
(0.0472)
17p loss 14 (11%) 109 0.716
(0.976)
0.536
(0.911)
1
(1.00)
0.401
(0.758)
0.552
(0.925)
0.00826
(0.0911)
0.84
(1.00)
0.0152
(0.138)
18p loss 7 (6%) 116 0.00539
(0.0781)
0.804
(1.00)
0.648
(0.95)
0.709
(0.971)
0.689
(0.97)
0.0241
(0.175)
1
(1.00)
0.0767
(0.368)
18q loss 7 (6%) 116 0.00539
(0.0781)
0.804
(1.00)
0.648
(0.95)
0.709
(0.971)
0.689
(0.97)
0.0247
(0.177)
1
(1.00)
0.0767
(0.368)
19p loss 3 (2%) 120 0.779
(1.00)
0.275
(0.643)
0.121
(0.433)
0.607
(0.938)
0.268
(0.64)
0.00045
(0.0147)
1
(1.00)
0.0175
(0.146)
19q loss 3 (2%) 120 0.779
(1.00)
0.275
(0.643)
0.121
(0.433)
0.607
(0.938)
0.268
(0.64)
0.00054
(0.0147)
1
(1.00)
0.0175
(0.146)
5p gain 11 (9%) 112 0.176
(0.533)
0.642
(0.95)
0.0624
(0.327)
0.116
(0.433)
0.0445
(0.279)
0.00013
(0.00758)
0.764
(1.00)
0.161
(0.501)
5q gain 9 (7%) 114 0.145
(0.475)
0.553
(0.925)
0.41
(0.765)
0.0859
(0.398)
0.0612
(0.324)
0.0003
(0.0147)
0.733
(0.989)
0.463
(0.821)
7p gain 16 (13%) 107 0.113
(0.433)
0.375
(0.724)
0.116
(0.433)
1
(1.00)
0.167
(0.512)
0.00049
(0.0147)
1
(1.00)
1
(1.00)
7q gain 16 (13%) 107 0.113
(0.433)
0.375
(0.724)
0.116
(0.433)
1
(1.00)
0.167
(0.512)
0.00067
(0.0171)
1
(1.00)
1
(1.00)
8p gain 12 (10%) 111 0.128
(0.442)
0.264
(0.64)
0.296
(0.661)
0.368
(0.722)
0.336
(0.697)
0.0187
(0.149)
0.8
(1.00)
1
(1.00)
8q gain 12 (10%) 111 0.128
(0.442)
0.264
(0.64)
0.296
(0.661)
0.368
(0.722)
0.336
(0.697)
0.019
(0.149)
0.803
(1.00)
1
(1.00)
12p gain 4 (3%) 119 0.193
(0.551)
0.388
(0.743)
0.209
(0.574)
0.62
(0.94)
0.605
(0.938)
0.0035
(0.0621)
1
(1.00)
0.295
(0.661)
12q gain 4 (3%) 119 0.193
(0.551)
0.388
(0.743)
0.209
(0.574)
0.62
(0.94)
0.605
(0.938)
0.00321
(0.0595)
1
(1.00)
0.295
(0.661)
17q gain 7 (6%) 116 0.438
(0.803)
0.574
(0.938)
0.648
(0.95)
1
(1.00)
0.229
(0.59)
0.00899
(0.0965)
0.708
(0.971)
1
(1.00)
19p gain 3 (2%) 120 0.684
(0.97)
0.354
(0.711)
1
(1.00)
0.607
(0.938)
0.268
(0.64)
0.0011
(0.0264)
1
(1.00)
1
(1.00)
19q gain 3 (2%) 120 0.684
(0.97)
0.354
(0.711)
1
(1.00)
0.607
(0.938)
0.268
(0.64)
0.00151
(0.0342)
1
(1.00)
1
(1.00)
20p gain 10 (8%) 113 0.631
(0.95)
0.867
(1.00)
0.224
(0.59)
1
(1.00)
0.307
(0.667)
6e-05
(0.00612)
0.596
(0.938)
0.192
(0.551)
20q gain 10 (8%) 113 0.631
(0.95)
0.867
(1.00)
0.224
(0.59)
1
(1.00)
0.307
(0.667)
8e-05
(0.00653)
0.594
(0.938)
0.192
(0.551)
21q gain 3 (2%) 120 0.782
(1.00)
0.221
(0.59)
0.121
(0.433)
0.107
(0.433)
1
(1.00)
0.005
(0.0781)
1
(1.00)
1
(1.00)
1p loss 5 (4%) 118 0.593
(0.938)
0.148
(0.475)
1
(1.00)
0.67
(0.97)
0.0459
(0.279)
0.0135
(0.132)
1
(1.00)
0.0535
(0.303)
9p loss 4 (3%) 119 0.693
(0.971)
0.131
(0.442)
0.209
(0.574)
0.349
(0.711)
0.605
(0.938)
0.00051
(0.0147)
1
(1.00)
0.295
(0.661)
12q loss 7 (6%) 116 0.327
(0.696)
0.0168
(0.146)
0.648
(0.95)
0.116
(0.433)
0.689
(0.97)
0.314
(0.673)
0.709
(0.971)
0.103
(0.433)
16q loss 13 (11%) 110 0.0664
(0.343)
0.845
(1.00)
0.479
(0.847)
0.772
(1.00)
0.13
(0.442)
1e-05
(0.00408)
0.821
(1.00)
0.0735
(0.361)
17q loss 6 (5%) 117 0.601
(0.938)
0.209
(0.574)
0.612
(0.938)
0.681
(0.97)
0.41
(0.765)
0.0478
(0.287)
0.65
(0.951)
0.00702
(0.0868)
21q loss 9 (7%) 114 0.454
(0.812)
0.0542
(0.303)
0.105
(0.433)
1
(1.00)
0.489
(0.857)
0.146
(0.475)
1
(1.00)
0.0258
(0.182)
22q loss 13 (11%) 110 0.83
(1.00)
0.0919
(0.416)
0.157
(0.492)
0.772
(1.00)
0.059
(0.318)
0.0698
(0.347)
1
(1.00)
0.0113
(0.116)
xq loss 5 (4%) 118 0.153
(0.488)
0.583
(0.938)
1
(1.00)
0.193
(0.551)
0.337
(0.697)
0.209
(0.574)
1
(1.00)
0.0336
(0.221)
1p gain 6 (5%) 117 0.304
(0.667)
0.696
(0.971)
0.119
(0.433)
0.425
(0.789)
1
(1.00)
0.274
(0.643)
0.647
(0.95)
0.356
(0.711)
18p gain 3 (2%) 120 0.721
(0.978)
0.679
(0.97)
0.528
(0.901)
1
(1.00)
0.268
(0.64)
0.079
(0.373)
1
(1.00)
0.23
(0.59)
18q gain 3 (2%) 120 0.721
(0.978)
0.679
(0.97)
0.528
(0.901)
1
(1.00)
0.268
(0.64)
0.0794
(0.373)
1
(1.00)
0.23
(0.59)
22q gain 4 (3%) 119 0.685
(0.97)
0.0938
(0.416)
0.575
(0.938)
0.349
(0.711)
1
(1.00)
0.0688
(0.347)
0.499
(0.869)
1
(1.00)
xq gain 4 (3%) 119 0.106
(0.433)
0.142
(0.472)
1
(1.00)
1
(1.00)
0.605
(0.938)
0.0957
(0.42)
1
(1.00)
1
(1.00)
4p loss 5 (4%) 118 0.44
(0.803)
0.522
(0.901)
1
(1.00)
1
(1.00)
1
(1.00)
0.041
(0.261)
1
(1.00)
1
(1.00)
4q loss 4 (3%) 119 0.462
(0.821)
0.948
(1.00)
1
(1.00)
0.62
(0.94)
0.605
(0.938)
0.0694
(0.347)
1
(1.00)
1
(1.00)
10p loss 3 (2%) 120 0.779
(1.00)
0.286
(0.661)
0.528
(0.901)
0.607
(0.938)
0.55
(0.925)
0.296
(0.661)
1
(1.00)
0.23
(0.59)
12p loss 8 (7%) 115 0.396
(0.753)
0.039
(0.252)
1
(1.00)
0.276
(0.643)
0.443
(0.803)
0.11
(0.433)
1
(1.00)
0.131
(0.442)
13q loss 14 (11%) 109 0.311
(0.671)
0.254
(0.635)
0.187
(0.551)
0.78
(1.00)
0.233
(0.591)
0.107
(0.433)
0.837
(1.00)
0.0592
(0.318)
16p loss 5 (4%) 118 0.602
(0.938)
0.544
(0.92)
0.302
(0.667)
0.367
(0.722)
0.0459
(0.279)
0.181
(0.539)
0.305
(0.667)
0.0535
(0.303)
xp loss 8 (7%) 115 0.0552
(0.304)
0.216
(0.588)
1
(1.00)
1
(1.00)
0.12
(0.433)
0.148
(0.475)
0.735
(0.989)
0.103
(0.433)
'1q gain' versus 'Time to Death'

P value = 2.8e-05 (logrank test), Q value = 0.0041

Table S1.  Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
1Q GAIN MUTATED 23 6 1.6 - 114.7 (30.6)
1Q GAIN WILD-TYPE 99 3 0.5 - 150.4 (42.1)

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'RADIATION_THERAPY'

P value = 0.0157 (Fisher's exact test), Q value = 0.14

Table S2.  Gene #2: '1q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 81 42
1Q GAIN MUTATED 10 13
1Q GAIN WILD-TYPE 71 29

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0041

Table S3.  Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
1Q GAIN MUTATED 1 2 1 6 6 7
1Q GAIN WILD-TYPE 16 36 14 24 6 4

Figure S3.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 0.000347 (logrank test), Q value = 0.015

Table S4.  Gene #3: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
3Q GAIN MUTATED 5 2 1.6 - 93.7 (28.0)
3Q GAIN WILD-TYPE 117 7 0.5 - 150.4 (41.2)

Figure S4.  Get High-res Image Gene #3: '3q gain' versus Clinical Feature #1: 'Time to Death'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00036 (Fisher's exact test), Q value = 0.015

Table S5.  Gene #3: '3q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
3Q GAIN MUTATED 0 0 0 0 3 2
3Q GAIN WILD-TYPE 17 38 15 30 9 9

Figure S5.  Get High-res Image Gene #3: '3q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0076

Table S6.  Gene #4: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
5P GAIN MUTATED 0 0 0 4 5 2
5P GAIN WILD-TYPE 17 38 15 26 7 9

Figure S6.  Get High-res Image Gene #4: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.015

Table S7.  Gene #5: '5q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
5Q GAIN MUTATED 0 0 0 3 5 1
5Q GAIN WILD-TYPE 17 38 15 27 7 10

Figure S7.  Get High-res Image Gene #5: '5q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00049 (Fisher's exact test), Q value = 0.015

Table S8.  Gene #6: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
7P GAIN MUTATED 0 2 1 7 6 0
7P GAIN WILD-TYPE 17 36 14 23 6 11

Figure S8.  Get High-res Image Gene #6: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00067 (Fisher's exact test), Q value = 0.017

Table S9.  Gene #7: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
7Q GAIN MUTATED 0 2 1 7 6 0
7Q GAIN WILD-TYPE 17 36 14 23 6 11

Figure S9.  Get High-res Image Gene #7: '7q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0187 (Fisher's exact test), Q value = 0.15

Table S10.  Gene #8: '8p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
8P GAIN MUTATED 0 1 2 4 1 4
8P GAIN WILD-TYPE 17 37 13 26 11 7

Figure S10.  Get High-res Image Gene #8: '8p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.019 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #9: '8q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
8Q GAIN MUTATED 0 1 2 4 1 4
8Q GAIN WILD-TYPE 17 37 13 26 11 7

Figure S11.  Get High-res Image Gene #9: '8q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00243 (Wilcoxon-test), Q value = 0.047

Table S12.  Gene #10: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
9P GAIN MUTATED 11 45.7 (15.0)
9P GAIN WILD-TYPE 111 59.5 (12.2)

Figure S12.  Get High-res Image Gene #10: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'RADIATION_THERAPY'

P value = 0.00755 (Fisher's exact test), Q value = 0.088

Table S13.  Gene #10: '9p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 81 42
9P GAIN MUTATED 3 8
9P GAIN WILD-TYPE 78 34

Figure S13.  Get High-res Image Gene #10: '9p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9p gain' versus 'RACE'

P value = 0.0323 (Fisher's exact test), Q value = 0.22

Table S14.  Gene #10: '9p gain' versus Clinical Feature #7: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 13 6 102
9P GAIN MUTATED 4 0 7
9P GAIN WILD-TYPE 9 6 95

Figure S14.  Get High-res Image Gene #10: '9p gain' versus Clinical Feature #7: 'RACE'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00243 (Wilcoxon-test), Q value = 0.047

Table S15.  Gene #11: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
9Q GAIN MUTATED 11 45.7 (15.0)
9Q GAIN WILD-TYPE 111 59.5 (12.2)

Figure S15.  Get High-res Image Gene #11: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'RADIATION_THERAPY'

P value = 0.00755 (Fisher's exact test), Q value = 0.088

Table S16.  Gene #11: '9q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 81 42
9Q GAIN MUTATED 3 8
9Q GAIN WILD-TYPE 78 34

Figure S16.  Get High-res Image Gene #11: '9q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q gain' versus 'RACE'

P value = 0.0313 (Fisher's exact test), Q value = 0.21

Table S17.  Gene #11: '9q gain' versus Clinical Feature #7: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 13 6 102
9Q GAIN MUTATED 4 0 7
9Q GAIN WILD-TYPE 9 6 95

Figure S17.  Get High-res Image Gene #11: '9q gain' versus Clinical Feature #7: 'RACE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0035 (Fisher's exact test), Q value = 0.062

Table S18.  Gene #12: '12p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
12P GAIN MUTATED 0 0 0 1 0 3
12P GAIN WILD-TYPE 17 38 15 29 12 8

Figure S18.  Get High-res Image Gene #12: '12p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00321 (Fisher's exact test), Q value = 0.06

Table S19.  Gene #13: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
12Q GAIN MUTATED 0 0 0 1 0 3
12Q GAIN WILD-TYPE 17 38 15 29 12 8

Figure S19.  Get High-res Image Gene #13: '12q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0188 (Wilcoxon-test), Q value = 0.15

Table S20.  Gene #14: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
14Q GAIN MUTATED 13 49.4 (15.4)
14Q GAIN WILD-TYPE 109 59.3 (12.4)

Figure S20.  Get High-res Image Gene #14: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0046 (Fisher's exact test), Q value = 0.075

Table S21.  Gene #14: '14q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
14Q GAIN MUTATED 0 1 1 8 3 0
14Q GAIN WILD-TYPE 17 37 14 22 9 11

Figure S21.  Get High-res Image Gene #14: '14q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'TUMOR_TISSUE_SITE'

P value = 0.0234 (Fisher's exact test), Q value = 0.18

Table S22.  Gene #15: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients ANTERIOR MEDIASTINUM THYMUS
ALL 27 96
15Q GAIN MUTATED 6 6
15Q GAIN WILD-TYPE 21 90

Figure S22.  Get High-res Image Gene #15: '15q gain' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'15q gain' versus 'RADIATION_THERAPY'

P value = 0.0216 (Fisher's exact test), Q value = 0.17

Table S23.  Gene #15: '15q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 81 42
15Q GAIN MUTATED 4 8
15Q GAIN WILD-TYPE 77 34

Figure S23.  Get High-res Image Gene #15: '15q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0144 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #15: '15q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
15Q GAIN MUTATED 1 1 1 3 5 1
15Q GAIN WILD-TYPE 16 37 14 27 7 10

Figure S24.  Get High-res Image Gene #15: '15q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00899 (Fisher's exact test), Q value = 0.097

Table S25.  Gene #16: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
17Q GAIN MUTATED 2 0 0 1 1 3
17Q GAIN WILD-TYPE 15 38 15 29 11 8

Figure S25.  Get High-res Image Gene #16: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0011 (Fisher's exact test), Q value = 0.026

Table S26.  Gene #19: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
19P GAIN MUTATED 0 0 0 0 3 0
19P GAIN WILD-TYPE 17 38 15 30 9 11

Figure S26.  Get High-res Image Gene #19: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00151 (Fisher's exact test), Q value = 0.034

Table S27.  Gene #20: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
19Q GAIN MUTATED 0 0 0 0 3 0
19Q GAIN WILD-TYPE 17 38 15 30 9 11

Figure S27.  Get High-res Image Gene #20: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0061

Table S28.  Gene #21: '20p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
20P GAIN MUTATED 0 0 0 2 4 4
20P GAIN WILD-TYPE 17 38 15 28 8 7

Figure S28.  Get High-res Image Gene #21: '20p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0065

Table S29.  Gene #22: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
20Q GAIN MUTATED 0 0 0 2 4 4
20Q GAIN WILD-TYPE 17 38 15 28 8 7

Figure S29.  Get High-res Image Gene #22: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.005 (Fisher's exact test), Q value = 0.078

Table S30.  Gene #23: '21q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
21Q GAIN MUTATED 0 0 0 0 1 2
21Q GAIN WILD-TYPE 17 38 15 30 11 9

Figure S30.  Get High-res Image Gene #23: '21q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0135 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #26: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
1P LOSS MUTATED 0 0 0 1 2 2
1P LOSS WILD-TYPE 17 38 15 29 10 9

Figure S31.  Get High-res Image Gene #26: '1p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0114 (Fisher's exact test), Q value = 0.12

Table S32.  Gene #27: '3p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
3P LOSS MUTATED 0 1 0 6 3 2
3P LOSS WILD-TYPE 17 37 15 24 9 9

Figure S32.  Get High-res Image Gene #27: '3p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'ETHNICITY'

P value = 0.00566 (Fisher's exact test), Q value = 0.078

Table S33.  Gene #27: '3p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
3P LOSS MUTATED 4 7
3P LOSS WILD-TYPE 5 93

Figure S33.  Get High-res Image Gene #27: '3p loss' versus Clinical Feature #8: 'ETHNICITY'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0281 (Fisher's exact test), Q value = 0.19

Table S34.  Gene #28: '3q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
3Q LOSS MUTATED 0 0 0 4 2 1
3Q LOSS WILD-TYPE 17 38 15 26 10 10

Figure S34.  Get High-res Image Gene #28: '3q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'ETHNICITY'

P value = 0.00702 (Fisher's exact test), Q value = 0.087

Table S35.  Gene #28: '3q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
3Q LOSS MUTATED 3 3
3Q LOSS WILD-TYPE 6 97

Figure S35.  Get High-res Image Gene #28: '3q loss' versus Clinical Feature #8: 'ETHNICITY'

'6p loss' versus 'Time to Death'

P value = 0.00414 (logrank test), Q value = 0.07

Table S36.  Gene #31: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
6P LOSS MUTATED 21 4 5.9 - 97.4 (28.0)
6P LOSS WILD-TYPE 101 5 0.5 - 150.4 (42.1)

Figure S36.  Get High-res Image Gene #31: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00041 (Fisher's exact test), Q value = 0.015

Table S37.  Gene #31: '6p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
6P LOSS MUTATED 1 2 0 8 5 5
6P LOSS WILD-TYPE 16 36 15 22 7 6

Figure S37.  Get High-res Image Gene #31: '6p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'ETHNICITY'

P value = 0.00777 (Fisher's exact test), Q value = 0.088

Table S38.  Gene #31: '6p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
6P LOSS MUTATED 5 14
6P LOSS WILD-TYPE 4 86

Figure S38.  Get High-res Image Gene #31: '6p loss' versus Clinical Feature #8: 'ETHNICITY'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00013 (Fisher's exact test), Q value = 0.0076

Table S39.  Gene #32: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
6Q LOSS MUTATED 0 2 0 8 5 5
6Q LOSS WILD-TYPE 17 36 15 22 7 6

Figure S39.  Get High-res Image Gene #32: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'ETHNICITY'

P value = 0.00593 (Fisher's exact test), Q value = 0.078

Table S40.  Gene #32: '6q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
6Q LOSS MUTATED 5 13
6Q LOSS WILD-TYPE 4 87

Figure S40.  Get High-res Image Gene #32: '6q loss' versus Clinical Feature #8: 'ETHNICITY'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00051 (Fisher's exact test), Q value = 0.015

Table S41.  Gene #33: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
9P LOSS MUTATED 0 0 0 0 1 3
9P LOSS WILD-TYPE 17 38 15 30 11 8

Figure S41.  Get High-res Image Gene #33: '9p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'TUMOR_TISSUE_SITE'

P value = 0.0239 (Fisher's exact test), Q value = 0.18

Table S42.  Gene #35: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

nPatients ANTERIOR MEDIASTINUM THYMUS
ALL 27 96
11P LOSS MUTATED 5 4
11P LOSS WILD-TYPE 22 92

Figure S42.  Get High-res Image Gene #35: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p loss' versus 'ETHNICITY'

P value = 0.00234 (Fisher's exact test), Q value = 0.047

Table S43.  Gene #35: '11p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
11P LOSS MUTATED 4 5
11P LOSS WILD-TYPE 5 95

Figure S43.  Get High-res Image Gene #35: '11p loss' versus Clinical Feature #8: 'ETHNICITY'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.014 (Wilcoxon-test), Q value = 0.13

Table S44.  Gene #36: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
11Q LOSS MUTATED 7 44.4 (16.5)
11Q LOSS WILD-TYPE 115 59.1 (12.4)

Figure S44.  Get High-res Image Gene #36: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00584 (Fisher's exact test), Q value = 0.078

Table S45.  Gene #36: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
11Q LOSS MUTATED 0 0 0 4 3 0
11Q LOSS WILD-TYPE 17 38 15 26 9 11

Figure S45.  Get High-res Image Gene #36: '11q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'ETHNICITY'

P value = 0.0118 (Fisher's exact test), Q value = 0.12

Table S46.  Gene #36: '11q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
11Q LOSS MUTATED 3 4
11Q LOSS WILD-TYPE 6 96

Figure S46.  Get High-res Image Gene #36: '11q loss' versus Clinical Feature #8: 'ETHNICITY'

'12q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0168 (Wilcoxon-test), Q value = 0.15

Table S47.  Gene #38: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 122 58.3 (13.0)
12Q LOSS MUTATED 7 44.6 (17.0)
12Q LOSS WILD-TYPE 115 59.1 (12.3)

Figure S47.  Get High-res Image Gene #38: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0041

Table S48.  Gene #41: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
16Q LOSS MUTATED 0 1 0 2 1 9
16Q LOSS WILD-TYPE 17 37 15 28 11 2

Figure S48.  Get High-res Image Gene #41: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00826 (Fisher's exact test), Q value = 0.091

Table S49.  Gene #42: '17p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
17P LOSS MUTATED 3 1 0 3 3 4
17P LOSS WILD-TYPE 14 37 15 27 9 7

Figure S49.  Get High-res Image Gene #42: '17p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'ETHNICITY'

P value = 0.0152 (Fisher's exact test), Q value = 0.14

Table S50.  Gene #42: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
17P LOSS MUTATED 4 10
17P LOSS WILD-TYPE 5 90

Figure S50.  Get High-res Image Gene #42: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

'17q loss' versus 'ETHNICITY'

P value = 0.00702 (Fisher's exact test), Q value = 0.087

Table S51.  Gene #43: '17q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
17Q LOSS MUTATED 3 3
17Q LOSS WILD-TYPE 6 97

Figure S51.  Get High-res Image Gene #43: '17q loss' versus Clinical Feature #8: 'ETHNICITY'

'18p loss' versus 'Time to Death'

P value = 0.00539 (logrank test), Q value = 0.078

Table S52.  Gene #44: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
18P LOSS MUTATED 7 2 5.9 - 82.7 (49.4)
18P LOSS WILD-TYPE 115 7 0.5 - 150.4 (40.1)

Figure S52.  Get High-res Image Gene #44: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0241 (Fisher's exact test), Q value = 0.18

Table S53.  Gene #44: '18p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
18P LOSS MUTATED 1 0 0 2 3 1
18P LOSS WILD-TYPE 16 38 15 28 9 10

Figure S53.  Get High-res Image Gene #44: '18p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'Time to Death'

P value = 0.00539 (logrank test), Q value = 0.078

Table S54.  Gene #45: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.4 (40.6)
18Q LOSS MUTATED 7 2 5.9 - 82.7 (49.4)
18Q LOSS WILD-TYPE 115 7 0.5 - 150.4 (40.1)

Figure S54.  Get High-res Image Gene #45: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0247 (Fisher's exact test), Q value = 0.18

Table S55.  Gene #45: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
18Q LOSS MUTATED 1 0 0 2 3 1
18Q LOSS WILD-TYPE 16 38 15 28 9 10

Figure S55.  Get High-res Image Gene #45: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00045 (Fisher's exact test), Q value = 0.015

Table S56.  Gene #46: '19p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
19P LOSS MUTATED 0 0 0 0 0 3
19P LOSS WILD-TYPE 17 38 15 30 12 8

Figure S56.  Get High-res Image Gene #46: '19p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'ETHNICITY'

P value = 0.0175 (Fisher's exact test), Q value = 0.15

Table S57.  Gene #46: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
19P LOSS MUTATED 2 1
19P LOSS WILD-TYPE 7 99

Figure S57.  Get High-res Image Gene #46: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.015

Table S58.  Gene #47: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients THYMOMA; TYPE A THYMOMA; TYPE AB THYMOMA; TYPE B1 THYMOMA; TYPE B2 THYMOMA; TYPE B3 THYMOMA; TYPE C
ALL 17 38 15 30 12 11
19Q LOSS MUTATED 0 0 0 0 0 3
19Q LOSS WILD-TYPE 17 38 15 30 12 8

Figure S58.  Get High-res Image Gene #47: '19q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'ETHNICITY'

P value = 0.0175 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #47: '19q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
19Q LOSS MUTATED 2 1
19Q LOSS WILD-TYPE 7 99

Figure S59.  Get High-res Image Gene #47: '19q loss' versus Clinical Feature #8: 'ETHNICITY'

'21q loss' versus 'ETHNICITY'

P value = 0.0258 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #48: '21q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
21Q LOSS MUTATED 3 6
21Q LOSS WILD-TYPE 6 94

Figure S60.  Get High-res Image Gene #48: '21q loss' versus Clinical Feature #8: 'ETHNICITY'

'22q loss' versus 'ETHNICITY'

P value = 0.0113 (Fisher's exact test), Q value = 0.12

Table S61.  Gene #49: '22q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
22Q LOSS MUTATED 4 9
22Q LOSS WILD-TYPE 5 91

Figure S61.  Get High-res Image Gene #49: '22q loss' versus Clinical Feature #8: 'ETHNICITY'

'xq loss' versus 'ETHNICITY'

P value = 0.0336 (Fisher's exact test), Q value = 0.22

Table S62.  Gene #51: 'xq loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
XQ LOSS MUTATED 2 2
XQ LOSS WILD-TYPE 7 98

Figure S62.  Get High-res Image Gene #51: 'xq loss' versus Clinical Feature #8: 'ETHNICITY'

Methods & Data
Input
  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/THYM-TP/22516316/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/22507339/THYM-TP.merged_data.txt

  • Number of patients = 123

  • Number of significantly arm-level cnvs = 51

  • Number of selected clinical features = 8

  • 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

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] 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)
[3] 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)