Correlation between copy number variations of arm-level result and selected clinical features
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 82 arm-level events and 5 clinical features across 246 patients, 71 significant findings detected with Q value < 0.25.

  • 1p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RACE'.

  • 3p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 5q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 6p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 6q gain cnv correlated to 'Time to Death'.

  • 7p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 7q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 8p gain cnv correlated to 'Time to Death'.

  • 8q gain cnv correlated to 'Time to Death'.

  • 9p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 9q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 11p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 11q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 12p gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'RACE'.

  • 12q gain cnv correlated to 'GENDER' and 'RACE'.

  • 13q gain cnv correlated to 'RACE'.

  • 14q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 16p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 17p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 18p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 18q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 20p gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 20q gain cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'GENDER'.

  • 21q gain cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 22q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xp gain cnv correlated to 'YEARS_TO_BIRTH'.

  • xq gain cnv correlated to 'ETHNICITY'.

  • 1p loss cnv correlated to 'GENDER'.

  • 2p loss cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • 2q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 3p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 3q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 6p loss cnv correlated to 'Time to Death'.

  • 9p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 9q loss cnv correlated to 'Time to Death'.

  • 10p loss cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • 10q loss cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • 13q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 15q loss cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 17q loss cnv correlated to 'Time to Death'.

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

  • 20p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 20q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 21q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 22q loss cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 71 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
1p gain 54 (22%) 192 0.0114
(0.122) 		0.0142
(0.129) 		0.542
(0.895) 		0.0428
(0.247) 		0.34
(0.73)
12p gain 42 (17%) 204 0.00564
(0.105) 		8.66e-05
(0.00581) 		0.615
(0.904) 		0.04
(0.241) 		0.198
(0.56)
20q gain 82 (33%) 164 0.0108
(0.122) 		0.000326
(0.0157) 		0.00976
(0.122) 		0.618
(0.905) 		1
(1.00)
6p gain 49 (20%) 197 0.00123
(0.0405) 		0.0119
(0.122) 		0.338
(0.73) 		0.555
(0.895) 		1
(1.00)
9p gain 55 (22%) 191 0.0372
(0.235) 		0.00105
(0.0392) 		0.172
(0.525) 		0.419
(0.768) 		1
(1.00)
11p gain 22 (9%) 224 0.00449
(0.0921) 		7.73e-05
(0.00581) 		0.376
(0.74) 		0.233
(0.613) 		1
(1.00)
11q gain 21 (9%) 225 0.000925
(0.0379) 		0.0219
(0.164) 		0.497
(0.849) 		0.355
(0.735) 		1
(1.00)
12q gain 33 (13%) 213 0.594
(0.895) 		0.0937
(0.415) 		0.0391
(0.241) 		0.0159
(0.136) 		0.141
(0.487)
14q gain 55 (22%) 191 0.0181
(0.152) 		0.0131
(0.127) 		0.759
(0.999) 		0.835
(1.00) 		1
(1.00)
16p gain 39 (16%) 207 0.00596
(0.106) 		0.025
(0.18) 		0.861
(1.00) 		0.497
(0.849) 		1
(1.00)
20p gain 61 (25%) 185 0.00177
(0.0453) 		0.00925
(0.122) 		0.0545
(0.298) 		0.357
(0.735) 		1
(1.00)
21q gain 55 (22%) 191 0.019
(0.155) 		0.036
(0.232) 		0.288
(0.678) 		0.0504
(0.281) 		0.593
(0.895)
2p loss 84 (34%) 162 0.343
(0.73) 		0.00815
(0.122) 		0.225
(0.603) 		0.031
(0.208) 		0.159
(0.512)
2q loss 67 (27%) 179 0.00138
(0.0405) 		0.000344
(0.0157) 		0.473
(0.839) 		0.104
(0.439) 		0.324
(0.73)
3q loss 49 (20%) 197 0.0149
(0.132) 		0.0136
(0.127) 		0.201
(0.562) 		0.815
(1.00) 		1
(1.00)
10p loss 116 (47%) 130 0.876
(1.00) 		0.0197
(0.155) 		0.00714
(0.113) 		0.195
(0.56) 		0.369
(0.735)
10q loss 126 (51%) 120 0.483
(0.846) 		0.00954
(0.122) 		0.0104
(0.122) 		0.24
(0.62) 		0.168
(0.523)
15q loss 42 (17%) 204 9.15e-05
(0.00581) 		0.00936
(0.122) 		0.401
(0.751) 		0.337
(0.73) 		0.587
(0.895)
3p gain 37 (15%) 209 0.704
(0.943) 		0.0405
(0.241) 		0.479
(0.846) 		0.0997
(0.426) 		1
(1.00)
3q gain 34 (14%) 212 0.97
(1.00) 		0.0134
(0.127) 		0.581
(0.895) 		0.12
(0.45) 		1
(1.00)
5p gain 95 (39%) 151 0.909
(1.00) 		0.00129
(0.0405) 		0.694
(0.941) 		0.724
(0.964) 		1
(1.00)
5q gain 70 (28%) 176 0.527
(0.882) 		0.0264
(0.183) 		0.395
(0.751) 		0.395
(0.751) 		1
(1.00)
6q gain 48 (20%) 198 0.0119
(0.122) 		0.0507
(0.281) 		0.147
(0.494) 		0.684
(0.932) 		1
(1.00)
7p gain 79 (32%) 167 0.373
(0.738) 		9e-06
(0.00123) 		0.892
(1.00) 		0.492
(0.849) 		0.662
(0.917)
7q gain 66 (27%) 180 0.115
(0.444) 		4.22e-07
(0.000173) 		0.149
(0.494) 		0.795
(1.00) 		0.136
(0.477)
8p gain 52 (21%) 194 0.022
(0.164) 		0.11
(0.439) 		1
(1.00) 		0.0462
(0.263) 		0.335
(0.73)
8q gain 63 (26%) 183 0.00688
(0.113) 		0.311
(0.716) 		0.56
(0.895) 		0.0952
(0.415) 		0.136
(0.477)
9q gain 71 (29%) 175 0.948
(1.00) 		6.69e-06
(0.00123) 		0.4
(0.751) 		0.684
(0.932) 		1
(1.00)
13q gain 13 (5%) 233 0.703
(0.943) 		0.213
(0.589) 		0.095
(0.415) 		0.0201
(0.155) 		1
(1.00)
17p gain 58 (24%) 188 0.149
(0.494) 		0.0247
(0.18) 		0.549
(0.895) 		0.242
(0.62) 		1
(1.00)
18p gain 49 (20%) 197 0.367
(0.735) 		0.0102
(0.122) 		0.426
(0.776) 		0.333
(0.73) 		0.585
(0.895)
18q gain 33 (13%) 213 0.634
(0.913) 		0.00954
(0.122) 		0.262
(0.648) 		0.367
(0.735) 		1
(1.00)
19p gain 82 (33%) 164 0.11
(0.439) 		9.92e-05
(0.00581) 		0.0776
(0.374) 		0.932
(1.00) 		0.332
(0.73)
19q gain 62 (25%) 184 0.387
(0.747) 		0.00244
(0.0555) 		0.141
(0.487) 		0.845
(1.00) 		1
(1.00)
22q gain 58 (24%) 188 0.604
(0.895) 		0.00202
(0.0486) 		0.452
(0.813) 		0.922
(1.00) 		0.112
(0.441)
xp gain 72 (29%) 174 0.639
(0.916) 		0.0418
(0.245) 		0.0916
(0.415) 		0.931
(1.00) 		0.332
(0.73)
xq gain 32 (13%) 214 0.316
(0.718) 		0.302
(0.7) 		0.57
(0.895) 		1
(1.00) 		0.0156
(0.136)
1p loss 30 (12%) 216 0.0645
(0.328) 		0.117
(0.445) 		0.0101
(0.122) 		0.278
(0.662) 		1
(1.00)
3p loss 56 (23%) 190 0.0933
(0.415) 		0.0193
(0.155) 		0.763
(0.999) 		0.913
(1.00) 		1
(1.00)
6p loss 57 (23%) 189 0.00655
(0.112) 		0.99
(1.00) 		0.545
(0.895) 		0.655
(0.917) 		1
(1.00)
9p loss 81 (33%) 165 0.25
(0.635) 		0.00372
(0.0802) 		0.224
(0.603) 		0.495
(0.849) 		1
(1.00)
9q loss 49 (20%) 197 0.028
(0.191) 		0.107
(0.439) 		0.633
(0.913) 		0.19
(0.553) 		1
(1.00)
13q loss 130 (53%) 116 0.602
(0.895) 		0.00172
(0.0453) 		0.0734
(0.363) 		0.941
(1.00) 		0.657
(0.917)
16q loss 120 (49%) 126 0.176
(0.526) 		0.00529
(0.103) 		0.056
(0.302) 		0.116
(0.444) 		0.672
(0.925)
17q loss 46 (19%) 200 0.0344
(0.227) 		0.0662
(0.331) 		0.625
(0.912) 		0.342
(0.73) 		0.585
(0.895)
18q loss 69 (28%) 177 0.0132
(0.127) 		0.108
(0.439) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20p loss 52 (21%) 194 0.596
(0.895) 		0.0115
(0.122) 		0.214
(0.589) 		0.544
(0.895) 		1
(1.00)
20q loss 24 (10%) 222 0.899
(1.00) 		0.0362
(0.232) 		0.202
(0.562) 		1
(1.00) 		1
(1.00)
21q loss 48 (20%) 198 0.186
(0.544) 		0.0257
(0.181) 		0.872
(1.00) 		0.902
(1.00) 		1
(1.00)
22q loss 63 (26%) 183 0.859
(1.00) 		0.274
(0.661) 		0.0406
(0.241) 		1
(1.00) 		0.593
(0.895)
1q gain 47 (19%) 199 0.776
(1.00) 		0.0649
(0.328) 		0.144
(0.492) 		0.905
(1.00) 		0.587
(0.895)
2p gain 21 (9%) 225 0.183
(0.544) 		0.163
(0.514) 		0.821
(1.00) 		0.645
(0.917) 		0.368
(0.735)
2q gain 21 (9%) 225 0.634
(0.913) 		0.235
(0.614) 		0.256
(0.648) 		0.428
(0.777) 		0.368
(0.735)
4p gain 65 (26%) 181 0.197
(0.56) 		0.633
(0.913) 		0.565
(0.895) 		0.857
(1.00) 		1
(1.00)
4q gain 44 (18%) 202 0.16
(0.512) 		0.366
(0.735) 		0.408
(0.76) 		1
(1.00) 		1
(1.00)
10p gain 22 (9%) 224 0.295
(0.686) 		0.511
(0.865) 		0.658
(0.917) 		0.822
(1.00) 		1
(1.00)
10q gain 11 (4%) 235 0.36
(0.735) 		0.941
(1.00) 		0.759
(0.999) 		1
(1.00) 		1
(1.00)
15q gain 61 (25%) 185 0.517
(0.872) 		0.0576
(0.303) 		0.0758
(0.37) 		0.654
(0.917) 		0.106
(0.439)
16q gain 20 (8%) 226 0.605
(0.895) 		0.82
(1.00) 		0.643
(0.917) 		1
(1.00) 		1
(1.00)
17q gain 53 (22%) 193 0.947
(1.00) 		0.174
(0.525) 		0.165
(0.517) 		0.133
(0.477) 		0.6
(0.895)
1q loss 37 (15%) 209 0.774
(1.00) 		0.483
(0.846) 		0.287
(0.678) 		0.789
(1.00) 		0.527
(0.882)
4p loss 41 (17%) 205 0.385
(0.747) 		0.134
(0.477) 		0.391
(0.75) 		0.383
(0.747) 		1
(1.00)
4q loss 50 (20%) 196 0.761
(0.999) 		0.192
(0.553) 		0.0572
(0.303) 		0.509
(0.865) 		0.585
(0.895)
5p loss 20 (8%) 226 0.461
(0.825) 		0.369
(0.735) 		0.353
(0.735) 		0.317
(0.718) 		1
(1.00)
5q loss 34 (14%) 212 0.276
(0.661) 		0.0788
(0.375) 		0.581
(0.895) 		0.58
(0.895) 		1
(1.00)
6q loss 50 (20%) 196 0.123
(0.46) 		0.766
(1.00) 		0.343
(0.73) 		0.911
(1.00) 		1
(1.00)
7p loss 31 (13%) 215 0.914
(1.00) 		0.357
(0.735) 		0.0848
(0.398) 		0.185
(0.544) 		1
(1.00)
7q loss 33 (13%) 213 0.0854
(0.398) 		0.42
(0.768) 		0.576
(0.895) 		0.698
(0.941) 		1
(1.00)
8p loss 58 (24%) 188 0.274
(0.661) 		0.492
(0.849) 		0.652
(0.917) 		0.0998
(0.426) 		0.587
(0.895)
8q loss 43 (17%) 203 0.782
(1.00) 		0.0942
(0.415) 		0.4
(0.751) 		0.132
(0.477) 		0.588
(0.895)
11p loss 91 (37%) 155 0.468
(0.835) 		0.259
(0.648) 		0.792
(1.00) 		0.933
(1.00) 		0.16
(0.512)
11q loss 87 (35%) 159 0.269
(0.66) 		0.697
(0.941) 		1
(1.00) 		0.667
(0.921) 		0.172
(0.525)
12p loss 63 (26%) 183 0.718
(0.959) 		0.136
(0.477) 		0.661
(0.917) 		0.173
(0.525) 		0.328
(0.73)
12q loss 52 (21%) 194 0.849
(1.00) 		0.263
(0.648) 		0.352
(0.735) 		0.238
(0.619) 		0.586
(0.895)
14q loss 59 (24%) 187 0.109
(0.439) 		0.42
(0.768) 		0.882
(1.00) 		0.388
(0.747) 		0.589
(0.895)
16p loss 72 (29%) 174 0.661
(0.917) 		0.161
(0.512) 		0.261
(0.648) 		0.148
(0.494) 		1
(1.00)
17p loss 55 (22%) 191 0.272
(0.661) 		0.217
(0.592) 		0.759
(0.999) 		0.451
(0.813) 		1
(1.00)
18p loss 60 (24%) 186 0.0645
(0.328) 		0.419
(0.768) 		0.882
(1.00) 		0.919
(1.00) 		1
(1.00)
19p loss 21 (9%) 225 0.682
(0.932) 		0.597
(0.895) 		0.821
(1.00) 		0.233
(0.613) 		1
(1.00)
19q loss 38 (15%) 208 0.98
(1.00) 		0.934
(1.00) 		0.861
(1.00) 		0.496
(0.849) 		0.218
(0.592)
xp loss 58 (24%) 188 0.615
(0.904) 		0.132
(0.477) 		0.292
(0.684) 		0.313
(0.716) 		0.588
(0.895)
xq loss 96 (39%) 150 0.233
(0.613) 		0.535
(0.891) 		0.116
(0.444) 		0.38
(0.745) 		0.159
(0.512)
'1p gain' versus 'Time to Death'

P value = 0.0114 (logrank test), Q value = 0.12

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

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
1P GAIN MUTATED 54 22 0.5 - 106.5 (18.3)
1P GAIN WILD-TYPE 190 60 0.1 - 188.2 (26.1)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0142 (Wilcoxon-test), Q value = 0.13

Table S2.  Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
1P GAIN MUTATED 54 65.2 (13.5)
1P GAIN WILD-TYPE 191 60.2 (14.6)

Figure S2.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p gain' versus 'RACE'

P value = 0.0428 (Fisher's exact test), Q value = 0.25

Table S3.  Gene #1: '1p gain' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
1P GAIN MUTATED 0 8 42
1P GAIN WILD-TYPE 6 10 152

Figure S3.  Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'RACE'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0405 (Wilcoxon-test), Q value = 0.24

Table S4.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
3P GAIN MUTATED 37 65.8 (13.0)
3P GAIN WILD-TYPE 208 60.5 (14.6)

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0134 (Wilcoxon-test), Q value = 0.13

Table S5.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
3Q GAIN MUTATED 34 66.9 (12.9)
3Q GAIN WILD-TYPE 211 60.4 (14.6)

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00129 (Wilcoxon-test), Q value = 0.041

Table S6.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
5P GAIN MUTATED 94 65.1 (12.9)
5P GAIN WILD-TYPE 151 58.9 (14.9)

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0264 (Wilcoxon-test), Q value = 0.18

Table S7.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
5Q GAIN MUTATED 70 64.7 (13.5)
5Q GAIN WILD-TYPE 175 59.9 (14.7)

Figure S7.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p gain' versus 'Time to Death'

P value = 0.00123 (logrank test), Q value = 0.041

Table S8.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
6P GAIN MUTATED 49 24 0.1 - 143.4 (19.9)
6P GAIN WILD-TYPE 195 58 0.1 - 188.2 (25.1)

Figure S8.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0119 (Wilcoxon-test), Q value = 0.12

Table S9.  Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
6P GAIN MUTATED 48 66.2 (12.9)
6P GAIN WILD-TYPE 197 60.1 (14.6)

Figure S9.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q gain' versus 'Time to Death'

P value = 0.0119 (logrank test), Q value = 0.12

Table S10.  Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
6Q GAIN MUTATED 47 21 0.6 - 143.4 (22.0)
6Q GAIN WILD-TYPE 197 61 0.1 - 188.2 (24.0)

Figure S10.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 9e-06 (Wilcoxon-test), Q value = 0.0012

Table S11.  Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
7P GAIN MUTATED 78 66.9 (12.6)
7P GAIN WILD-TYPE 167 58.7 (14.6)

Figure S11.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 4.22e-07 (Wilcoxon-test), Q value = 0.00017

Table S12.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
7Q GAIN MUTATED 66 68.8 (10.3)
7Q GAIN WILD-TYPE 179 58.5 (14.8)

Figure S12.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p gain' versus 'Time to Death'

P value = 0.022 (logrank test), Q value = 0.16

Table S13.  Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
8P GAIN MUTATED 52 22 0.1 - 106.5 (17.0)
8P GAIN WILD-TYPE 192 60 0.1 - 188.2 (25.2)

Figure S13.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #1: 'Time to Death'

'8q gain' versus 'Time to Death'

P value = 0.00688 (logrank test), Q value = 0.11

Table S14.  Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
8Q GAIN MUTATED 63 27 0.1 - 106.5 (15.9)
8Q GAIN WILD-TYPE 181 55 0.1 - 188.2 (26.5)

Figure S14.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'Time to Death'

P value = 0.0372 (logrank test), Q value = 0.23

Table S15.  Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
9P GAIN MUTATED 54 25 1.1 - 96.9 (21.5)
9P GAIN WILD-TYPE 190 57 0.1 - 188.2 (24.5)

Figure S15.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #1: 'Time to Death'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00105 (Wilcoxon-test), Q value = 0.039

Table S16.  Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
9P GAIN MUTATED 54 66.7 (14.1)
9P GAIN WILD-TYPE 191 59.8 (14.3)

Figure S16.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 6.69e-06 (Wilcoxon-test), Q value = 0.0012

Table S17.  Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
9Q GAIN MUTATED 71 67.6 (13.7)
9Q GAIN WILD-TYPE 174 58.8 (14.0)

Figure S17.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'Time to Death'

P value = 0.00449 (logrank test), Q value = 0.092

Table S18.  Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
11P GAIN MUTATED 22 13 1.1 - 123.8 (16.1)
11P GAIN WILD-TYPE 222 69 0.1 - 188.2 (25.1)

Figure S18.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 7.73e-05 (Wilcoxon-test), Q value = 0.0058

Table S19.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
11P GAIN MUTATED 22 72.2 (12.9)
11P GAIN WILD-TYPE 223 60.2 (14.2)

Figure S19.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'Time to Death'

P value = 0.000925 (logrank test), Q value = 0.038

Table S20.  Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
11Q GAIN MUTATED 21 14 1.1 - 123.8 (18.1)
11Q GAIN WILD-TYPE 223 68 0.1 - 188.2 (25.1)

Figure S20.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0219 (Wilcoxon-test), Q value = 0.16

Table S21.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
11Q GAIN MUTATED 21 67.6 (15.5)
11Q GAIN WILD-TYPE 224 60.7 (14.3)

Figure S21.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'Time to Death'

P value = 0.00564 (logrank test), Q value = 0.11

Table S22.  Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
12P GAIN MUTATED 42 21 0.1 - 106.5 (16.9)
12P GAIN WILD-TYPE 202 61 0.1 - 188.2 (24.7)

Figure S22.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #1: 'Time to Death'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 8.66e-05 (Wilcoxon-test), Q value = 0.0058

Table S23.  Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
12P GAIN MUTATED 42 69.0 (12.1)
12P GAIN WILD-TYPE 203 59.7 (14.5)

Figure S23.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'RACE'

P value = 0.04 (Fisher's exact test), Q value = 0.24

Table S24.  Gene #23: '12p gain' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
12P GAIN MUTATED 2 0 36
12P GAIN WILD-TYPE 4 18 158

Figure S24.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #4: 'RACE'

'12q gain' versus 'GENDER'

P value = 0.0391 (Fisher's exact test), Q value = 0.24

Table S25.  Gene #24: '12q gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
12Q GAIN MUTATED 12 21
12Q GAIN WILD-TYPE 120 93

Figure S25.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'GENDER'

'12q gain' versus 'RACE'

P value = 0.0159 (Fisher's exact test), Q value = 0.14

Table S26.  Gene #24: '12q gain' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
12Q GAIN MUTATED 3 0 27
12Q GAIN WILD-TYPE 3 18 167

Figure S26.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'RACE'

'13q gain' versus 'RACE'

P value = 0.0201 (Fisher's exact test), Q value = 0.16

Table S27.  Gene #25: '13q gain' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
13Q GAIN MUTATED 0 4 8
13Q GAIN WILD-TYPE 6 14 186

Figure S27.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #4: 'RACE'

'14q gain' versus 'Time to Death'

P value = 0.0181 (logrank test), Q value = 0.15

Table S28.  Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
14Q GAIN MUTATED 55 27 0.6 - 108.1 (19.7)
14Q GAIN WILD-TYPE 189 55 0.1 - 188.2 (25.1)

Figure S28.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #1: 'Time to Death'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0131 (Wilcoxon-test), Q value = 0.13

Table S29.  Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
14Q GAIN MUTATED 55 65.6 (15.4)
14Q GAIN WILD-TYPE 190 60.1 (14.0)

Figure S29.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'Time to Death'

P value = 0.00596 (logrank test), Q value = 0.11

Table S30.  Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
16P GAIN MUTATED 39 21 0.5 - 86.1 (23.5)
16P GAIN WILD-TYPE 205 61 0.1 - 188.2 (23.1)

Figure S30.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.025 (Wilcoxon-test), Q value = 0.18

Table S31.  Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
16P GAIN MUTATED 39 66.2 (13.8)
16P GAIN WILD-TYPE 206 60.4 (14.5)

Figure S31.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0247 (Wilcoxon-test), Q value = 0.18

Table S32.  Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
17P GAIN MUTATED 57 65.3 (12.9)
17P GAIN WILD-TYPE 188 60.1 (14.8)

Figure S32.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.12

Table S33.  Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
18P GAIN MUTATED 49 65.9 (12.5)
18P GAIN WILD-TYPE 196 60.2 (14.7)

Figure S33.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00954 (Wilcoxon-test), Q value = 0.12

Table S34.  Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
18Q GAIN MUTATED 32 67.1 (13.7)
18Q GAIN WILD-TYPE 213 60.4 (14.4)

Figure S34.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p gain' versus 'YEARS_TO_BIRTH'

P value = 9.92e-05 (Wilcoxon-test), Q value = 0.0058

Table S35.  Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
19P GAIN MUTATED 81 66.1 (12.7)
19P GAIN WILD-TYPE 164 58.9 (14.8)

Figure S35.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00244 (Wilcoxon-test), Q value = 0.055

Table S36.  Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
19Q GAIN MUTATED 61 66.2 (12.3)
19Q GAIN WILD-TYPE 184 59.7 (14.8)

Figure S36.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'Time to Death'

P value = 0.00177 (logrank test), Q value = 0.045

Table S37.  Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
20P GAIN MUTATED 61 27 0.1 - 106.5 (19.7)
20P GAIN WILD-TYPE 183 55 0.1 - 188.2 (25.1)

Figure S37.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00925 (Wilcoxon-test), Q value = 0.12

Table S38.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
20P GAIN MUTATED 61 65.8 (13.6)
20P GAIN WILD-TYPE 184 59.8 (14.5)

Figure S38.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'Time to Death'

P value = 0.0108 (logrank test), Q value = 0.12

Table S39.  Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
20Q GAIN MUTATED 82 35 0.1 - 143.4 (20.1)
20Q GAIN WILD-TYPE 162 47 0.1 - 188.2 (25.2)

Figure S39.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #1: 'Time to Death'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000326 (Wilcoxon-test), Q value = 0.016

Table S40.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
20Q GAIN MUTATED 82 66.0 (13.1)
20Q GAIN WILD-TYPE 163 58.9 (14.6)

Figure S40.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'GENDER'

P value = 0.00976 (Fisher's exact test), Q value = 0.12

Table S41.  Gene #37: '20q gain' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
20Q GAIN MUTATED 34 48
20Q GAIN WILD-TYPE 98 66

Figure S41.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'GENDER'

'21q gain' versus 'Time to Death'

P value = 0.019 (logrank test), Q value = 0.16

Table S42.  Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
21Q GAIN MUTATED 55 25 0.1 - 108.1 (19.9)
21Q GAIN WILD-TYPE 189 57 0.1 - 188.2 (24.3)

Figure S42.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #1: 'Time to Death'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.036 (Wilcoxon-test), Q value = 0.23

Table S43.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
21Q GAIN MUTATED 54 65.0 (12.3)
21Q GAIN WILD-TYPE 191 60.3 (14.9)

Figure S43.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00202 (Wilcoxon-test), Q value = 0.049

Table S44.  Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
22Q GAIN MUTATED 58 66.3 (12.6)
22Q GAIN WILD-TYPE 187 59.8 (14.7)

Figure S44.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp gain' versus 'YEARS_TO_BIRTH'

P value = 0.0418 (Wilcoxon-test), Q value = 0.24

Table S45.  Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
XP GAIN MUTATED 71 64.3 (13.4)
XP GAIN WILD-TYPE 174 60.1 (14.8)

Figure S45.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq gain' versus 'ETHNICITY'

P value = 0.0156 (Fisher's exact test), Q value = 0.14

Table S46.  Gene #41: 'xq gain' versus Clinical Feature #5: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 5 191
XQ GAIN MUTATED 3 22
XQ GAIN WILD-TYPE 2 169

Figure S46.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #5: 'ETHNICITY'

'1p loss' versus 'GENDER'

P value = 0.0101 (Fisher's exact test), Q value = 0.12

Table S47.  Gene #42: '1p loss' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
1P LOSS MUTATED 23 7
1P LOSS WILD-TYPE 109 107

Figure S47.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'GENDER'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00815 (Wilcoxon-test), Q value = 0.12

Table S48.  Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
2P LOSS MUTATED 83 64.8 (13.7)
2P LOSS WILD-TYPE 162 59.5 (14.6)

Figure S48.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'RACE'

P value = 0.031 (Fisher's exact test), Q value = 0.21

Table S49.  Gene #44: '2p loss' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
2P LOSS MUTATED 0 10 66
2P LOSS WILD-TYPE 6 8 128

Figure S49.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #4: 'RACE'

'2q loss' versus 'Time to Death'

P value = 0.00138 (logrank test), Q value = 0.041

Table S50.  Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
2Q LOSS MUTATED 66 28 0.1 - 96.9 (18.8)
2Q LOSS WILD-TYPE 178 54 0.1 - 188.2 (25.2)

Figure S50.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000344 (Wilcoxon-test), Q value = 0.016

Table S51.  Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
2Q LOSS MUTATED 66 66.6 (13.5)
2Q LOSS WILD-TYPE 179 59.4 (14.4)

Figure S51.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0193 (Wilcoxon-test), Q value = 0.16

Table S52.  Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
3P LOSS MUTATED 56 64.7 (15.7)
3P LOSS WILD-TYPE 189 60.3 (14.0)

Figure S52.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'Time to Death'

P value = 0.0149 (logrank test), Q value = 0.13

Table S53.  Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
3Q LOSS MUTATED 48 22 1.1 - 188.2 (17.8)
3Q LOSS WILD-TYPE 196 60 0.1 - 143.4 (25.2)

Figure S53.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #1: 'Time to Death'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0136 (Wilcoxon-test), Q value = 0.13

Table S54.  Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
3Q LOSS MUTATED 49 65.3 (14.7)
3Q LOSS WILD-TYPE 196 60.3 (14.3)

Figure S54.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'Time to Death'

P value = 0.00655 (logrank test), Q value = 0.11

Table S55.  Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
6P LOSS MUTATED 57 11 0.1 - 188.2 (26.6)
6P LOSS WILD-TYPE 187 71 0.1 - 143.4 (21.4)

Figure S55.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00372 (Wilcoxon-test), Q value = 0.08

Table S56.  Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
9P LOSS MUTATED 81 65.1 (13.6)
9P LOSS WILD-TYPE 164 59.5 (14.6)

Figure S56.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'Time to Death'

P value = 0.028 (logrank test), Q value = 0.19

Table S57.  Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
9Q LOSS MUTATED 49 23 0.1 - 188.2 (16.9)
9Q LOSS WILD-TYPE 195 59 0.1 - 135.5 (24.3)

Figure S57.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0197 (Wilcoxon-test), Q value = 0.16

Table S58.  Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
10P LOSS MUTATED 116 63.5 (14.5)
10P LOSS WILD-TYPE 129 59.4 (14.2)

Figure S58.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'GENDER'

P value = 0.00714 (Fisher's exact test), Q value = 0.11

Table S59.  Gene #60: '10p loss' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
10P LOSS MUTATED 73 43
10P LOSS WILD-TYPE 59 71

Figure S59.  Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'GENDER'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00954 (Wilcoxon-test), Q value = 0.12

Table S60.  Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
10Q LOSS MUTATED 126 63.8 (13.3)
10Q LOSS WILD-TYPE 119 58.7 (15.2)

Figure S60.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'GENDER'

P value = 0.0104 (Fisher's exact test), Q value = 0.12

Table S61.  Gene #61: '10q loss' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
10Q LOSS MUTATED 78 48
10Q LOSS WILD-TYPE 54 66

Figure S61.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'GENDER'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00172 (Wilcoxon-test), Q value = 0.045

Table S62.  Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
13Q LOSS MUTATED 130 64.0 (14.0)
13Q LOSS WILD-TYPE 115 58.3 (14.5)

Figure S62.  Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'Time to Death'

P value = 9.15e-05 (logrank test), Q value = 0.0058

Table S63.  Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
15Q LOSS MUTATED 40 23 0.1 - 143.4 (20.0)
15Q LOSS WILD-TYPE 204 59 0.1 - 188.2 (24.7)

Figure S63.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00936 (Wilcoxon-test), Q value = 0.12

Table S64.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
15Q LOSS MUTATED 42 66.5 (13.0)
15Q LOSS WILD-TYPE 203 60.2 (14.6)

Figure S64.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00529 (Wilcoxon-test), Q value = 0.1

Table S65.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
16Q LOSS MUTATED 119 63.7 (13.7)
16Q LOSS WILD-TYPE 126 59.0 (14.9)

Figure S65.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'Time to Death'

P value = 0.0344 (logrank test), Q value = 0.23

Table S66.  Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
17Q LOSS MUTATED 46 20 0.1 - 88.6 (21.1)
17Q LOSS WILD-TYPE 198 62 0.1 - 188.2 (23.8)

Figure S66.  Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'Time to Death'

P value = 0.0132 (logrank test), Q value = 0.13

Table S67.  Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
18Q LOSS MUTATED 69 30 0.1 - 188.2 (18.9)
18Q LOSS WILD-TYPE 175 52 0.1 - 135.5 (25.7)

Figure S67.  Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'20p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0115 (Wilcoxon-test), Q value = 0.12

Table S68.  Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
20P LOSS MUTATED 52 65.5 (11.9)
20P LOSS WILD-TYPE 193 60.2 (14.9)

Figure S68.  Get High-res Image Gene #77: '20p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0362 (Wilcoxon-test), Q value = 0.23

Table S69.  Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
20Q LOSS MUTATED 24 67.4 (10.8)
20Q LOSS WILD-TYPE 221 60.7 (14.7)

Figure S69.  Get High-res Image Gene #78: '20q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0257 (Wilcoxon-test), Q value = 0.18

Table S70.  Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
21Q LOSS MUTATED 48 65.6 (11.6)
21Q LOSS WILD-TYPE 197 60.3 (14.9)

Figure S70.  Get High-res Image Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'22q loss' versus 'GENDER'

P value = 0.0406 (Fisher's exact test), Q value = 0.24

Table S71.  Gene #80: '22q loss' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
22Q LOSS MUTATED 41 22
22Q LOSS WILD-TYPE 91 92

Figure S71.  Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'GENDER'

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/SARC-TP/15098587/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/SARC-TP/15087563/SARC-TP.merged_data.txt

  • Number of patients = 246

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 5

  • 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.

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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