Correlation between copy number variation genes (focal events) and selected clinical features
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 30 focal events and 12 clinical features across 528 patients, 75 significant findings detected with Q value < 0.25.

  • amp_1q24.1 cnv correlated to 'Time to Death'.

  • amp_1q32.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_3q26.32 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE', and 'PATHOLOGY_M_STAGE'.

  • amp_4q32.1 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • amp_5q35.1 cnv correlated to 'Time to Death',  'GENDER', and 'RACE'.

  • amp_7q36.3 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • amp_8q24.22 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE', and 'PATHOLOGY_T_STAGE'.

  • amp_10p14 cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.

  • amp_xp22.2 cnv correlated to 'PATHOLOGIC_STAGE' and 'RACE'.

  • amp_xp11.4 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_M_STAGE'.

  • del_1p36.23 cnv correlated to 'Time to Death'.

  • del_1p31.1 cnv correlated to 'PATHOLOGY_T_STAGE'.

  • del_3p26.3 cnv correlated to 'PATHOLOGY_T_STAGE' and 'RACE'.

  • del_3p22.2 cnv correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'RACE'.

  • del_3p14.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.

  • del_3p12.2 cnv correlated to 'GENDER'.

  • del_3q11.2 cnv correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • del_4q34.3 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'RACE'.

  • del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.

  • del_6q26 cnv correlated to 'PATHOLOGY_N_STAGE',  'GENDER', and 'NUMBER_PACK_YEARS_SMOKED'.

  • del_8p23.2 cnv correlated to 'Time to Death' and 'ETHNICITY'.

  • del_9p23 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • del_9p21.3 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', and 'GENDER'.

  • del_10q23.31 cnv correlated to 'PATHOLOGIC_STAGE' and 'PATHOLOGY_T_STAGE'.

  • del_13q14.2 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • del_14q31.1 cnv correlated to 'Time to Death',  'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE',  'KARNOFSKY_PERFORMANCE_SCORE', and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 30 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 75 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		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 Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
del 9p21 3 159 (30%) 369 4.95e-07
(8.91e-05) 		0.0385
(0.213) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.0126
(0.108) 		0.000159
(0.00337) 		0.000768
(0.00953) 		0.357
(0.773) 		0.91
(1.00) 		0.935
(1.00) 		0.0583
(0.262) 		0.827
(1.00)
del 14q31 1 228 (43%) 300 0.000653
(0.00866) 		0.0959
(0.346) 		2e-05
(0.00072) 		6e-05
(0.00144) 		0.000258
(0.00512) 		0.00114
(0.0132) 		0.17
(0.507) 		0.0366
(0.206) 		0.37
(0.775) 		0.199
(0.538) 		0.0396
(0.214) 		1
(1.00)
del 9p23 152 (29%) 376 2.29e-05
(0.00075) 		0.0226
(0.156) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.0879
(0.331) 		0.00173
(0.0195) 		0.0019
(0.0208) 		0.357
(0.773) 		0.707
(1.00) 		0.872
(1.00) 		0.321
(0.723) 		0.655
(0.965)
del 4q34 3 78 (15%) 450 0.000289
(0.00521) 		0.56
(0.927) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.714
(1.00) 		0.0278
(0.178) 		0.371
(0.775) 		0.827
(1.00) 		0.0245
(0.167) 		0.579
(0.929)
amp 3q26 32 87 (16%) 441 0.118
(0.396) 		0.991
(1.00) 		5e-05
(0.00129) 		0.00011
(0.00247) 		0.0516
(0.248) 		0.000414
(0.00648) 		0.903
(1.00) 		0.759
(1.00) 		1
(1.00) 		0.569
(0.927) 		1
(1.00)
amp 7q36 3 176 (33%) 352 0.734
(1.00) 		0.56
(0.927) 		0.0122
(0.108) 		0.0442
(0.221) 		0.306
(0.692) 		0.00391
(0.0402) 		0.0125
(0.108) 		0.305
(0.692) 		0.154
(0.474) 		0.0635
(0.276) 		0.0704
(0.288) 		0.27
(0.652)
amp 8q24 22 79 (15%) 449 0.025
(0.167) 		0.00692
(0.0692) 		0.00063
(0.00866) 		0.00051
(0.00734) 		0.728
(1.00) 		0.0578
(0.262) 		0.0747
(0.299) 		0.559
(0.927) 		0.8
(1.00) 		0.256
(0.623) 		0.229
(0.582)
del 13q14 2 82 (16%) 446 0.00102
(0.0123) 		0.88
(1.00) 		3e-05
(9e-04) 		1e-05
(4e-04) 		0.19
(0.534) 		0.0429
(0.221) 		1
(1.00) 		0.715
(1.00) 		0.478
(0.867) 		0.0884
(0.331) 		0.398
(0.796)
amp 5q35 1 332 (63%) 196 0.0318
(0.198) 		0.183
(0.532) 		0.329
(0.732) 		0.239
(0.588) 		0.192
(0.534) 		0.306
(0.692) 		0.0484
(0.239) 		0.697
(1.00) 		0.155
(0.474) 		0.47
(0.858) 		0.0021
(0.0222) 		1
(1.00)
del 3p22 2 465 (88%) 63 0.636
(0.958) 		0.53
(0.927) 		0.017
(0.138) 		0.00037
(0.00605) 		1
(1.00) 		0.563
(0.927) 		0.89
(1.00) 		0.44
(0.838) 		0.619
(0.951) 		4e-05
(0.00111) 		1
(1.00)
del 6q26 151 (29%) 377 0.884
(1.00) 		0.236
(0.588) 		0.369
(0.775) 		0.565
(0.927) 		0.0177
(0.138) 		0.588
(0.929) 		0.0274
(0.178) 		0.213
(0.553) 		0.0337
(0.199) 		0.643
(0.958) 		0.0693
(0.288) 		0.12
(0.396)
del 6q26 151 (29%) 377 0.908
(1.00) 		0.194
(0.534) 		0.371
(0.775) 		0.565
(0.927) 		0.0177
(0.138) 		0.588
(0.929) 		0.0161
(0.134) 		0.213
(0.553) 		0.0337
(0.199) 		0.643
(0.958) 		0.0696
(0.288) 		0.12
(0.396)
amp 10p14 20 (4%) 508 0.778
(1.00) 		0.0424
(0.221) 		0.185
(0.532) 		0.0295
(0.186) 		0.191
(0.534) 		0.536
(0.927) 		0.643
(0.958) 		0.362
(0.775) 		0.38
(0.781) 		1
(1.00)
amp xp22 2 31 (6%) 497 0.68
(0.993) 		0.822
(1.00) 		0.022
(0.156) 		0.0555
(0.256) 		1
(1.00) 		0.116
(0.393) 		1
(1.00) 		0.943
(1.00) 		0.0507
(0.247) 		0.615
(0.95)
amp xp11 4 33 (6%) 495 0.709
(1.00) 		0.976
(1.00) 		0.018
(0.138) 		0.0697
(0.288) 		1
(1.00) 		0.0434
(0.221) 		0.852
(1.00) 		0.943
(1.00) 		0.0978
(0.347) 		0.382
(0.781)
del 3p26 3 455 (86%) 73 0.48
(0.867) 		0.466
(0.855) 		0.136
(0.442) 		0.00922
(0.0897) 		0.718
(1.00) 		0.856
(1.00) 		0.794
(1.00) 		0.329
(0.732) 		0.803
(1.00) 		0.00037
(0.00605) 		0.398
(0.796)
del 3p14 1 373 (71%) 155 0.811
(1.00) 		0.995
(1.00) 		0.197
(0.537) 		0.044
(0.221) 		0.286
(0.682) 		0.416
(0.815) 		0.000674
(0.00866) 		0.597
(0.936) 		0.913
(1.00) 		0.865
(1.00) 		0.0983
(0.347) 		0.827
(1.00)
del 3q11 2 161 (30%) 367 0.694
(1) 		0.00991
(0.0938) 		0.382
(0.781) 		0.0873
(0.331) 		0.409
(0.808) 		0.689
(0.996) 		8.29e-08
(2.98e-05) 		0.143
(0.451) 		0.588
(0.929) 		0.189
(0.534) 		0.372
(0.775)
del 8p23 2 154 (29%) 374 0.0327
(0.199) 		0.131
(0.428) 		0.0995
(0.348) 		0.0733
(0.296) 		0.785
(1.00) 		0.14
(0.451) 		0.232
(0.585) 		0.569
(0.927) 		0.647
(0.958) 		0.865
(1.00) 		0.0538
(0.255) 		0.0361
(0.206)
del 10q23 31 96 (18%) 432 0.17
(0.507) 		0.46
(0.853) 		0.0124
(0.108) 		0.00027
(0.00512) 		1
(1.00) 		0.434
(0.83) 		0.0593
(0.264) 		0.738
(1.00) 		0.148
(0.458) 		0.427
(0.822)
amp 1q24 1 62 (12%) 466 0.0196
(0.147) 		0.0803
(0.318) 		0.116
(0.393) 		0.0961
(0.346) 		0.0624
(0.274) 		0.194
(0.534) 		0.575
(0.929) 		0.426
(0.822) 		0.533
(0.927) 		0.52
(0.922)
amp 1q32 1 62 (12%) 466 0.065
(0.278) 		0.0211
(0.152) 		0.0829
(0.321) 		0.0815
(0.319) 		0.462
(0.853) 		0.352
(0.772) 		0.575
(0.929) 		0.426
(0.822) 		0.533
(0.927) 		0.2
(0.538)
amp 4q32 1 16 (3%) 512 0.239
(0.588) 		0.298
(0.692) 		0.641
(0.958) 		0.395
(0.796) 		0.545
(0.927) 		0.726
(1.00) 		0.598
(0.936) 		0.0352
(0.204) 		1
(1.00) 		1
(1.00)
del 1p36 23 103 (20%) 425 0.0212
(0.152) 		0.142
(0.451) 		0.3
(0.692) 		0.101
(0.348) 		0.766
(1.00) 		0.218
(0.557) 		0.208
(0.553) 		0.496
(0.889) 		0.919
(1.00) 		0.952
(1.00) 		0.215
(0.553)
del 1p31 1 77 (15%) 451 0.24
(0.588) 		0.176
(0.517) 		0.554
(0.927) 		0.0397
(0.214) 		0.3
(0.692) 		0.73
(1.00) 		0.0544
(0.255) 		0.929
(1.00) 		0.605
(0.943) 		0.0916
(0.336)
del 3p12 2 305 (58%) 223 0.369
(0.775) 		0.858
(1.00) 		0.644
(0.958) 		0.209
(0.553) 		0.449
(0.846) 		0.457
(0.853) 		0.000479
(0.00719) 		0.177
(0.517) 		1
(1.00) 		0.871
(1.00) 		0.291
(0.688) 		0.538
(0.927)
amp xq11 2 29 (5%) 499 0.621
(0.951) 		0.297
(0.692) 		0.284
(0.682) 		0.348
(0.768) 		1
(1.00) 		0.411
(0.808) 		1
(1.00) 		0.558
(0.927) 		0.0905
(0.336) 		0.612
(0.95)
amp xq28 37 (7%) 491 0.589
(0.929) 		0.504
(0.898) 		0.457
(0.853) 		0.642
(0.958) 		1
(1.00) 		0.211
(0.553) 		0.859
(1.00) 		0.558
(0.927) 		1
(1.00) 		0.394
(0.796)
del 1q43 42 (8%) 486 0.969
(1.00) 		0.545
(0.927) 		0.979
(1.00) 		0.146
(0.457) 		1
(1.00) 		0.657
(0.965) 		1
(1.00) 		0.684
(0.993) 		0.708
(1.00) 		0.723
(1.00)
del 2q37 3 50 (9%) 478 0.855
(1.00) 		0.718
(1.00) 		0.445
(0.844) 		0.684
(0.993) 		1
(1.00) 		0.403
(0.802) 		0.163
(0.492) 		0.76
(1.00) 		0.492
(0.886)
'amp_1q24.1' versus 'Time to Death'

P value = 0.0196 (logrank test), Q value = 0.15

Table S1.  Gene #1: 'amp_1q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
AMP PEAK 1(1Q24.1) MUTATED 62 29 0.4 - 129.4 (28.9)
AMP PEAK 1(1Q24.1) WILD-TYPE 464 146 0.1 - 149.2 (38.8)

Figure S1.  Get High-res Image Gene #1: 'amp_1q24.1' versus Clinical Feature #1: 'Time to Death'

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 0.0211 (Wilcoxon-test), Q value = 0.15

Table S2.  Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
AMP PEAK 2(1Q32.1) MUTATED 62 63.4 (11.9)
AMP PEAK 2(1Q32.1) WILD-TYPE 465 60.1 (12.1)

Figure S2.  Get High-res Image Gene #2: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.32' versus 'PATHOLOGIC_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0013

Table S3.  Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
AMP PEAK 3(3Q26.32) MUTATED 28 6 26 27
AMP PEAK 3(3Q26.32) WILD-TYPE 235 51 99 56

Figure S3.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.0025

Table S4.  Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
AMP PEAK 3(3Q26.32) MUTATED 29 8 46 4
AMP PEAK 3(3Q26.32) WILD-TYPE 239 61 134 7

Figure S4.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0516 (Fisher's exact test), Q value = 0.25

Table S5.  Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
AMP PEAK 3(3Q26.32) MUTATED 43 7
AMP PEAK 3(3Q26.32) WILD-TYPE 191 10

Figure S5.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.000414 (Fisher's exact test), Q value = 0.0065

Table S6.  Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
AMP PEAK 3(3Q26.32) MUTATED 59 25
AMP PEAK 3(3Q26.32) WILD-TYPE 359 53

Figure S6.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_4q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0352 (Wilcoxon-test), Q value = 0.2

Table S7.  Gene #4: 'amp_4q32.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 53 85.3 (26.0)
AMP PEAK 4(4Q32.1) MUTATED 4 45.0 (52.0)
AMP PEAK 4(4Q32.1) WILD-TYPE 49 88.6 (20.4)

Figure S7.  Get High-res Image Gene #4: 'amp_4q32.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_5q35.1' versus 'Time to Death'

P value = 0.0318 (logrank test), Q value = 0.2

Table S8.  Gene #5: 'amp_5q35.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
AMP PEAK 5(5Q35.1) MUTATED 332 104 0.1 - 149.2 (43.6)
AMP PEAK 5(5Q35.1) WILD-TYPE 194 71 0.1 - 126.3 (31.8)

Figure S8.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #1: 'Time to Death'

'amp_5q35.1' versus 'GENDER'

P value = 0.0484 (Fisher's exact test), Q value = 0.24

Table S9.  Gene #5: 'amp_5q35.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
AMP PEAK 5(5Q35.1) MUTATED 108 224
AMP PEAK 5(5Q35.1) WILD-TYPE 81 115

Figure S9.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #7: 'GENDER'

'amp_5q35.1' versus 'RACE'

P value = 0.0021 (Fisher's exact test), Q value = 0.022

Table S10.  Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
AMP PEAK 5(5Q35.1) MUTATED 3 25 299
AMP PEAK 5(5Q35.1) WILD-TYPE 5 31 158

Figure S10.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

'amp_7q36.3' versus 'PATHOLOGIC_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #6: 'amp_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
AMP PEAK 6(7Q36.3) MUTATED 74 17 46 39
AMP PEAK 6(7Q36.3) WILD-TYPE 189 40 79 44

Figure S11.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q36.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0442 (Fisher's exact test), Q value = 0.22

Table S12.  Gene #6: 'amp_7q36.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
AMP PEAK 6(7Q36.3) MUTATED 76 22 74 4
AMP PEAK 6(7Q36.3) WILD-TYPE 192 47 106 7

Figure S12.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_7q36.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.00391 (Fisher's exact test), Q value = 0.04

Table S13.  Gene #6: 'amp_7q36.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
AMP PEAK 6(7Q36.3) MUTATED 130 38
AMP PEAK 6(7Q36.3) WILD-TYPE 288 40

Figure S13.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7q36.3' versus 'GENDER'

P value = 0.0125 (Fisher's exact test), Q value = 0.11

Table S14.  Gene #6: 'amp_7q36.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
AMP PEAK 6(7Q36.3) MUTATED 50 126
AMP PEAK 6(7Q36.3) WILD-TYPE 139 213

Figure S14.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #7: 'GENDER'

'amp_8q24.22' versus 'Time to Death'

P value = 0.025 (logrank test), Q value = 0.17

Table S15.  Gene #7: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
AMP PEAK 7(8Q24.22) MUTATED 79 33 0.5 - 115.7 (31.1)
AMP PEAK 7(8Q24.22) WILD-TYPE 447 142 0.1 - 149.2 (39.5)

Figure S15.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.22' versus 'YEARS_TO_BIRTH'

P value = 0.00692 (Wilcoxon-test), Q value = 0.069

Table S16.  Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
AMP PEAK 7(8Q24.22) MUTATED 79 63.8 (11.4)
AMP PEAK 7(8Q24.22) WILD-TYPE 448 59.9 (12.1)

Figure S16.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'PATHOLOGIC_STAGE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0087

Table S17.  Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
AMP PEAK 7(8Q24.22) MUTATED 23 11 26 19
AMP PEAK 7(8Q24.22) WILD-TYPE 240 46 99 64

Figure S17.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0073

Table S18.  Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
AMP PEAK 7(8Q24.22) MUTATED 24 12 41 2
AMP PEAK 7(8Q24.22) WILD-TYPE 244 57 139 9

Figure S18.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'YEARS_TO_BIRTH'

P value = 0.0424 (Wilcoxon-test), Q value = 0.22

Table S19.  Gene #8: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
AMP PEAK 8(10P14) MUTATED 20 65.5 (10.5)
AMP PEAK 8(10P14) WILD-TYPE 507 60.3 (12.1)

Figure S19.  Get High-res Image Gene #8: 'amp_10p14' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.0295 (Fisher's exact test), Q value = 0.19

Table S20.  Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
AMP PEAK 8(10P14) MUTATED 9 5 4 2
AMP PEAK 8(10P14) WILD-TYPE 259 64 176 9

Figure S20.  Get High-res Image Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xp22.2' versus 'PATHOLOGIC_STAGE'

P value = 0.022 (Fisher's exact test), Q value = 0.16

Table S21.  Gene #9: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
AMP PEAK 9(XP22.2) MUTATED 9 5 7 10
AMP PEAK 9(XP22.2) WILD-TYPE 254 52 118 73

Figure S21.  Get High-res Image Gene #9: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp22.2' versus 'RACE'

P value = 0.0507 (Fisher's exact test), Q value = 0.25

Table S22.  Gene #9: 'amp_xp22.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
AMP PEAK 9(XP22.2) MUTATED 2 1 28
AMP PEAK 9(XP22.2) WILD-TYPE 6 55 429

Figure S22.  Get High-res Image Gene #9: 'amp_xp22.2' versus Clinical Feature #11: 'RACE'

'amp_xp11.4' versus 'PATHOLOGIC_STAGE'

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

Table S23.  Gene #10: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
AMP PEAK 10(XP11.4) MUTATED 10 5 7 11
AMP PEAK 10(XP11.4) WILD-TYPE 253 52 118 72

Figure S23.  Get High-res Image Gene #10: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp11.4' versus 'PATHOLOGY_M_STAGE'

P value = 0.0434 (Fisher's exact test), Q value = 0.22

Table S24.  Gene #10: 'amp_xp11.4' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
AMP PEAK 10(XP11.4) MUTATED 22 9
AMP PEAK 10(XP11.4) WILD-TYPE 396 69

Figure S24.  Get High-res Image Gene #10: 'amp_xp11.4' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_1p36.23' versus 'Time to Death'

P value = 0.0212 (logrank test), Q value = 0.15

Table S25.  Gene #13: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 1(1P36.23) MUTATED 103 46 0.5 - 130.7 (40.4)
DEL PEAK 1(1P36.23) WILD-TYPE 423 129 0.1 - 149.2 (38.4)

Figure S25.  Get High-res Image Gene #13: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

'del_1p31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.21

Table S26.  Gene #14: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 2(1P31.1) MUTATED 38 12 22 5
DEL PEAK 2(1P31.1) WILD-TYPE 230 57 158 6

Figure S26.  Get High-res Image Gene #14: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p26.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00922 (Fisher's exact test), Q value = 0.09

Table S27.  Gene #17: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 5(3P26.3) MUTATED 225 62 162 6
DEL PEAK 5(3P26.3) WILD-TYPE 43 7 18 5

Figure S27.  Get High-res Image Gene #17: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p26.3' versus 'RACE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0061

Table S28.  Gene #17: 'del_3p26.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
DEL PEAK 5(3P26.3) MUTATED 6 38 404
DEL PEAK 5(3P26.3) WILD-TYPE 2 18 53

Figure S28.  Get High-res Image Gene #17: 'del_3p26.3' versus Clinical Feature #11: 'RACE'

'del_3p22.2' versus 'PATHOLOGIC_STAGE'

P value = 0.017 (Fisher's exact test), Q value = 0.14

Table S29.  Gene #18: 'del_3p22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 6(3P22.2) MUTATED 223 49 119 74
DEL PEAK 6(3P22.2) WILD-TYPE 40 8 6 9

Figure S29.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0061

Table S30.  Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 6(3P22.2) MUTATED 228 61 170 6
DEL PEAK 6(3P22.2) WILD-TYPE 40 8 10 5

Figure S30.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p22.2' versus 'RACE'

P value = 4e-05 (Fisher's exact test), Q value = 0.0011

Table S31.  Gene #18: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
DEL PEAK 6(3P22.2) MUTATED 6 38 414
DEL PEAK 6(3P22.2) WILD-TYPE 2 18 43

Figure S31.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

'del_3p14.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.044 (Fisher's exact test), Q value = 0.22

Table S32.  Gene #19: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 7(3P14.1) MUTATED 184 50 135 4
DEL PEAK 7(3P14.1) WILD-TYPE 84 19 45 7

Figure S32.  Get High-res Image Gene #19: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p14.1' versus 'GENDER'

P value = 0.000674 (Fisher's exact test), Q value = 0.0087

Table S33.  Gene #19: 'del_3p14.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 7(3P14.1) MUTATED 116 257
DEL PEAK 7(3P14.1) WILD-TYPE 73 82

Figure S33.  Get High-res Image Gene #19: 'del_3p14.1' versus Clinical Feature #7: 'GENDER'

'del_3p12.2' versus 'GENDER'

P value = 0.000479 (Fisher's exact test), Q value = 0.0072

Table S34.  Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 8(3P12.2) MUTATED 90 215
DEL PEAK 8(3P12.2) WILD-TYPE 99 124

Figure S34.  Get High-res Image Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

'del_3q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.00991 (Wilcoxon-test), Q value = 0.094

Table S35.  Gene #21: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
DEL PEAK 9(3Q11.2) MUTATED 161 62.8 (12.9)
DEL PEAK 9(3Q11.2) WILD-TYPE 366 59.5 (11.6)

Figure S35.  Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q11.2' versus 'GENDER'

P value = 8.29e-08 (Fisher's exact test), Q value = 3e-05

Table S36.  Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 9(3Q11.2) MUTATED 31 130
DEL PEAK 9(3Q11.2) WILD-TYPE 158 209

Figure S36.  Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'Time to Death'

P value = 0.000289 (logrank test), Q value = 0.0052

Table S37.  Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 10(4Q34.3) MUTATED 78 41 0.6 - 133.7 (37.6)
DEL PEAK 10(4Q34.3) WILD-TYPE 448 134 0.1 - 149.2 (38.5)

Figure S37.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S38.  Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 10(4Q34.3) MUTATED 19 7 30 22
DEL PEAK 10(4Q34.3) WILD-TYPE 244 50 95 61

Figure S38.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S39.  Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 10(4Q34.3) MUTATED 20 9 43 6
DEL PEAK 10(4Q34.3) WILD-TYPE 248 60 137 5

Figure S39.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0278 (Fisher's exact test), Q value = 0.18

Table S40.  Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
DEL PEAK 10(4Q34.3) MUTATED 59 19
DEL PEAK 10(4Q34.3) WILD-TYPE 359 59

Figure S40.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'RACE'

P value = 0.0245 (Fisher's exact test), Q value = 0.17

Table S41.  Gene #22: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
DEL PEAK 10(4Q34.3) MUTATED 1 2 73
DEL PEAK 10(4Q34.3) WILD-TYPE 7 54 384

Figure S41.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.14

Table S42.  Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
DEL PEAK 11(6Q26) MUTATED 56 9
DEL PEAK 11(6Q26) WILD-TYPE 178 8

Figure S42.  Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.0274 (Fisher's exact test), Q value = 0.18

Table S43.  Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 11(6Q26) MUTATED 43 108
DEL PEAK 11(6Q26) WILD-TYPE 146 231

Figure S43.  Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0337 (Wilcoxon-test), Q value = 0.2

Table S44.  Gene #23: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 21 28.3 (16.1)
DEL PEAK 11(6Q26) MUTATED 5 16.0 (13.7)
DEL PEAK 11(6Q26) WILD-TYPE 16 32.2 (15.2)

Figure S44.  Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0177 (Fisher's exact test), Q value = 0.14

Table S45.  Gene #24: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
DEL PEAK 12(6Q26) MUTATED 56 9
DEL PEAK 12(6Q26) WILD-TYPE 178 8

Figure S45.  Get High-res Image Gene #24: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.0161 (Fisher's exact test), Q value = 0.13

Table S46.  Gene #24: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 12(6Q26) MUTATED 42 109
DEL PEAK 12(6Q26) WILD-TYPE 147 230

Figure S46.  Get High-res Image Gene #24: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0337 (Wilcoxon-test), Q value = 0.2

Table S47.  Gene #24: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 21 28.3 (16.1)
DEL PEAK 12(6Q26) MUTATED 5 16.0 (13.7)
DEL PEAK 12(6Q26) WILD-TYPE 16 32.2 (15.2)

Figure S47.  Get High-res Image Gene #24: 'del_6q26' versus Clinical Feature #9: 'NUMBER_PACK_YEARS_SMOKED'

'del_8p23.2' versus 'Time to Death'

P value = 0.0327 (logrank test), Q value = 0.2

Table S48.  Gene #25: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 13(8P23.2) MUTATED 154 61 0.1 - 118.8 (36.7)
DEL PEAK 13(8P23.2) WILD-TYPE 372 114 0.1 - 149.2 (39.5)

Figure S48.  Get High-res Image Gene #25: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'ETHNICITY'

P value = 0.0361 (Fisher's exact test), Q value = 0.21

Table S49.  Gene #25: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 350
DEL PEAK 13(8P23.2) MUTATED 12 89
DEL PEAK 13(8P23.2) WILD-TYPE 14 261

Figure S49.  Get High-res Image Gene #25: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

'del_9p23' versus 'Time to Death'

P value = 2.29e-05 (logrank test), Q value = 0.00075

Table S50.  Gene #26: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 14(9P23) MUTATED 151 73 0.5 - 133.7 (38.6)
DEL PEAK 14(9P23) WILD-TYPE 375 102 0.1 - 149.2 (38.3)

Figure S50.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0226 (Wilcoxon-test), Q value = 0.16

Table S51.  Gene #26: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
DEL PEAK 14(9P23) MUTATED 151 62.3 (11.7)
DEL PEAK 14(9P23) WILD-TYPE 376 59.8 (12.2)

Figure S51.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S52.  Gene #26: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 14(9P23) MUTATED 52 12 50 38
DEL PEAK 14(9P23) WILD-TYPE 211 45 75 45

Figure S52.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S53.  Gene #26: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 14(9P23) MUTATED 55 16 76 5
DEL PEAK 14(9P23) WILD-TYPE 213 53 104 6

Figure S53.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.02

Table S54.  Gene #26: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
DEL PEAK 14(9P23) MUTATED 111 35
DEL PEAK 14(9P23) WILD-TYPE 307 43

Figure S54.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'GENDER'

P value = 0.0019 (Fisher's exact test), Q value = 0.021

Table S55.  Gene #26: 'del_9p23' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 14(9P23) MUTATED 39 113
DEL PEAK 14(9P23) WILD-TYPE 150 226

Figure S55.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'Time to Death'

P value = 4.95e-07 (logrank test), Q value = 8.9e-05

Table S56.  Gene #27: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 15(9P21.3) MUTATED 158 79 0.5 - 133.7 (37.0)
DEL PEAK 15(9P21.3) WILD-TYPE 368 96 0.1 - 149.2 (38.8)

Figure S56.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0385 (Wilcoxon-test), Q value = 0.21

Table S57.  Gene #27: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 527 60.5 (12.1)
DEL PEAK 15(9P21.3) MUTATED 158 62.1 (11.6)
DEL PEAK 15(9P21.3) WILD-TYPE 369 59.8 (12.3)

Figure S57.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S58.  Gene #27: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 15(9P21.3) MUTATED 53 11 54 41
DEL PEAK 15(9P21.3) WILD-TYPE 210 46 71 42

Figure S58.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S59.  Gene #27: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 15(9P21.3) MUTATED 56 15 82 6
DEL PEAK 15(9P21.3) WILD-TYPE 212 54 98 5

Figure S59.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0126 (Fisher's exact test), Q value = 0.11

Table S60.  Gene #27: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
DEL PEAK 15(9P21.3) MUTATED 66 10
DEL PEAK 15(9P21.3) WILD-TYPE 168 7

Figure S60.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.000159 (Fisher's exact test), Q value = 0.0034

Table S61.  Gene #27: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
DEL PEAK 15(9P21.3) MUTATED 115 39
DEL PEAK 15(9P21.3) WILD-TYPE 303 39

Figure S61.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.000768 (Fisher's exact test), Q value = 0.0095

Table S62.  Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 189 339
DEL PEAK 15(9P21.3) MUTATED 40 119
DEL PEAK 15(9P21.3) WILD-TYPE 149 220

Figure S62.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_10q23.31' versus 'PATHOLOGIC_STAGE'

P value = 0.0124 (Fisher's exact test), Q value = 0.11

Table S63.  Gene #28: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 16(10Q23.31) MUTATED 34 11 31 20
DEL PEAK 16(10Q23.31) WILD-TYPE 229 46 94 63

Figure S63.  Get High-res Image Gene #28: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.0051

Table S64.  Gene #28: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 16(10Q23.31) MUTATED 34 12 44 6
DEL PEAK 16(10Q23.31) WILD-TYPE 234 57 136 5

Figure S64.  Get High-res Image Gene #28: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'Time to Death'

P value = 0.00102 (logrank test), Q value = 0.012

Table S65.  Gene #29: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 17(13Q14.2) MUTATED 81 38 0.5 - 112.1 (31.8)
DEL PEAK 17(13Q14.2) WILD-TYPE 445 137 0.1 - 149.2 (39.5)

Figure S65.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 9e-04

Table S66.  Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 17(13Q14.2) MUTATED 27 3 30 22
DEL PEAK 17(13Q14.2) WILD-TYPE 236 54 95 61

Figure S66.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 4e-04

Table S67.  Gene #29: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 17(13Q14.2) MUTATED 29 4 42 7
DEL PEAK 17(13Q14.2) WILD-TYPE 239 65 138 4

Figure S67.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0429 (Fisher's exact test), Q value = 0.22

Table S68.  Gene #29: 'del_13q14.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
DEL PEAK 17(13Q14.2) MUTATED 61 19
DEL PEAK 17(13Q14.2) WILD-TYPE 357 59

Figure S68.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'Time to Death'

P value = 0.000653 (logrank test), Q value = 0.0087

Table S69.  Gene #30: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 526 175 0.1 - 149.2 (38.5)
DEL PEAK 18(14Q31.1) MUTATED 227 97 0.4 - 133.7 (36.4)
DEL PEAK 18(14Q31.1) WILD-TYPE 299 78 0.1 - 149.2 (41.6)

Figure S69.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00072

Table S70.  Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 263 57 125 83
DEL PEAK 18(14Q31.1) MUTATED 86 27 66 49
DEL PEAK 18(14Q31.1) WILD-TYPE 177 30 59 34

Figure S70.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0014

Table S71.  Gene #30: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 268 69 180 11
DEL PEAK 18(14Q31.1) MUTATED 91 35 98 4
DEL PEAK 18(14Q31.1) WILD-TYPE 177 34 82 7

Figure S71.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.000258 (Fisher's exact test), Q value = 0.0051

Table S72.  Gene #30: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 234 17
DEL PEAK 18(14Q31.1) MUTATED 100 15
DEL PEAK 18(14Q31.1) WILD-TYPE 134 2

Figure S72.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q31.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.00114 (Fisher's exact test), Q value = 0.013

Table S73.  Gene #30: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 418 78
DEL PEAK 18(14Q31.1) MUTATED 171 48
DEL PEAK 18(14Q31.1) WILD-TYPE 247 30

Figure S73.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0366 (Wilcoxon-test), Q value = 0.21

Table S74.  Gene #30: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 53 85.3 (26.0)
DEL PEAK 18(14Q31.1) MUTATED 21 72.4 (37.5)
DEL PEAK 18(14Q31.1) WILD-TYPE 32 93.8 (6.1)

Figure S74.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q31.1' versus 'RACE'

P value = 0.0396 (Fisher's exact test), Q value = 0.21

Table S75.  Gene #30: 'del_14q31.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 56 457
DEL PEAK 18(14Q31.1) MUTATED 2 16 206
DEL PEAK 18(14Q31.1) WILD-TYPE 6 40 251

Figure S75.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #11: 'RACE'

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/KIRC-TP/19781826/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/19775258/KIRC-TP.merged_data.txt

  • Number of patients = 528

  • Number of significantly focal cnvs = 30

  • Number of selected clinical features = 12

  • 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.

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)
Made with Nozzle