Correlation between copy number variations of arm-level result and selected clinical features
Thymoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C18P5ZS7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18P5ZS7
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 52 arm-level events and 8 clinical features across 123 patients, 61 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'Time to Death' 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'.

  • 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'.

  • xp loss cnv correlated to 'Time to Death'.

  • 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 52 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 61 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
9p gain 11 (9%) 112 0.358
(0.716) 		0.00243
(0.0482) 		1
(1.00) 		1
(1.00) 		0.00755
(0.0857) 		0.105
(0.411) 		0.0316
(0.223) 		1
(1.00)
9q gain 11 (9%) 112 0.358
(0.716) 		0.00243
(0.0482) 		1
(1.00) 		1
(1.00) 		0.00755
(0.0857) 		0.106
(0.411) 		0.0327
(0.227) 		1
(1.00)
15q gain 12 (10%) 111 0.332
(0.702) 		0.88
(1.00) 		0.0234
(0.184) 		1
(1.00) 		0.0216
(0.173) 		0.0151
(0.144) 		1
(1.00) 		1
(1.00)
6p loss 20 (16%) 103 0.00337
(0.0584) 		0.0754
(0.353) 		0.769
(1.00) 		0.811
(1.00) 		0.306
(0.666) 		7e-05
(0.00485) 		0.873
(1.00) 		0.00593
(0.0772)
11q loss 7 (6%) 116 0.439
(0.805) 		0.014
(0.139) 		0.178
(0.528) 		0.442
(0.805) 		0.229
(0.59) 		0.00594
(0.0772) 		0.705
(0.97) 		0.0118
(0.119)
1q gain 22 (18%) 101 1.8e-05
(0.00375) 		0.547
(0.924) 		0.571
(0.935) 		0.347
(0.712) 		0.045
(0.272) 		0.00012
(0.00713) 		0.464
(0.825) 		0.669
(0.968)
3q gain 5 (4%) 118 0.000373
(0.0141) 		0.093
(0.395) 		0.585
(0.935) 		0.67
(0.968) 		1
(1.00) 		0.00036
(0.0141) 		1
(1.00) 		1
(1.00)
14q gain 13 (11%) 110 0.417
(0.782) 		0.0188
(0.16) 		1
(1.00) 		0.772
(1.00) 		0.13
(0.426) 		0.00459
(0.0682) 		0.801
(1.00) 		1
(1.00)
3p loss 12 (10%) 111 0.14
(0.45) 		0.232
(0.591) 		0.296
(0.664) 		0.765
(1.00) 		0.336
(0.702) 		0.0112
(0.118) 		1
(1.00) 		0.00566
(0.0772)
3q loss 7 (6%) 116 0.45
(0.814) 		0.205
(0.569) 		0.178
(0.528) 		0.116
(0.411) 		0.229
(0.59) 		0.0287
(0.206) 		0.707
(0.97) 		0.00702
(0.0857)
6q loss 19 (15%) 104 0.0426
(0.269) 		0.105
(0.411) 		0.563
(0.935) 		0.804
(1.00) 		0.44
(0.805) 		3e-05
(0.00416) 		0.569
(0.935) 		0.00444
(0.0682)
11p loss 9 (7%) 114 0.401
(0.766) 		0.155
(0.49) 		0.0239
(0.184) 		1
(1.00) 		0.489
(0.855) 		0.0515
(0.297) 		1
(1.00) 		0.00234
(0.0482)
17p loss 14 (11%) 109 0.705
(0.97) 		0.536
(0.914) 		1
(1.00) 		0.401
(0.766) 		0.552
(0.924) 		0.00762
(0.0857) 		0.838
(1.00) 		0.0152
(0.144)
18p loss 7 (6%) 116 0.00421
(0.0674) 		0.804
(1.00) 		0.648
(0.955) 		0.709
(0.97) 		0.689
(0.968) 		0.0244
(0.185) 		1
(1.00) 		0.0767
(0.353)
18q loss 7 (6%) 116 0.00421
(0.0674) 		0.804
(1.00) 		0.648
(0.955) 		0.709
(0.97) 		0.689
(0.968) 		0.025
(0.186) 		1
(1.00) 		0.0767
(0.353)
19p loss 3 (2%) 120 0.79
(1.00) 		0.275
(0.649) 		0.121
(0.416) 		0.607
(0.935) 		0.268
(0.642) 		0.00063
(0.0166) 		1
(1.00) 		0.0175
(0.152)
19q loss 3 (2%) 120 0.79
(1.00) 		0.275
(0.649) 		0.121
(0.416) 		0.607
(0.935) 		0.268
(0.642) 		0.00064
(0.0166) 		1
(1.00) 		0.0175
(0.152)
5p gain 11 (9%) 112 0.174
(0.524) 		0.642
(0.955) 		0.0624
(0.329) 		0.116
(0.411) 		0.0445
(0.272) 		0.00019
(0.00988) 		0.761
(1.00) 		0.161
(0.5)
5q gain 9 (7%) 114 0.148
(0.47) 		0.553
(0.924) 		0.41
(0.775) 		0.0859
(0.376) 		0.0612
(0.327) 		0.00024
(0.0111) 		0.732
(0.992) 		0.463
(0.825)
7p gain 16 (13%) 107 0.114
(0.411) 		0.375
(0.732) 		0.116
(0.411) 		1
(1.00) 		0.167
(0.507) 		0.00054
(0.016) 		1
(1.00) 		1
(1.00)
7q gain 16 (13%) 107 0.114
(0.411) 		0.375
(0.732) 		0.116
(0.411) 		1
(1.00) 		0.167
(0.507) 		0.00051
(0.016) 		1
(1.00) 		1
(1.00)
8p gain 12 (10%) 111 0.131
(0.426) 		0.264
(0.642) 		0.296
(0.664) 		0.368
(0.726) 		0.336
(0.702) 		0.0195
(0.162) 		0.805
(1.00) 		1
(1.00)
8q gain 12 (10%) 111 0.131
(0.426) 		0.264
(0.642) 		0.296
(0.664) 		0.368
(0.726) 		0.336
(0.702) 		0.0199
(0.162) 		0.803
(1.00) 		1
(1.00)
12p gain 4 (3%) 119 0.196
(0.553) 		0.388
(0.751) 		0.209
(0.569) 		0.62
(0.935) 		0.605
(0.935) 		0.00318
(0.0584) 		1
(1.00) 		0.295
(0.664)
12q gain 4 (3%) 119 0.196
(0.553) 		0.388
(0.751) 		0.209
(0.569) 		0.62
(0.935) 		0.605
(0.935) 		0.00323
(0.0584) 		1
(1.00) 		0.295
(0.664)
17q gain 7 (6%) 116 0.435
(0.805) 		0.574
(0.935) 		0.648
(0.955) 		1
(1.00) 		0.229
(0.59) 		0.00851
(0.0932) 		0.707
(0.97) 		1
(1.00)
19p gain 3 (2%) 120 0.683
(0.968) 		0.354
(0.716) 		1
(1.00) 		0.607
(0.935) 		0.268
(0.642) 		0.00142
(0.0328) 		1
(1.00) 		1
(1.00)
19q gain 3 (2%) 120 0.683
(0.968) 		0.354
(0.716) 		1
(1.00) 		0.607
(0.935) 		0.268
(0.642) 		0.0012
(0.0294) 		1
(1.00) 		1
(1.00)
20p gain 10 (8%) 113 0.617
(0.935) 		0.867
(1.00) 		0.224
(0.59) 		1
(1.00) 		0.307
(0.666) 		5e-05
(0.00416) 		0.598
(0.935) 		0.192
(0.553)
20q gain 10 (8%) 113 0.617
(0.935) 		0.867
(1.00) 		0.224
(0.59) 		1
(1.00) 		0.307
(0.666) 		5e-05
(0.00416) 		0.597
(0.935) 		0.192
(0.553)
21q gain 3 (2%) 120 0.781
(1.00) 		0.221
(0.59) 		0.121
(0.416) 		0.107
(0.411) 		1
(1.00) 		0.00508
(0.0729) 		1
(1.00) 		1
(1.00)
9p loss 4 (3%) 119 0.691
(0.968) 		0.131
(0.426) 		0.209
(0.569) 		0.349
(0.712) 		0.605
(0.935) 		0.00054
(0.016) 		1
(1.00) 		0.295
(0.664)
12q loss 7 (6%) 116 0.321
(0.685) 		0.0168
(0.152) 		0.648
(0.955) 		0.116
(0.411) 		0.689
(0.968) 		0.316
(0.677) 		0.708
(0.97) 		0.103
(0.411)
16q loss 13 (11%) 110 0.0654
(0.34) 		0.845
(1.00) 		0.479
(0.845) 		0.772
(1.00) 		0.13
(0.426) 		1e-05
(0.00375) 		0.823
(1.00) 		0.0735
(0.353)
17q loss 6 (5%) 117 0.605
(0.935) 		0.209
(0.569) 		0.612
(0.935) 		0.681
(0.968) 		0.41
(0.775) 		0.0472
(0.277) 		0.65
(0.956) 		0.00702
(0.0857)
21q loss 9 (7%) 114 0.459
(0.825) 		0.0542
(0.304) 		0.105
(0.411) 		1
(1.00) 		0.489
(0.855) 		0.144
(0.46) 		1
(1.00) 		0.0258
(0.189)
22q loss 13 (11%) 110 0.831
(1.00) 		0.0919
(0.394) 		0.157
(0.49) 		0.772
(1.00) 		0.059
(0.32) 		0.07
(0.351) 		1
(1.00) 		0.0113
(0.118)
xp loss 7 (6%) 116 0.0336
(0.229) 		0.0809
(0.358) 		1
(1.00) 		1
(1.00) 		0.0452
(0.272) 		0.0719
(0.352) 		1
(1.00) 		0.0767
(0.353)
xq loss 4 (3%) 119 0.0697
(0.351) 		0.241
(0.608) 		0.575
(0.935) 		0.349
(0.712) 		0.115
(0.411) 		0.0415
(0.269) 		1
(1.00) 		0.0175
(0.152)
1p gain 8 (7%) 115 0.129
(0.426) 		0.877
(1.00) 		0.0692
(0.351) 		0.479
(0.845) 		0.443
(0.805) 		0.0915
(0.394) 		1
(1.00) 		0.103
(0.411)
18p gain 3 (2%) 120 0.719
(0.978) 		0.679
(0.968) 		0.528
(0.904) 		1
(1.00) 		0.268
(0.642) 		0.0781
(0.353) 		1
(1.00) 		0.23
(0.59)
18q gain 3 (2%) 120 0.719
(0.978) 		0.679
(0.968) 		0.528
(0.904) 		1
(1.00) 		0.268
(0.642) 		0.078
(0.353) 		1
(1.00) 		0.23
(0.59)
22q gain 5 (4%) 118 0.639
(0.955) 		0.342
(0.712) 		1
(1.00) 		0.193
(0.553) 		0.66
(0.963) 		0.0572
(0.317) 		0.583
(0.935) 		1
(1.00)
xp gain 3 (2%) 120 0.736
(0.994) 		0.655
(0.96) 		0.528
(0.904) 		0.107
(0.411) 		1
(1.00) 		0.0945
(0.397) 		1
(1.00) 		1
(1.00)
xq gain 5 (4%) 118 0.204
(0.569) 		0.416
(0.782) 		0.302
(0.665) 		0.67
(0.968) 		1
(1.00) 		0.166
(0.507) 		1
(1.00) 		1
(1.00)
1p loss 4 (3%) 119 0.61
(0.935) 		0.0793
(0.355) 		1
(1.00) 		0.349
(0.712) 		0.115
(0.411) 		0.0414
(0.269) 		1
(1.00) 		0.295
(0.664)
4p loss 5 (4%) 118 0.438
(0.805) 		0.522
(0.904) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0425
(0.269) 		1
(1.00) 		1
(1.00)
4q loss 4 (3%) 119 0.46
(0.825) 		0.948
(1.00) 		1
(1.00) 		0.62
(0.935) 		0.605
(0.935) 		0.0708
(0.351) 		1
(1.00) 		1
(1.00)
10p loss 3 (2%) 120 0.79
(1.00) 		0.286
(0.664) 		0.528
(0.904) 		0.607
(0.935) 		0.55
(0.924) 		0.297
(0.664) 		1
(1.00) 		0.23
(0.59)
12p loss 8 (7%) 115 0.39
(0.751) 		0.039
(0.262) 		1
(1.00) 		0.276
(0.649) 		0.443
(0.805) 		0.11
(0.411) 		1
(1.00) 		0.131
(0.426)
13q loss 14 (11%) 109 0.311
(0.671) 		0.254
(0.636) 		0.187
(0.549) 		0.78
(1.00) 		0.233
(0.591) 		0.107
(0.411) 		0.84
(1.00) 		0.0592
(0.32)
16p loss 5 (4%) 118 0.6
(0.935) 		0.544
(0.923) 		0.302
(0.665) 		0.367
(0.726) 		0.0459
(0.273) 		0.183
(0.54) 		0.302
(0.665) 		0.0535
(0.304)
'1q gain' versus 'Time to Death'

P value = 1.8e-05 (logrank test), Q value = 0.0037

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

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
1Q GAIN MUTATED 22 6 1.6 - 114.7 (29.3)
1Q GAIN WILD-TYPE 100 3 0.5 - 150.0 (41.7)

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

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00012 (Fisher's exact test), Q value = 0.0071

Table S2.  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 5 7
1Q GAIN WILD-TYPE 16 36 14 24 7 4

Figure S2.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'Time to Death'

P value = 0.000373 (logrank test), Q value = 0.014

Table S3.  Gene #3: '3q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
3Q GAIN MUTATED 5 2 1.6 - 93.7 (28.0)
3Q GAIN WILD-TYPE 117 7 0.5 - 150.0 (41.2)

Figure S3.  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 = 0.014

Table S4.  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 S4.  Get High-res Image Gene #3: '3q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0099

Table S5.  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 S5.  Get High-res Image Gene #4: '5p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00024 (Fisher's exact test), Q value = 0.011

Table S6.  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 S6.  Get High-res Image Gene #5: '5q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.016

Table S7.  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 S7.  Get High-res Image Gene #6: '7p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00051 (Fisher's exact test), Q value = 0.016

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

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0195 (Fisher's exact test), Q value = 0.16

Table S9.  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 S9.  Get High-res Image Gene #8: '8p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0199 (Fisher's exact test), Q value = 0.16

Table S10.  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 S10.  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 = 0.048

Table S11.  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 S11.  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 = 0.086

Table S12.  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 S12.  Get High-res Image Gene #10: '9p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9p gain' versus 'RACE'

P value = 0.0316 (Fisher's exact test), Q value = 0.22

Table S13.  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 S13.  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 = 0.048

Table S14.  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 S14.  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 = 0.086

Table S15.  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 S15.  Get High-res Image Gene #11: '9q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'9q gain' versus 'RACE'

P value = 0.0327 (Fisher's exact test), Q value = 0.23

Table S16.  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 S16.  Get High-res Image Gene #11: '9q gain' versus Clinical Feature #7: 'RACE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00318 (Fisher's exact test), Q value = 0.058

Table S17.  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 S17.  Get High-res Image Gene #12: '12p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00323 (Fisher's exact test), Q value = 0.058

Table S18.  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 S18.  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 = 0.16

Table S19.  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 S19.  Get High-res Image Gene #14: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00459 (Fisher's exact test), Q value = 0.068

Table S20.  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 S20.  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 S21.  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 S21.  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 S22.  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 S22.  Get High-res Image Gene #15: '15q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0151 (Fisher's exact test), Q value = 0.14

Table S23.  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 S23.  Get High-res Image Gene #15: '15q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00851 (Fisher's exact test), Q value = 0.093

Table S24.  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 S24.  Get High-res Image Gene #16: '17q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00142 (Fisher's exact test), Q value = 0.033

Table S25.  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 S25.  Get High-res Image Gene #19: '19p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0012 (Fisher's exact test), Q value = 0.029

Table S26.  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 S26.  Get High-res Image Gene #20: '19q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0042

Table S27.  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 S27.  Get High-res Image Gene #21: '20p gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0042

Table S28.  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 S28.  Get High-res Image Gene #22: '20q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00508 (Fisher's exact test), Q value = 0.073

Table S29.  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 S29.  Get High-res Image Gene #23: '21q gain' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0112 (Fisher's exact test), Q value = 0.12

Table S30.  Gene #28: '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 S30.  Get High-res Image Gene #28: '3p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'ETHNICITY'

P value = 0.00566 (Fisher's exact test), Q value = 0.077

Table S31.  Gene #28: '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 S31.  Get High-res Image Gene #28: '3p loss' versus Clinical Feature #8: 'ETHNICITY'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0287 (Fisher's exact test), Q value = 0.21

Table S32.  Gene #29: '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 S32.  Get High-res Image Gene #29: '3q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'ETHNICITY'

P value = 0.00702 (Fisher's exact test), Q value = 0.086

Table S33.  Gene #29: '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 S33.  Get High-res Image Gene #29: '3q loss' versus Clinical Feature #8: 'ETHNICITY'

'6p loss' versus 'Time to Death'

P value = 0.00337 (logrank test), Q value = 0.058

Table S34.  Gene #32: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
6P LOSS MUTATED 20 4 5.9 - 97.4 (30.0)
6P LOSS WILD-TYPE 102 5 0.5 - 150.0 (41.7)

Figure S34.  Get High-res Image Gene #32: '6p loss' versus Clinical Feature #1: 'Time to Death'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0049

Table S35.  Gene #32: '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 1 0 8 5 5
6P LOSS WILD-TYPE 16 37 15 22 7 6

Figure S35.  Get High-res Image Gene #32: '6p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'ETHNICITY'

P value = 0.00593 (Fisher's exact test), Q value = 0.077

Table S36.  Gene #32: '6p loss' versus Clinical Feature #8: 'ETHNICITY'

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

Figure S36.  Get High-res Image Gene #32: '6p loss' versus Clinical Feature #8: 'ETHNICITY'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0042

Table S37.  Gene #33: '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 1 0 8 5 5
6Q LOSS WILD-TYPE 17 37 15 22 7 6

Figure S37.  Get High-res Image Gene #33: '6q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'ETHNICITY'

P value = 0.00444 (Fisher's exact test), Q value = 0.068

Table S38.  Gene #33: '6q loss' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 9 100
6Q LOSS MUTATED 5 12
6Q LOSS WILD-TYPE 4 88

Figure S38.  Get High-res Image Gene #33: '6q loss' versus Clinical Feature #8: 'ETHNICITY'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00054 (Fisher's exact test), Q value = 0.016

Table S39.  Gene #34: '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 S39.  Get High-res Image Gene #34: '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 S40.  Gene #36: '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 S40.  Get High-res Image Gene #36: '11p loss' versus Clinical Feature #3: 'TUMOR_TISSUE_SITE'

'11p loss' versus 'ETHNICITY'

P value = 0.00234 (Fisher's exact test), Q value = 0.048

Table S41.  Gene #36: '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 S41.  Get High-res Image Gene #36: '11p loss' versus Clinical Feature #8: 'ETHNICITY'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.014 (Wilcoxon-test), Q value = 0.14

Table S42.  Gene #37: '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 S42.  Get High-res Image Gene #37: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00594 (Fisher's exact test), Q value = 0.077

Table S43.  Gene #37: '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 S43.  Get High-res Image Gene #37: '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 S44.  Gene #37: '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 S44.  Get High-res Image Gene #37: '11q loss' versus Clinical Feature #8: 'ETHNICITY'

'12q loss' versus 'YEARS_TO_BIRTH'

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

Table S45.  Gene #39: '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 S45.  Get High-res Image Gene #39: '12q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0037

Table S46.  Gene #42: '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 S46.  Get High-res Image Gene #42: '16q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00762 (Fisher's exact test), Q value = 0.086

Table S47.  Gene #43: '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 S47.  Get High-res Image Gene #43: '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 S48.  Gene #43: '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 S48.  Get High-res Image Gene #43: '17p loss' versus Clinical Feature #8: 'ETHNICITY'

'17q loss' versus 'ETHNICITY'

P value = 0.00702 (Fisher's exact test), Q value = 0.086

Table S49.  Gene #44: '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 S49.  Get High-res Image Gene #44: '17q loss' versus Clinical Feature #8: 'ETHNICITY'

'18p loss' versus 'Time to Death'

P value = 0.00421 (logrank test), Q value = 0.067

Table S50.  Gene #45: '18p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
18P LOSS MUTATED 7 2 5.9 - 82.7 (49.4)
18P LOSS WILD-TYPE 115 7 0.5 - 150.0 (40.1)

Figure S50.  Get High-res Image Gene #45: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0244 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #45: '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 S51.  Get High-res Image Gene #45: '18p loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'18q loss' versus 'Time to Death'

P value = 0.00421 (logrank test), Q value = 0.067

Table S52.  Gene #46: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
18Q LOSS MUTATED 7 2 5.9 - 82.7 (49.4)
18Q LOSS WILD-TYPE 115 7 0.5 - 150.0 (40.1)

Figure S52.  Get High-res Image Gene #46: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.025 (Fisher's exact test), Q value = 0.19

Table S53.  Gene #46: '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 S53.  Get High-res Image Gene #46: '18q loss' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00063 (Fisher's exact test), Q value = 0.017

Table S54.  Gene #47: '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 S54.  Get High-res Image Gene #47: '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 S55.  Gene #47: '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 S55.  Get High-res Image Gene #47: '19p loss' versus Clinical Feature #8: 'ETHNICITY'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00064 (Fisher's exact test), Q value = 0.017

Table S56.  Gene #48: '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 S56.  Get High-res Image Gene #48: '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 S57.  Gene #48: '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 S57.  Get High-res Image Gene #48: '19q loss' versus Clinical Feature #8: 'ETHNICITY'

'21q loss' versus 'ETHNICITY'

P value = 0.0258 (Fisher's exact test), Q value = 0.19

Table S58.  Gene #49: '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 S58.  Get High-res Image Gene #49: '21q loss' versus Clinical Feature #8: 'ETHNICITY'

'22q loss' versus 'ETHNICITY'

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

Table S59.  Gene #50: '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 S59.  Get High-res Image Gene #50: '22q loss' versus Clinical Feature #8: 'ETHNICITY'

'xp loss' versus 'Time to Death'

P value = 0.0336 (logrank test), Q value = 0.23

Table S60.  Gene #51: 'xp loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 122 9 0.5 - 150.0 (40.6)
XP LOSS MUTATED 7 2 21.1 - 93.7 (52.9)
XP LOSS WILD-TYPE 115 7 0.5 - 150.0 (38.3)

Figure S60.  Get High-res Image Gene #51: 'xp loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'ETHNICITY'

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

Table S61.  Gene #52: 'xq loss' versus Clinical Feature #8: 'ETHNICITY'

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

Figure S61.  Get High-res Image Gene #52: '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/19781935/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THYM-TP/19775615/THYM-TP.merged_data.txt

  • Number of patients = 123

  • Number of significantly arm-level cnvs = 52

  • 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)
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