Correlation between copy number variation genes (focal events) and selected clinical features
Sarcoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1TT4Q2W
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1TT4Q2W
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 66 focal events and 5 clinical features across 246 patients, 68 significant findings detected with Q value < 0.25.

  • amp_1p32.1 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_1q21.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_2p11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_3p12.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_4q12 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_5p15.33 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_6p21.1 cnv correlated to 'Time to Death'.

  • amp_7q31.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_8p11.22 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_8q24.21 cnv correlated to 'Time to Death'.

  • amp_11q22.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_12q15 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'GENDER', and 'RACE'.

  • amp_13q34 cnv correlated to 'RACE'.

  • amp_15q26.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_17p12 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_17p11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_17q24.3 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • amp_19q12 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_20q13.33 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'GENDER'.

  • amp_21q21.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_xq21.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_1p36.32 cnv correlated to 'Time to Death' and 'GENDER'.

  • del_1q44 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_2p25.3 cnv correlated to 'GENDER' and 'RACE'.

  • del_2q37.3 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_2q37.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_3q13.31 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_4q35.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_9p24.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_9q34.3 cnv correlated to 'RACE'.

  • del_10p15.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH' and 'RACE'.

  • del_10q26.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_11p15.5 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_11q24.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_12p13.1 cnv correlated to 'GENDER'.

  • del_12q12 cnv correlated to 'Time to Death' and 'RACE'.

  • del_12q24.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_13q14.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_16q11.2 cnv correlated to 'RACE'.

  • del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_17p13.1 cnv correlated to 'GENDER'.

  • del_17q11.2 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_17q25.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_18q23 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_19p13.3 cnv correlated to 'GENDER'.

  • del_21q22.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_xq21.1 cnv correlated to 'Time to Death' and 'GENDER'.

  • del_xq22.3 cnv correlated to 'Time to Death' and 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 66 focal events and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 68 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
amp 12q15 92 (37%) 154 0.0197
(0.143) 		0.0101
(0.108) 		0.000563
(0.0223) 		0.013
(0.122) 		1
(1.00)
amp 20q13 33 96 (39%) 150 0.0242
(0.154) 		0.000555
(0.0223) 		0.0133
(0.122) 		1
(1.00) 		1
(1.00)
amp 1p32 1 91 (37%) 155 0.000391
(0.0223) 		0.000348
(0.0223) 		0.145
(0.457) 		0.136
(0.445) 		0.159
(0.46)
amp 5p15 33 114 (46%) 132 0.0313
(0.178) 		0.00296
(0.061) 		0.201
(0.54) 		0.94
(1.00) 		1
(1.00)
amp 8p11 22 78 (32%) 168 0.00675
(0.0857) 		0.00107
(0.0294) 		1
(1.00) 		0.112
(0.406) 		1
(1.00)
amp 11q22 2 35 (14%) 211 0.00594
(0.0857) 		0.0108
(0.108) 		0.855
(1.00) 		0.308
(0.668) 		0.498
(0.787)
amp 17q24 3 75 (30%) 171 0.539
(0.82) 		0.0459
(0.223) 		0.0373
(0.192) 		0.557
(0.836) 		1
(1.00)
del 1p36 32 64 (26%) 182 0.0177
(0.138) 		0.131
(0.437) 		0.000763
(0.0229) 		0.674
(0.874) 		0.324
(0.668)
del 2p25 3 93 (38%) 153 0.577
(0.857) 		0.0701
(0.322) 		0.018
(0.138) 		0.00768
(0.0905) 		0.0703
(0.322)
del 2q37 3 103 (42%) 143 0.0347
(0.188) 		0.00847
(0.0964) 		1
(1.00) 		0.598
(0.865) 		0.385
(0.697)
del 10q23 31 133 (54%) 113 0.222
(0.56) 		0.0208
(0.143) 		0.25
(0.592) 		0.0271
(0.162) 		0.163
(0.464)
del 12q12 53 (22%) 193 0.0205
(0.143) 		0.138
(0.447) 		0.644
(0.868) 		0.0221
(0.144) 		0.586
(0.863)
del 18q23 82 (33%) 164 0.0155
(0.131) 		0.0037
(0.0642) 		0.498
(0.787) 		1
(1.00) 		0.665
(0.868)
del xq21 1 111 (45%) 135 0.00606
(0.0857) 		0.134
(0.443) 		0.0206
(0.143) 		0.412
(0.712) 		0.371
(0.695)
del xq22 3 120 (49%) 126 0.0173
(0.138) 		0.972
(1.00) 		0.0303
(0.175) 		0.655
(0.868) 		0.369
(0.695)
amp 1q21 3 99 (40%) 147 0.781
(0.954) 		0.0361
(0.192) 		0.0901
(0.362) 		0.94
(1.00) 		0.402
(0.71)
amp 2p11 2 60 (24%) 186 0.465
(0.764) 		0.000633
(0.0223) 		0.298
(0.668) 		0.143
(0.452) 		1
(1.00)
amp 3p12 1 67 (27%) 179 0.346
(0.685) 		4.65e-06
(0.000768) 		0.315
(0.668) 		0.797
(0.96) 		0.324
(0.668)
amp 4q12 75 (30%) 171 0.496
(0.787) 		0.0223
(0.144) 		0.406
(0.712) 		0.557
(0.836) 		1
(1.00)
amp 6p21 1 58 (24%) 188 0.00707
(0.0864) 		0.0732
(0.323) 		0.369
(0.695) 		0.124
(0.426) 		0.595
(0.865)
amp 7q31 2 75 (30%) 171 0.125
(0.426) 		1.3e-06
(0.000429) 		1
(1.00) 		1
(1.00) 		0.647
(0.868)
amp 8q24 21 80 (33%) 166 0.00641
(0.0857) 		0.377
(0.695) 		0.682
(0.88) 		0.171
(0.475) 		0.337
(0.683)
amp 13q34 51 (21%) 195 0.58
(0.859) 		0.152
(0.46) 		0.0842
(0.347) 		0.0408
(0.201) 		0.591
(0.865)
amp 15q26 3 81 (33%) 165 0.444
(0.736) 		0.0348
(0.188) 		0.224
(0.56) 		0.619
(0.868) 		0.351
(0.689)
amp 17p12 97 (39%) 149 0.305
(0.668) 		0.025
(0.156) 		0.896
(1.00) 		0.723
(0.908) 		0.388
(0.699)
amp 17p11 2 99 (40%) 147 0.323
(0.668) 		0.0276
(0.162) 		0.362
(0.695) 		0.444
(0.736) 		1
(1.00)
amp 19q12 90 (37%) 156 0.167
(0.471) 		0.000677
(0.0223) 		0.289
(0.662) 		0.774
(0.949) 		0.653
(0.868)
amp 21q21 1 71 (29%) 175 0.156
(0.46) 		0.0152
(0.131) 		0.0921
(0.362) 		0.622
(0.868) 		0.324
(0.668)
amp xq21 1 43 (17%) 203 0.0777
(0.329) 		0.0257
(0.157) 		0.4
(0.71) 		0.415
(0.713) 		0.188
(0.513)
del 1q44 76 (31%) 170 0.251
(0.592) 		0.00638
(0.0857) 		0.89
(1.00) 		0.24
(0.581) 		1
(1.00)
del 2q37 3 105 (43%) 141 0.153
(0.46) 		0.00256
(0.0563) 		0.699
(0.896) 		0.573
(0.856) 		1
(1.00)
del 3q13 31 51 (21%) 195 0.228
(0.562) 		0.0172
(0.138) 		0.529
(0.815) 		0.633
(0.868) 		1
(1.00)
del 4q35 1 91 (37%) 155 0.109
(0.4) 		0.00194
(0.0457) 		0.598
(0.865) 		0.315
(0.668) 		0.159
(0.46)
del 9p24 3 96 (39%) 150 0.322
(0.668) 		0.00191
(0.0457) 		0.793
(0.96) 		1
(1.00) 		0.651
(0.868)
del 9p21 3 112 (46%) 134 0.0719
(0.323) 		0.00362
(0.0642) 		0.7
(0.896) 		0.535
(0.82) 		1
(1.00)
del 9q34 3 60 (24%) 186 0.155
(0.46) 		0.257
(0.598) 		0.458
(0.755) 		0.0368
(0.192) 		1
(1.00)
del 10p15 3 123 (50%) 123 0.723
(0.908) 		0.04
(0.201) 		0.159
(0.46) 		0.342
(0.685) 		0.192
(0.52)
del 10q26 3 128 (52%) 118 0.521
(0.811) 		0.00447
(0.0738) 		0.443
(0.736) 		0.122
(0.422) 		0.168
(0.471)
del 11p15 5 104 (42%) 142 0.38
(0.695) 		0.0102
(0.108) 		0.606
(0.868) 		0.636
(0.868) 		0.379
(0.695)
del 11q24 2 118 (48%) 128 0.801
(0.961) 		0.0152
(0.131) 		0.609
(0.868) 		1
(1.00) 		0.372
(0.695)
del 12p13 1 84 (34%) 162 0.61
(0.868) 		0.141
(0.451) 		0.0318
(0.178) 		0.711
(0.9) 		0.663
(0.868)
del 12q24 33 68 (28%) 178 0.372
(0.695) 		0.00659
(0.0857) 		0.153
(0.46) 		0.393
(0.704) 		0.324
(0.668)
del 13q14 2 175 (71%) 71 0.756
(0.938) 		0.00326
(0.0633) 		0.0921
(0.362) 		0.42
(0.718) 		0.101
(0.379)
del 16q11 2 125 (51%) 121 0.774
(0.949) 		0.16
(0.46) 		0.0963
(0.37) 		0.0196
(0.143) 		1
(1.00)
del 16q23 1 130 (53%) 116 0.226
(0.56) 		0.000632
(0.0223) 		0.0734
(0.323) 		0.241
(0.581) 		0.654
(0.868)
del 17p13 1 124 (50%) 122 0.116
(0.418) 		0.477
(0.779) 		0.0406
(0.201) 		0.157
(0.46) 		1
(1.00)
del 17q11 2 78 (32%) 168 0.256
(0.598) 		0.013
(0.122) 		0.493
(0.787) 		0.704
(0.897) 		1
(1.00)
del 17q25 3 61 (25%) 185 0.104
(0.385) 		0.0215
(0.144) 		0.658
(0.868) 		0.602
(0.868) 		0.332
(0.675)
del 19p13 3 70 (28%) 176 0.512
(0.801) 		0.707
(0.897) 		0.0105
(0.108) 		0.803
(0.961) 		0.326
(0.668)
del 21q22 3 65 (26%) 181 0.984
(1.00) 		0.00053
(0.0223) 		0.885
(1.00) 		0.926
(1.00) 		1
(1.00)
amp 1q24 3 100 (41%) 146 0.345
(0.685) 		0.215
(0.56) 		0.795
(0.96) 		0.523
(0.811) 		1
(1.00)
amp 6q25 1 73 (30%) 173 0.425
(0.72) 		0.101
(0.379) 		0.0941
(0.365) 		0.867
(1.00) 		0.629
(0.868)
amp 19p13 2 101 (41%) 145 0.539
(0.82) 		0.297
(0.668) 		0.12
(0.421) 		0.676
(0.874) 		0.651
(0.868)
amp xp21 2 94 (38%) 152 0.657
(0.868) 		0.0802
(0.335) 		0.36
(0.695) 		0.827
(0.981) 		0.402
(0.71)
del 3p21 31 64 (26%) 182 0.223
(0.56) 		0.381
(0.695) 		0.885
(1.00) 		0.665
(0.868) 		1
(1.00)
del 3q29 52 (21%) 194 0.943
(1.00) 		0.767
(0.948) 		0.434
(0.731) 		0.303
(0.668) 		1
(1.00)
del 5p15 33 33 (13%) 213 0.365
(0.695) 		0.936
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
del 6p25 3 76 (31%) 170 0.288
(0.662) 		0.655
(0.868) 		0.89
(1.00) 		0.658
(0.868) 		0.181
(0.499)
del 6q14 1 75 (30%) 171 0.506
(0.795) 		0.293
(0.667) 		1
(1.00) 		0.813
(0.968) 		1
(1.00)
del 7q36 3 68 (28%) 178 0.224
(0.56) 		0.496
(0.787) 		0.479
(0.779) 		0.426
(0.72) 		1
(1.00)
del 8p23 3 78 (32%) 168 0.0907
(0.362) 		0.076
(0.327) 		0.493
(0.787) 		0.646
(0.868) 		1
(1.00)
del 14q24 1 77 (31%) 169 0.343
(0.685) 		0.88
(1.00) 		0.216
(0.56) 		0.648
(0.868) 		0.325
(0.668)
del 19q13 43 102 (41%) 144 0.0569
(0.272) 		0.411
(0.712) 		0.3
(0.668) 		0.225
(0.56) 		0.377
(0.695)
del 21q11 2 48 (20%) 198 0.795
(0.96) 		0.128
(0.433) 		0.748
(0.932) 		0.554
(0.836) 		0.249
(0.592)
del 22q13 32 79 (32%) 167 0.209
(0.555) 		0.218
(0.56) 		0.0764
(0.327) 		1
(1.00) 		1
(1.00)
del xp21 1 52 (21%) 194 0.732
(0.914) 		0.0613
(0.289) 		0.12
(0.421) 		0.411
(0.712) 		0.239
(0.581)
'amp_1p32.1' versus 'Time to Death'

P value = 0.000391 (logrank test), Q value = 0.022

Table S1.  Gene #1: 'amp_1p32.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 1(1P32.1) MUTATED 91 39 0.5 - 106.5 (19.3)
AMP PEAK 1(1P32.1) WILD-TYPE 153 43 0.1 - 188.2 (27.8)

Figure S1.  Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #1: 'Time to Death'

'amp_1p32.1' versus 'YEARS_TO_BIRTH'

P value = 0.000348 (Wilcoxon-test), Q value = 0.022

Table S2.  Gene #1: 'amp_1p32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 1(1P32.1) MUTATED 91 65.7 (12.9)
AMP PEAK 1(1P32.1) WILD-TYPE 154 58.7 (14.8)

Figure S2.  Get High-res Image Gene #1: 'amp_1p32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0361 (Wilcoxon-test), Q value = 0.19

Table S3.  Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 2(1Q21.3) MUTATED 98 63.5 (12.6)
AMP PEAK 2(1Q21.3) WILD-TYPE 147 59.9 (15.5)

Figure S3.  Get High-res Image Gene #2: 'amp_1q21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_2p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.000633 (Wilcoxon-test), Q value = 0.022

Table S4.  Gene #4: 'amp_2p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 4(2P11.2) MUTATED 60 67.1 (12.2)
AMP PEAK 4(2P11.2) WILD-TYPE 185 59.4 (14.7)

Figure S4.  Get High-res Image Gene #4: 'amp_2p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3p12.1' versus 'YEARS_TO_BIRTH'

P value = 4.65e-06 (Wilcoxon-test), Q value = 0.00077

Table S5.  Gene #5: 'amp_3p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 5(3P12.1) MUTATED 66 68.2 (13.4)
AMP PEAK 5(3P12.1) WILD-TYPE 179 58.8 (14.1)

Figure S5.  Get High-res Image Gene #5: 'amp_3p12.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_4q12' versus 'YEARS_TO_BIRTH'

P value = 0.0223 (Wilcoxon-test), Q value = 0.14

Table S6.  Gene #6: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 6(4Q12) MUTATED 74 64.8 (11.7)
AMP PEAK 6(4Q12) WILD-TYPE 171 59.8 (15.3)

Figure S6.  Get High-res Image Gene #6: 'amp_4q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_5p15.33' versus 'Time to Death'

P value = 0.0313 (logrank test), Q value = 0.18

Table S7.  Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 7(5P15.33) MUTATED 113 44 0.1 - 188.2 (20.3)
AMP PEAK 7(5P15.33) WILD-TYPE 131 38 0.1 - 143.4 (25.1)

Figure S7.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #1: 'Time to Death'

'amp_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00296 (Wilcoxon-test), Q value = 0.061

Table S8.  Gene #7: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 7(5P15.33) MUTATED 113 64.3 (13.2)
AMP PEAK 7(5P15.33) WILD-TYPE 132 58.7 (15.1)

Figure S8.  Get High-res Image Gene #7: 'amp_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_6p21.1' versus 'Time to Death'

P value = 0.00707 (logrank test), Q value = 0.086

Table S9.  Gene #8: 'amp_6p21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 8(6P21.1) MUTATED 57 26 0.1 - 143.4 (19.9)
AMP PEAK 8(6P21.1) WILD-TYPE 187 56 0.1 - 188.2 (25.1)

Figure S9.  Get High-res Image Gene #8: 'amp_6p21.1' versus Clinical Feature #1: 'Time to Death'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 1.3e-06 (Wilcoxon-test), Q value = 0.00043

Table S10.  Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 10(7Q31.2) MUTATED 75 67.6 (11.7)
AMP PEAK 10(7Q31.2) WILD-TYPE 170 58.5 (14.8)

Figure S10.  Get High-res Image Gene #10: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8p11.22' versus 'Time to Death'

P value = 0.00675 (logrank test), Q value = 0.086

Table S11.  Gene #11: 'amp_8p11.22' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 11(8P11.22) MUTATED 78 34 0.1 - 106.5 (19.5)
AMP PEAK 11(8P11.22) WILD-TYPE 166 48 0.1 - 188.2 (26.1)

Figure S11.  Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #1: 'Time to Death'

'amp_8p11.22' versus 'YEARS_TO_BIRTH'

P value = 0.00107 (Wilcoxon-test), Q value = 0.029

Table S12.  Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 11(8P11.22) MUTATED 77 66.1 (12.0)
AMP PEAK 11(8P11.22) WILD-TYPE 168 59.1 (15.0)

Figure S12.  Get High-res Image Gene #11: 'amp_8p11.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.21' versus 'Time to Death'

P value = 0.00641 (logrank test), Q value = 0.086

Table S13.  Gene #12: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 12(8Q24.21) MUTATED 79 31 0.1 - 88.3 (16.9)
AMP PEAK 12(8Q24.21) WILD-TYPE 165 51 0.1 - 188.2 (27.8)

Figure S13.  Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #1: 'Time to Death'

'amp_11q22.2' versus 'Time to Death'

P value = 0.00594 (logrank test), Q value = 0.086

Table S14.  Gene #13: 'amp_11q22.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 13(11Q22.2) MUTATED 34 17 0.1 - 106.5 (18.7)
AMP PEAK 13(11Q22.2) WILD-TYPE 210 65 0.1 - 188.2 (25.2)

Figure S14.  Get High-res Image Gene #13: 'amp_11q22.2' versus Clinical Feature #1: 'Time to Death'

'amp_11q22.2' versus 'YEARS_TO_BIRTH'

P value = 0.0108 (Wilcoxon-test), Q value = 0.11

Table S15.  Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 13(11Q22.2) MUTATED 35 66.7 (14.5)
AMP PEAK 13(11Q22.2) WILD-TYPE 210 60.4 (14.3)

Figure S15.  Get High-res Image Gene #13: 'amp_11q22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'Time to Death'

P value = 0.0197 (logrank test), Q value = 0.14

Table S16.  Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 14(12Q15) MUTATED 91 38 0.1 - 108.1 (20.1)
AMP PEAK 14(12Q15) WILD-TYPE 153 44 0.1 - 188.2 (25.1)

Figure S16.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #1: 'Time to Death'

'amp_12q15' versus 'YEARS_TO_BIRTH'

P value = 0.0101 (Wilcoxon-test), Q value = 0.11

Table S17.  Gene #14: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 14(12Q15) MUTATED 92 64.3 (13.5)
AMP PEAK 14(12Q15) WILD-TYPE 153 59.5 (14.8)

Figure S17.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_12q15' versus 'GENDER'

P value = 0.000563 (Fisher's exact test), Q value = 0.022

Table S18.  Gene #14: 'amp_12q15' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
AMP PEAK 14(12Q15) MUTATED 36 56
AMP PEAK 14(12Q15) WILD-TYPE 96 58

Figure S18.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #3: 'GENDER'

'amp_12q15' versus 'RACE'

P value = 0.013 (Fisher's exact test), Q value = 0.12

Table S19.  Gene #14: 'amp_12q15' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
AMP PEAK 14(12Q15) MUTATED 3 1 66
AMP PEAK 14(12Q15) WILD-TYPE 3 17 128

Figure S19.  Get High-res Image Gene #14: 'amp_12q15' versus Clinical Feature #4: 'RACE'

'amp_13q34' versus 'RACE'

P value = 0.0408 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #15: 'amp_13q34' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
AMP PEAK 15(13Q34) MUTATED 0 8 41
AMP PEAK 15(13Q34) WILD-TYPE 6 10 153

Figure S20.  Get High-res Image Gene #15: 'amp_13q34' versus Clinical Feature #4: 'RACE'

'amp_15q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.0348 (Wilcoxon-test), Q value = 0.19

Table S21.  Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 16(15Q26.3) MUTATED 80 63.7 (14.7)
AMP PEAK 16(15Q26.3) WILD-TYPE 165 60.2 (14.3)

Figure S21.  Get High-res Image Gene #16: 'amp_15q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p12' versus 'YEARS_TO_BIRTH'

P value = 0.025 (Wilcoxon-test), Q value = 0.16

Table S22.  Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 17(17P12) MUTATED 96 64.0 (13.9)
AMP PEAK 17(17P12) WILD-TYPE 149 59.6 (14.7)

Figure S22.  Get High-res Image Gene #17: 'amp_17p12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17p11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0276 (Wilcoxon-test), Q value = 0.16

Table S23.  Gene #18: 'amp_17p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 18(17P11.2) MUTATED 98 63.8 (13.9)
AMP PEAK 18(17P11.2) WILD-TYPE 147 59.6 (14.7)

Figure S23.  Get High-res Image Gene #18: 'amp_17p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.0459 (Wilcoxon-test), Q value = 0.22

Table S24.  Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 19(17Q24.3) MUTATED 74 64.1 (14.2)
AMP PEAK 19(17Q24.3) WILD-TYPE 171 60.1 (14.5)

Figure S24.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q24.3' versus 'GENDER'

P value = 0.0373 (Fisher's exact test), Q value = 0.19

Table S25.  Gene #19: 'amp_17q24.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
AMP PEAK 19(17Q24.3) MUTATED 48 27
AMP PEAK 19(17Q24.3) WILD-TYPE 84 87

Figure S25.  Get High-res Image Gene #19: 'amp_17q24.3' versus Clinical Feature #3: 'GENDER'

'amp_19q12' versus 'YEARS_TO_BIRTH'

P value = 0.000677 (Wilcoxon-test), Q value = 0.022

Table S26.  Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 21(19Q12) MUTATED 89 65.0 (13.0)
AMP PEAK 21(19Q12) WILD-TYPE 156 59.2 (14.9)

Figure S26.  Get High-res Image Gene #21: 'amp_19q12' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.33' versus 'Time to Death'

P value = 0.0242 (logrank test), Q value = 0.15

Table S27.  Gene #22: 'amp_20q13.33' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
AMP PEAK 22(20Q13.33) MUTATED 96 37 0.1 - 143.4 (19.3)
AMP PEAK 22(20Q13.33) WILD-TYPE 148 45 0.1 - 188.2 (28.0)

Figure S27.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #1: 'Time to Death'

'amp_20q13.33' versus 'YEARS_TO_BIRTH'

P value = 0.000555 (Wilcoxon-test), Q value = 0.022

Table S28.  Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 22(20Q13.33) MUTATED 96 65.3 (13.5)
AMP PEAK 22(20Q13.33) WILD-TYPE 149 58.8 (14.6)

Figure S28.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_20q13.33' versus 'GENDER'

P value = 0.0133 (Fisher's exact test), Q value = 0.12

Table S29.  Gene #22: 'amp_20q13.33' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
AMP PEAK 22(20Q13.33) MUTATED 42 54
AMP PEAK 22(20Q13.33) WILD-TYPE 90 60

Figure S29.  Get High-res Image Gene #22: 'amp_20q13.33' versus Clinical Feature #3: 'GENDER'

'amp_21q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0152 (Wilcoxon-test), Q value = 0.13

Table S30.  Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 23(21Q21.1) MUTATED 70 64.8 (11.8)
AMP PEAK 23(21Q21.1) WILD-TYPE 175 59.9 (15.2)

Figure S30.  Get High-res Image Gene #23: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_xq21.1' versus 'YEARS_TO_BIRTH'

P value = 0.0257 (Wilcoxon-test), Q value = 0.16

Table S31.  Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
AMP PEAK 25(XQ21.1) MUTATED 43 65.7 (11.1)
AMP PEAK 25(XQ21.1) WILD-TYPE 202 60.4 (15.0)

Figure S31.  Get High-res Image Gene #25: 'amp_xq21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.32' versus 'Time to Death'

P value = 0.0177 (logrank test), Q value = 0.14

Table S32.  Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 1(1P36.32) MUTATED 64 17 0.1 - 188.2 (26.9)
DEL PEAK 1(1P36.32) WILD-TYPE 180 65 0.1 - 135.5 (20.0)

Figure S32.  Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #1: 'Time to Death'

'del_1p36.32' versus 'GENDER'

P value = 0.000763 (Fisher's exact test), Q value = 0.023

Table S33.  Gene #26: 'del_1p36.32' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 1(1P36.32) MUTATED 46 18
DEL PEAK 1(1P36.32) WILD-TYPE 86 96

Figure S33.  Get High-res Image Gene #26: 'del_1p36.32' versus Clinical Feature #3: 'GENDER'

'del_1q44' versus 'YEARS_TO_BIRTH'

P value = 0.00638 (Wilcoxon-test), Q value = 0.086

Table S34.  Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 2(1Q44) MUTATED 76 65.0 (13.8)
DEL PEAK 2(1Q44) WILD-TYPE 169 59.6 (14.5)

Figure S34.  Get High-res Image Gene #27: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2p25.3' versus 'GENDER'

P value = 0.018 (Fisher's exact test), Q value = 0.14

Table S35.  Gene #28: 'del_2p25.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 3(2P25.3) MUTATED 59 34
DEL PEAK 3(2P25.3) WILD-TYPE 73 80

Figure S35.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #3: 'GENDER'

'del_2p25.3' versus 'RACE'

P value = 0.00768 (Fisher's exact test), Q value = 0.091

Table S36.  Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
DEL PEAK 3(2P25.3) MUTATED 1 13 73
DEL PEAK 3(2P25.3) WILD-TYPE 5 5 121

Figure S36.  Get High-res Image Gene #28: 'del_2p25.3' versus Clinical Feature #4: 'RACE'

'del_2q37.3' versus 'Time to Death'

P value = 0.0347 (logrank test), Q value = 0.19

Table S37.  Gene #29: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 4(2Q37.3) MUTATED 102 41 0.1 - 102.0 (21.3)
DEL PEAK 4(2Q37.3) WILD-TYPE 142 41 0.1 - 188.2 (25.2)

Figure S37.  Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00847 (Wilcoxon-test), Q value = 0.096

Table S38.  Gene #29: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 4(2Q37.3) MUTATED 102 64.2 (13.9)
DEL PEAK 4(2Q37.3) WILD-TYPE 143 59.3 (14.6)

Figure S38.  Get High-res Image Gene #29: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00256 (Wilcoxon-test), Q value = 0.056

Table S39.  Gene #30: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 5(2Q37.3) MUTATED 104 64.5 (13.9)
DEL PEAK 5(2Q37.3) WILD-TYPE 141 59.0 (14.5)

Figure S39.  Get High-res Image Gene #30: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q13.31' versus 'YEARS_TO_BIRTH'

P value = 0.0172 (Wilcoxon-test), Q value = 0.14

Table S40.  Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 7(3Q13.31) MUTATED 50 64.7 (16.0)
DEL PEAK 7(3Q13.31) WILD-TYPE 195 60.4 (14.0)

Figure S40.  Get High-res Image Gene #32: 'del_3q13.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_4q35.1' versus 'YEARS_TO_BIRTH'

P value = 0.00194 (Wilcoxon-test), Q value = 0.046

Table S41.  Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 9(4Q35.1) MUTATED 90 64.8 (15.0)
DEL PEAK 9(4Q35.1) WILD-TYPE 155 59.3 (13.8)

Figure S41.  Get High-res Image Gene #34: 'del_4q35.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p24.3' versus 'YEARS_TO_BIRTH'

P value = 0.00191 (Wilcoxon-test), Q value = 0.046

Table S42.  Gene #40: 'del_9p24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 15(9P24.3) MUTATED 96 65.0 (12.8)
DEL PEAK 15(9P24.3) WILD-TYPE 149 58.9 (15.0)

Figure S42.  Get High-res Image Gene #40: 'del_9p24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.00362 (Wilcoxon-test), Q value = 0.064

Table S43.  Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 16(9P21.3) MUTATED 112 64.3 (13.3)
DEL PEAK 16(9P21.3) WILD-TYPE 133 58.8 (15.0)

Figure S43.  Get High-res Image Gene #41: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9q34.3' versus 'RACE'

P value = 0.0368 (Fisher's exact test), Q value = 0.19

Table S44.  Gene #42: 'del_9q34.3' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
DEL PEAK 17(9Q34.3) MUTATED 1 9 44
DEL PEAK 17(9Q34.3) WILD-TYPE 5 9 150

Figure S44.  Get High-res Image Gene #42: 'del_9q34.3' versus Clinical Feature #4: 'RACE'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 0.04 (Wilcoxon-test), Q value = 0.2

Table S45.  Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 18(10P15.3) MUTATED 122 63.0 (14.0)
DEL PEAK 18(10P15.3) WILD-TYPE 123 59.6 (14.8)

Figure S45.  Get High-res Image Gene #43: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0208 (Wilcoxon-test), Q value = 0.14

Table S46.  Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 19(10Q23.31) MUTATED 133 63.4 (13.0)
DEL PEAK 19(10Q23.31) WILD-TYPE 112 58.8 (15.8)

Figure S46.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'RACE'

P value = 0.0271 (Fisher's exact test), Q value = 0.16

Table S47.  Gene #44: 'del_10q23.31' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
DEL PEAK 19(10Q23.31) MUTATED 2 15 107
DEL PEAK 19(10Q23.31) WILD-TYPE 4 3 87

Figure S47.  Get High-res Image Gene #44: 'del_10q23.31' versus Clinical Feature #4: 'RACE'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 0.00447 (Wilcoxon-test), Q value = 0.074

Table S48.  Gene #45: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 20(10Q26.3) MUTATED 127 64.0 (12.7)
DEL PEAK 20(10Q26.3) WILD-TYPE 118 58.4 (15.7)

Figure S48.  Get High-res Image Gene #45: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.11

Table S49.  Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 21(11P15.5) MUTATED 103 63.8 (14.5)
DEL PEAK 21(11P15.5) WILD-TYPE 142 59.5 (14.3)

Figure S49.  Get High-res Image Gene #46: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q24.2' versus 'YEARS_TO_BIRTH'

P value = 0.0152 (Wilcoxon-test), Q value = 0.13

Table S50.  Gene #47: 'del_11q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 22(11Q24.2) MUTATED 117 63.6 (13.6)
DEL PEAK 22(11Q24.2) WILD-TYPE 128 59.2 (15.0)

Figure S50.  Get High-res Image Gene #47: 'del_11q24.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_12p13.1' versus 'GENDER'

P value = 0.0318 (Fisher's exact test), Q value = 0.18

Table S51.  Gene #48: 'del_12p13.1' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 23(12P13.1) MUTATED 37 47
DEL PEAK 23(12P13.1) WILD-TYPE 95 67

Figure S51.  Get High-res Image Gene #48: 'del_12p13.1' versus Clinical Feature #3: 'GENDER'

'del_12q12' versus 'Time to Death'

P value = 0.0205 (logrank test), Q value = 0.14

Table S52.  Gene #49: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 24(12Q12) MUTATED 53 23 0.1 - 86.1 (21.3)
DEL PEAK 24(12Q12) WILD-TYPE 191 59 0.1 - 188.2 (24.3)

Figure S52.  Get High-res Image Gene #49: 'del_12q12' versus Clinical Feature #1: 'Time to Death'

'del_12q12' versus 'RACE'

P value = 0.0221 (Fisher's exact test), Q value = 0.14

Table S53.  Gene #49: 'del_12q12' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
DEL PEAK 24(12Q12) MUTATED 0 8 36
DEL PEAK 24(12Q12) WILD-TYPE 6 10 158

Figure S53.  Get High-res Image Gene #49: 'del_12q12' versus Clinical Feature #4: 'RACE'

'del_12q24.33' versus 'YEARS_TO_BIRTH'

P value = 0.00659 (Wilcoxon-test), Q value = 0.086

Table S54.  Gene #50: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 25(12Q24.33) MUTATED 68 65.3 (12.7)
DEL PEAK 25(12Q24.33) WILD-TYPE 177 59.8 (14.9)

Figure S54.  Get High-res Image Gene #50: 'del_12q24.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 0.00326 (Wilcoxon-test), Q value = 0.063

Table S55.  Gene #51: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 26(13Q14.2) MUTATED 174 63.1 (13.5)
DEL PEAK 26(13Q14.2) WILD-TYPE 71 56.9 (15.9)

Figure S55.  Get High-res Image Gene #51: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_16q11.2' versus 'RACE'

P value = 0.0196 (Fisher's exact test), Q value = 0.14

Table S56.  Gene #53: 'del_16q11.2' versus Clinical Feature #4: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 6 18 194
DEL PEAK 28(16Q11.2) MUTATED 1 14 101
DEL PEAK 28(16Q11.2) WILD-TYPE 5 4 93

Figure S56.  Get High-res Image Gene #53: 'del_16q11.2' versus Clinical Feature #4: 'RACE'

'del_16q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.000632 (Wilcoxon-test), Q value = 0.022

Table S57.  Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 29(16Q23.1) MUTATED 129 64.3 (13.6)
DEL PEAK 29(16Q23.1) WILD-TYPE 116 58.0 (14.7)

Figure S57.  Get High-res Image Gene #54: 'del_16q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17p13.1' versus 'GENDER'

P value = 0.0406 (Fisher's exact test), Q value = 0.2

Table S58.  Gene #55: 'del_17p13.1' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 30(17P13.1) MUTATED 75 49
DEL PEAK 30(17P13.1) WILD-TYPE 57 65

Figure S58.  Get High-res Image Gene #55: 'del_17p13.1' versus Clinical Feature #3: 'GENDER'

'del_17q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.013 (Wilcoxon-test), Q value = 0.12

Table S59.  Gene #56: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 31(17Q11.2) MUTATED 78 64.4 (14.7)
DEL PEAK 31(17Q11.2) WILD-TYPE 167 59.9 (14.2)

Figure S59.  Get High-res Image Gene #56: 'del_17q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_17q25.3' versus 'YEARS_TO_BIRTH'

P value = 0.0215 (Wilcoxon-test), Q value = 0.14

Table S60.  Gene #57: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 32(17Q25.3) MUTATED 60 64.6 (13.2)
DEL PEAK 32(17Q25.3) WILD-TYPE 185 60.2 (14.8)

Figure S60.  Get High-res Image Gene #57: 'del_17q25.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_18q23' versus 'Time to Death'

P value = 0.0155 (logrank test), Q value = 0.13

Table S61.  Gene #58: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 33(18Q23) MUTATED 81 34 0.1 - 188.2 (19.3)
DEL PEAK 33(18Q23) WILD-TYPE 163 48 0.1 - 135.5 (26.5)

Figure S61.  Get High-res Image Gene #58: 'del_18q23' versus Clinical Feature #1: 'Time to Death'

'del_18q23' versus 'YEARS_TO_BIRTH'

P value = 0.0037 (Wilcoxon-test), Q value = 0.064

Table S62.  Gene #58: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 33(18Q23) MUTATED 82 64.8 (14.4)
DEL PEAK 33(18Q23) WILD-TYPE 163 59.5 (14.3)

Figure S62.  Get High-res Image Gene #58: 'del_18q23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19p13.3' versus 'GENDER'

P value = 0.0105 (Fisher's exact test), Q value = 0.11

Table S63.  Gene #59: 'del_19p13.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 34(19P13.3) MUTATED 47 23
DEL PEAK 34(19P13.3) WILD-TYPE 85 91

Figure S63.  Get High-res Image Gene #59: 'del_19p13.3' versus Clinical Feature #3: 'GENDER'

'del_21q22.3' versus 'YEARS_TO_BIRTH'

P value = 0.00053 (Wilcoxon-test), Q value = 0.022

Table S64.  Gene #62: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 245 61.3 (14.5)
DEL PEAK 37(21Q22.3) MUTATED 65 66.7 (11.4)
DEL PEAK 37(21Q22.3) WILD-TYPE 180 59.4 (15.0)

Figure S64.  Get High-res Image Gene #62: 'del_21q22.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xq21.1' versus 'Time to Death'

P value = 0.00606 (logrank test), Q value = 0.086

Table S65.  Gene #65: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 40(XQ21.1) MUTATED 109 26 0.1 - 188.2 (25.2)
DEL PEAK 40(XQ21.1) WILD-TYPE 135 56 0.1 - 135.5 (20.3)

Figure S65.  Get High-res Image Gene #65: 'del_xq21.1' versus Clinical Feature #1: 'Time to Death'

'del_xq21.1' versus 'GENDER'

P value = 0.0206 (Fisher's exact test), Q value = 0.14

Table S66.  Gene #65: 'del_xq21.1' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 40(XQ21.1) MUTATED 69 42
DEL PEAK 40(XQ21.1) WILD-TYPE 63 72

Figure S66.  Get High-res Image Gene #65: 'del_xq21.1' versus Clinical Feature #3: 'GENDER'

'del_xq22.3' versus 'Time to Death'

P value = 0.0173 (logrank test), Q value = 0.14

Table S67.  Gene #66: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 244 82 0.1 - 188.2 (23.3)
DEL PEAK 41(XQ22.3) MUTATED 119 32 0.1 - 188.2 (25.7)
DEL PEAK 41(XQ22.3) WILD-TYPE 125 50 0.1 - 135.5 (19.5)

Figure S67.  Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #1: 'Time to Death'

'del_xq22.3' versus 'GENDER'

P value = 0.0303 (Fisher's exact test), Q value = 0.18

Table S68.  Gene #66: 'del_xq22.3' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 132 114
DEL PEAK 41(XQ22.3) MUTATED 73 47
DEL PEAK 41(XQ22.3) WILD-TYPE 59 67

Figure S68.  Get High-res Image Gene #66: 'del_xq22.3' versus Clinical Feature #3: 'GENDER'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/15098582/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 focal cnvs = 66

  • Number of selected clinical features = 5

  • Exclude genes 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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