Correlation between copy number variation genes (focal events) and selected clinical features
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1H99471
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/C1H99471
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 524 patients, 64 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 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE', and 'PATHOLOGY_M_STAGE'.

  • amp_5q35.1 cnv correlated to 'RACE'.

  • amp_7q36.3 cnv correlated to 'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_M_STAGE',  'GENDER', and 'RACE'.

  • amp_8q24.22 cnv correlated to 'YEARS_TO_BIRTH',  'NEOPLASM_DISEASESTAGE', and 'PATHOLOGY_T_STAGE'.

  • amp_10p14 cnv correlated to 'PATHOLOGY_T_STAGE'.

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

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

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

  • del_1p31.1 cnv correlated to 'PATHOLOGY_T_STAGE' and 'GENDER'.

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

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

  • del_3p14.1 cnv correlated to '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',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_M_STAGE', and 'RACE'.

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

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

  • del_8p23.2 cnv correlated to 'ETHNICITY'.

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

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

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

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

  • del_14q31.1 cnv correlated to 'Time to Death',  'NEOPLASM_DISEASESTAGE',  'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'PATHOLOGY_M_STAGE', 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, 64 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		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 9p23 151 (29%) 373 4.59e-05
(0.00138) 		0.0272
(0.192) 		1e-05
(4e-04) 		2e-05
(0.000655) 		0.102
(0.386) 		0.00173
(0.0195) 		0.0025
(0.0273) 		0.523
(0.938) 		0.805
(1.00) 		0.764
(1.00) 		0.308
(0.723) 		0.655
(1.00)
del 9p21 3 159 (30%) 365 4.67e-07
(8.4e-05) 		0.0486
(0.257) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.0297
(0.198) 		0.000159
(0.00337) 		0.000741
(0.0103) 		0.523
(0.938) 		0.805
(1.00) 		0.764
(1.00) 		0.108
(0.397) 		0.826
(1.00)
del 14q31 1 226 (43%) 298 0.000743
(0.0103) 		0.0958
(0.371) 		2e-05
(0.000655) 		0.00015
(0.00337) 		0.000116
(0.00279) 		0.00114
(0.0132) 		0.199
(0.569) 		0.185
(0.547) 		0.217
(0.577) 		0.23
(0.59) 		0.0217
(0.166) 		1
(1.00)
del 4q34 3 78 (15%) 446 0.000192
(0.00383) 		0.602
(0.975) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.725
(1.00) 		0.0278
(0.192) 		0.371
(0.831) 		0.437
(0.845) 		0.0437
(0.246) 		0.583
(0.971)
amp 7q36 3 174 (33%) 350 0.811
(1.00) 		0.539
(0.941) 		0.0178
(0.142) 		0.0517
(0.262) 		0.446
(0.858) 		0.00391
(0.0402) 		0.0201
(0.158) 		0.17
(0.515) 		0.123
(0.426) 		0.0381
(0.233) 		0.27
(0.679)
del 13q14 2 82 (16%) 442 0.000433
(0.00677) 		0.834
(1.00) 		1e-05
(4e-04) 		1e-05
(4e-04) 		0.33
(0.761) 		0.0429
(0.246) 		1
(1.00) 		1
(1.00) 		0.114
(0.406) 		0.399
(0.834)
amp 3q26 32 86 (16%) 438 0.19
(0.557) 		0.976
(1.00) 		8e-05
(0.00206) 		0.00021
(0.00398) 		0.0572
(0.276) 		0.000414
(0.00677) 		0.806
(1.00) 		0.355
(0.804) 		0.491
(0.914) 		1
(1.00)
amp 8q24 22 78 (15%) 446 0.0606
(0.276) 		0.00739
(0.0739) 		0.001
(0.0122) 		0.00085
(0.0113) 		0.736
(1.00) 		0.0578
(0.276) 		0.0957
(0.371) 		0.713
(1.00) 		0.207
(0.57) 		0.229
(0.59)
del 3p22 2 463 (88%) 61 0.864
(1.00) 		0.395
(0.834) 		0.0232
(0.174) 		0.00035
(0.0063) 		1
(1.00) 		0.563
(0.964) 		1
(1.00) 		0.3
(0.716) 		0.513
(0.932) 		7e-05
(0.00194) 		1
(1.00)
amp xp22 2 30 (6%) 494 0.549
(0.954) 		0.82
(1.00) 		0.0411
(0.242) 		0.0788
(0.352) 		1
(1.00) 		0.116
(0.408) 		1
(1.00) 		0.96
(1.00) 		0.017
(0.139) 		0.612
(0.975)
amp xp11 4 32 (6%) 492 0.871
(1.00) 		0.98
(1.00) 		0.0332
(0.217) 		0.104
(0.391) 		1
(1.00) 		0.0434
(0.246) 		1
(1.00) 		0.96
(1.00) 		0.051
(0.262) 		0.382
(0.834)
del 1p31 1 76 (15%) 448 0.123
(0.426) 		0.148
(0.481) 		0.647
(1.00) 		0.0388
(0.233) 		0.491
(0.914) 		0.73
(1.00) 		0.0381
(0.233) 		0.422
(0.839) 		0.597
(0.974) 		0.0901
(0.369)
del 3p26 3 453 (86%) 71 0.378
(0.834) 		0.353
(0.804) 		0.143
(0.471) 		0.0117
(0.108) 		0.73
(1.00) 		0.856
(1.00) 		0.79
(1.00) 		0.156
(0.489) 		0.513
(0.932) 		0.00102
(0.0122) 		0.397
(0.834)
del 3q11 2 161 (31%) 363 0.653
(1.00) 		0.0126
(0.113) 		0.381
(0.834) 		0.0886
(0.369) 		0.598
(0.974) 		0.689
(1.00) 		7.65e-08
(2.75e-05) 		0.856
(1.00) 		0.693
(1.00) 		0.298
(0.715) 		0.372
(0.831)
del 6q26 151 (29%) 373 0.857
(1.00) 		0.275
(0.684) 		0.413
(0.839) 		0.607
(0.975) 		0.00899
(0.0852) 		0.588
(0.971) 		0.027
(0.192) 		0.208
(0.57) 		0.0556
(0.274) 		0.881
(1.00) 		0.153
(0.489) 		0.177
(0.527)
del 6q26 151 (29%) 373 0.881
(1.00) 		0.228
(0.59) 		0.416
(0.839) 		0.605
(0.975) 		0.00899
(0.0852) 		0.588
(0.971) 		0.0158
(0.132) 		0.208
(0.57) 		0.0556
(0.274) 		0.881
(1.00) 		0.155
(0.489) 		0.177
(0.527)
del 10q23 31 96 (18%) 428 0.0934
(0.369) 		0.505
(0.927) 		0.0136
(0.117) 		0.00042
(0.00677) 		1
(1.00) 		0.434
(0.844) 		0.0592
(0.276) 		0.966
(1.00) 		0.199
(0.569) 		0.432
(0.844)
amp 1q24 1 62 (12%) 462 0.038
(0.233) 		0.0892
(0.369) 		0.141
(0.469) 		0.101
(0.386) 		0.0791
(0.352) 		0.194
(0.562) 		0.575
(0.964) 		0.796
(1.00) 		0.575
(0.964) 		0.524
(0.938)
amp 1q32 1 62 (12%) 462 0.0928
(0.369) 		0.0242
(0.178) 		0.087
(0.369) 		0.0878
(0.369) 		0.711
(1.00) 		0.352
(0.804) 		0.575
(0.964) 		0.796
(1.00) 		0.575
(0.964) 		0.205
(0.57)
amp 5q35 1 330 (63%) 194 0.0465
(0.254) 		0.203
(0.57) 		0.432
(0.844) 		0.272
(0.68) 		0.31
(0.723) 		0.306
(0.723) 		0.0591
(0.276) 		0.898
(1.00) 		0.0839
(0.364) 		0.294
(0.71) 		0.00313
(0.0331) 		1
(1.00)
amp 10p14 20 (4%) 504 0.741
(1.00) 		0.0452
(0.25) 		0.389
(0.834) 		0.0287
(0.195) 		0.21
(0.571) 		0.536
(0.941) 		0.643
(1.00) 		0.281
(0.693) 		0.45
(0.862) 		1
(1.00)
del 1p36 23 102 (19%) 422 0.013
(0.114) 		0.125
(0.43) 		0.311
(0.723) 		0.0928
(0.369) 		1
(1.00) 		0.218
(0.577) 		0.136
(0.463) 		0.422
(0.839) 		0.951
(1.00) 		0.215
(0.577)
del 3p14 1 371 (71%) 153 0.759
(1.00) 		0.93
(1.00) 		0.241
(0.612) 		0.0514
(0.262) 		0.427
(0.844) 		0.416
(0.839) 		0.00091
(0.0117) 		0.815
(1.00) 		0.722
(1.00) 		0.16
(0.495) 		0.828
(1.00)
del 3p12 2 304 (58%) 220 0.536
(0.941) 		0.738
(1.00) 		0.644
(1.00) 		0.221
(0.58) 		0.623
(0.988) 		0.457
(0.871) 		0.00062
(0.0093) 		0.486
(0.914) 		0.722
(1.00) 		1
(1.00) 		0.394
(0.834) 		0.419
(0.839)
del 8p23 2 154 (29%) 370 0.0484
(0.257) 		0.156
(0.489) 		0.109
(0.397) 		0.0827
(0.363) 		1
(1.00) 		0.14
(0.469) 		0.231
(0.59) 		0.978
(1.00) 		0.843
(1.00) 		0.653
(1.00) 		0.105
(0.391) 		0.0373
(0.233)
amp 4q32 1 16 (3%) 508 0.166
(0.506) 		0.285
(0.699) 		0.641
(1.00) 		0.396
(0.834) 		0.568
(0.964) 		0.726
(1.00) 		0.598
(0.974) 		0.114
(0.406) 		1
(1.00) 		1
(1.00)
amp xq11 2 28 (5%) 496 0.63
(0.995) 		0.289
(0.704) 		0.374
(0.832) 		0.403
(0.834) 		1
(1.00) 		0.411
(0.839) 		1
(1.00) 		0.96
(1.00) 		0.0604
(0.276) 		0.611
(0.975)
amp xq28 36 (7%) 488 0.536
(0.941) 		0.504
(0.927) 		0.567
(0.964) 		0.729
(1.00) 		1
(1.00) 		0.211
(0.571) 		0.721
(1.00) 		0.96
(1.00) 		1
(1.00) 		0.39
(0.834)
del 1q43 42 (8%) 482 0.791
(1.00) 		0.576
(0.964) 		1
(1.00) 		0.146
(0.477) 		1
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.537
(0.941) 		0.7
(1.00) 		0.72
(1.00)
del 2q37 3 50 (10%) 474 0.708
(1.00) 		0.682
(1.00) 		0.48
(0.909) 		0.702
(1.00) 		1
(1.00) 		0.403
(0.834) 		0.162
(0.5) 		0.828
(1.00) 		0.492
(0.914)
'amp_1q24.1' versus 'Time to Death'

P value = 0.038 (logrank test), Q value = 0.23

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

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
AMP PEAK 1(1Q24.1) MUTATED 62 28 0.4 - 90.3 (28.3)
AMP PEAK 1(1Q24.1) WILD-TYPE 460 140 0.1 - 120.6 (36.9)

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 = 0.0242 (Wilcoxon-test), Q value = 0.18

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

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
AMP PEAK 2(1Q32.1) MUTATED 62 63.4 (11.9)
AMP PEAK 2(1Q32.1) WILD-TYPE 461 60.2 (12.1)

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

'amp_3q26.32' versus 'NEOPLASM_DISEASESTAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.0021

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

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
AMP PEAK 3(3Q26.32) MUTATED 28 6 27 25
AMP PEAK 3(3Q26.32) WILD-TYPE 232 51 100 55

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

'amp_3q26.32' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.004

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

nPatients T1 T2 T3 T4
ALL 265 69 179 11
AMP PEAK 3(3Q26.32) MUTATED 29 8 45 4
AMP PEAK 3(3Q26.32) WILD-TYPE 236 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_M_STAGE'

P value = 0.000414 (Fisher's exact test), Q value = 0.0068

Table S5.  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 S5.  Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.1' versus 'RACE'

P value = 0.00313 (Fisher's exact test), Q value = 0.033

Table S6.  Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
AMP PEAK 5(5Q35.1) MUTATED 3 23 299
AMP PEAK 5(5Q35.1) WILD-TYPE 5 29 158

Figure S6.  Get High-res Image Gene #5: 'amp_5q35.1' versus Clinical Feature #11: 'RACE'

'amp_7q36.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0178 (Fisher's exact test), Q value = 0.14

Table S7.  Gene #6: 'amp_7q36.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
AMP PEAK 6(7Q36.3) MUTATED 73 17 47 37
AMP PEAK 6(7Q36.3) WILD-TYPE 187 40 80 43

Figure S7.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_7q36.3' versus 'PATHOLOGY_M_STAGE'

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

Table S8.  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 S8.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7q36.3' versus 'GENDER'

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

Table S9.  Gene #6: 'amp_7q36.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
AMP PEAK 6(7Q36.3) MUTATED 50 124
AMP PEAK 6(7Q36.3) WILD-TYPE 138 212

Figure S9.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #7: 'GENDER'

'amp_7q36.3' versus 'RACE'

P value = 0.0381 (Fisher's exact test), Q value = 0.23

Table S10.  Gene #6: 'amp_7q36.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
AMP PEAK 6(7Q36.3) MUTATED 4 10 158
AMP PEAK 6(7Q36.3) WILD-TYPE 4 42 299

Figure S10.  Get High-res Image Gene #6: 'amp_7q36.3' versus Clinical Feature #11: 'RACE'

'amp_8q24.22' versus 'YEARS_TO_BIRTH'

P value = 0.00739 (Wilcoxon-test), Q value = 0.074

Table S11.  Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
AMP PEAK 7(8Q24.22) MUTATED 78 63.9 (11.5)
AMP PEAK 7(8Q24.22) WILD-TYPE 445 60.0 (12.1)

Figure S11.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.001 (Fisher's exact test), Q value = 0.012

Table S12.  Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
AMP PEAK 7(8Q24.22) MUTATED 23 11 26 18
AMP PEAK 7(8Q24.22) WILD-TYPE 237 46 101 62

Figure S12.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 0.00085 (Fisher's exact test), Q value = 0.011

Table S13.  Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
AMP PEAK 7(8Q24.22) MUTATED 24 12 40 2
AMP PEAK 7(8Q24.22) WILD-TYPE 241 57 139 9

Figure S13.  Get High-res Image Gene #7: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.0287 (Fisher's exact test), Q value = 0.2

Table S14.  Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
AMP PEAK 8(10P14) MUTATED 9 5 4 2
AMP PEAK 8(10P14) WILD-TYPE 256 64 175 9

Figure S14.  Get High-res Image Gene #8: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xp22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0411 (Fisher's exact test), Q value = 0.24

Table S15.  Gene #9: 'amp_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
AMP PEAK 9(XP22.2) MUTATED 9 5 7 9
AMP PEAK 9(XP22.2) WILD-TYPE 251 52 120 71

Figure S15.  Get High-res Image Gene #9: 'amp_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_xp22.2' versus 'RACE'

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

Table S16.  Gene #9: 'amp_xp22.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
AMP PEAK 9(XP22.2) MUTATED 2 0 28
AMP PEAK 9(XP22.2) WILD-TYPE 6 52 429

Figure S16.  Get High-res Image Gene #9: 'amp_xp22.2' versus Clinical Feature #11: 'RACE'

'amp_xp11.4' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0332 (Fisher's exact test), Q value = 0.22

Table S17.  Gene #10: 'amp_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
AMP PEAK 10(XP11.4) MUTATED 10 5 7 10
AMP PEAK 10(XP11.4) WILD-TYPE 250 52 120 70

Figure S17.  Get High-res Image Gene #10: 'amp_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_xp11.4' versus 'PATHOLOGY_M_STAGE'

P value = 0.0434 (Fisher's exact test), Q value = 0.25

Table S18.  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 S18.  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 = 0.013 (logrank test), Q value = 0.11

Table S19.  Gene #13: 'del_1p36.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 1(1P36.23) MUTATED 102 45 0.2 - 102.5 (37.1)
DEL PEAK 1(1P36.23) WILD-TYPE 420 123 0.1 - 120.6 (36.0)

Figure S19.  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 = 0.0388 (Fisher's exact test), Q value = 0.23

Table S20.  Gene #14: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 2(1P31.1) MUTATED 37 12 22 5
DEL PEAK 2(1P31.1) WILD-TYPE 228 57 157 6

Figure S20.  Get High-res Image Gene #14: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p31.1' versus 'GENDER'

P value = 0.0381 (Fisher's exact test), Q value = 0.23

Table S21.  Gene #14: 'del_1p31.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 2(1P31.1) MUTATED 19 57
DEL PEAK 2(1P31.1) WILD-TYPE 169 279

Figure S21.  Get High-res Image Gene #14: 'del_1p31.1' versus Clinical Feature #7: 'GENDER'

'del_3p26.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.0117 (Fisher's exact test), Q value = 0.11

Table S22.  Gene #17: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 5(3P26.3) MUTATED 224 62 161 6
DEL PEAK 5(3P26.3) WILD-TYPE 41 7 18 5

Figure S22.  Get High-res Image Gene #17: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p26.3' versus 'RACE'

P value = 0.00102 (Fisher's exact test), Q value = 0.012

Table S23.  Gene #17: 'del_3p26.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
DEL PEAK 5(3P26.3) MUTATED 6 36 404
DEL PEAK 5(3P26.3) WILD-TYPE 2 16 53

Figure S23.  Get High-res Image Gene #17: 'del_3p26.3' versus Clinical Feature #11: 'RACE'

'del_3p22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0232 (Fisher's exact test), Q value = 0.17

Table S24.  Gene #18: 'del_3p22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 6(3P22.2) MUTATED 222 49 121 71
DEL PEAK 6(3P22.2) WILD-TYPE 38 8 6 9

Figure S24.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00035 (Fisher's exact test), Q value = 0.0063

Table S25.  Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 6(3P22.2) MUTATED 227 61 169 6
DEL PEAK 6(3P22.2) WILD-TYPE 38 8 10 5

Figure S25.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p22.2' versus 'RACE'

P value = 7e-05 (Fisher's exact test), Q value = 0.0019

Table S26.  Gene #18: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
DEL PEAK 6(3P22.2) MUTATED 6 36 414
DEL PEAK 6(3P22.2) WILD-TYPE 2 16 43

Figure S26.  Get High-res Image Gene #18: 'del_3p22.2' versus Clinical Feature #11: 'RACE'

'del_3p14.1' versus 'GENDER'

P value = 0.00091 (Fisher's exact test), Q value = 0.012

Table S27.  Gene #19: 'del_3p14.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 7(3P14.1) MUTATED 116 255
DEL PEAK 7(3P14.1) WILD-TYPE 72 81

Figure S27.  Get High-res Image Gene #19: 'del_3p14.1' versus Clinical Feature #7: 'GENDER'

'del_3p12.2' versus 'GENDER'

P value = 0.00062 (Fisher's exact test), Q value = 0.0093

Table S28.  Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 8(3P12.2) MUTATED 90 214
DEL PEAK 8(3P12.2) WILD-TYPE 98 122

Figure S28.  Get High-res Image Gene #20: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

'del_3q11.2' versus 'YEARS_TO_BIRTH'

P value = 0.0126 (Wilcoxon-test), Q value = 0.11

Table S29.  Gene #21: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
DEL PEAK 9(3Q11.2) MUTATED 161 62.8 (12.9)
DEL PEAK 9(3Q11.2) WILD-TYPE 362 59.6 (11.6)

Figure S29.  Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_3q11.2' versus 'GENDER'

P value = 7.65e-08 (Fisher's exact test), Q value = 2.8e-05

Table S30.  Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 9(3Q11.2) MUTATED 31 130
DEL PEAK 9(3Q11.2) WILD-TYPE 157 206

Figure S30.  Get High-res Image Gene #21: 'del_3q11.2' versus Clinical Feature #7: 'GENDER'

'del_4q34.3' versus 'Time to Death'

P value = 0.000192 (logrank test), Q value = 0.0038

Table S31.  Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 10(4Q34.3) MUTATED 78 40 0.6 - 112.8 (33.0)
DEL PEAK 10(4Q34.3) WILD-TYPE 444 128 0.1 - 120.6 (36.5)

Figure S31.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'NEOPLASM_DISEASESTAGE'

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

Table S32.  Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 10(4Q34.3) MUTATED 19 7 31 21
DEL PEAK 10(4Q34.3) WILD-TYPE 241 50 96 59

Figure S32.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

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

Table S33.  Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 10(4Q34.3) MUTATED 20 9 43 6
DEL PEAK 10(4Q34.3) WILD-TYPE 245 60 136 5

Figure S33.  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 = 0.19

Table S34.  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 S34.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'RACE'

P value = 0.0437 (Fisher's exact test), Q value = 0.25

Table S35.  Gene #22: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
DEL PEAK 10(4Q34.3) MUTATED 1 2 73
DEL PEAK 10(4Q34.3) WILD-TYPE 7 50 384

Figure S35.  Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #11: 'RACE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.00899 (Fisher's exact test), Q value = 0.085

Table S36.  Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
DEL PEAK 11(6Q26) MUTATED 55 10
DEL PEAK 11(6Q26) WILD-TYPE 177 8

Figure S36.  Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.027 (Fisher's exact test), Q value = 0.19

Table S37.  Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 11(6Q26) MUTATED 43 108
DEL PEAK 11(6Q26) WILD-TYPE 145 228

Figure S37.  Get High-res Image Gene #23: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.00899 (Fisher's exact test), Q value = 0.085

Table S38.  Gene #24: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
DEL PEAK 12(6Q26) MUTATED 55 10
DEL PEAK 12(6Q26) WILD-TYPE 177 8

Figure S38.  Get High-res Image Gene #24: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'GENDER'

P value = 0.0158 (Fisher's exact test), Q value = 0.13

Table S39.  Gene #24: 'del_6q26' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 12(6Q26) MUTATED 42 109
DEL PEAK 12(6Q26) WILD-TYPE 146 227

Figure S39.  Get High-res Image Gene #24: 'del_6q26' versus Clinical Feature #7: 'GENDER'

'del_8p23.2' versus 'ETHNICITY'

P value = 0.0373 (Fisher's exact test), Q value = 0.23

Table S40.  Gene #25: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 345
DEL PEAK 13(8P23.2) MUTATED 12 89
DEL PEAK 13(8P23.2) WILD-TYPE 14 256

Figure S40.  Get High-res Image Gene #25: 'del_8p23.2' versus Clinical Feature #12: 'ETHNICITY'

'del_9p23' versus 'Time to Death'

P value = 4.59e-05 (logrank test), Q value = 0.0014

Table S41.  Gene #26: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 14(9P23) MUTATED 150 69 0.2 - 109.9 (36.3)
DEL PEAK 14(9P23) WILD-TYPE 372 99 0.1 - 120.6 (36.4)

Figure S41.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0272 (Wilcoxon-test), Q value = 0.19

Table S42.  Gene #26: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 523 60.6 (12.1)
DEL PEAK 14(9P23) MUTATED 150 62.4 (11.7)
DEL PEAK 14(9P23) WILD-TYPE 373 59.9 (12.2)

Figure S42.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'NEOPLASM_DISEASESTAGE'

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

Table S43.  Gene #26: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 14(9P23) MUTATED 52 12 51 36
DEL PEAK 14(9P23) WILD-TYPE 208 45 76 44

Figure S43.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00065

Table S44.  Gene #26: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 14(9P23) MUTATED 55 16 75 5
DEL PEAK 14(9P23) WILD-TYPE 210 53 104 6

Figure S44.  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 S45.  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 S45.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'GENDER'

P value = 0.0025 (Fisher's exact test), Q value = 0.027

Table S46.  Gene #26: 'del_9p23' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 14(9P23) MUTATED 39 112
DEL PEAK 14(9P23) WILD-TYPE 149 224

Figure S46.  Get High-res Image Gene #26: 'del_9p23' versus Clinical Feature #7: 'GENDER'

'del_9p21.3' versus 'Time to Death'

P value = 4.67e-07 (logrank test), Q value = 8.4e-05

Table S47.  Gene #27: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 15(9P21.3) MUTATED 158 76 0.2 - 109.9 (31.8)
DEL PEAK 15(9P21.3) WILD-TYPE 364 92 0.1 - 120.6 (37.1)

Figure S47.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'NEOPLASM_DISEASESTAGE'

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

Table S48.  Gene #27: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 15(9P21.3) MUTATED 53 11 55 40
DEL PEAK 15(9P21.3) WILD-TYPE 207 46 72 40

Figure S48.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

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

Table S49.  Gene #27: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 15(9P21.3) MUTATED 56 15 82 6
DEL PEAK 15(9P21.3) WILD-TYPE 209 54 97 5

Figure S49.  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 = 0.0297 (Fisher's exact test), Q value = 0.2

Table S50.  Gene #27: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
DEL PEAK 15(9P21.3) MUTATED 66 10
DEL PEAK 15(9P21.3) WILD-TYPE 166 8

Figure S50.  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 S51.  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 S51.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'GENDER'

P value = 0.000741 (Fisher's exact test), Q value = 0.01

Table S52.  Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 188 336
DEL PEAK 15(9P21.3) MUTATED 40 119
DEL PEAK 15(9P21.3) WILD-TYPE 148 217

Figure S52.  Get High-res Image Gene #27: 'del_9p21.3' versus Clinical Feature #7: 'GENDER'

'del_10q23.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0136 (Fisher's exact test), Q value = 0.12

Table S53.  Gene #28: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 16(10Q23.31) MUTATED 34 11 32 19
DEL PEAK 16(10Q23.31) WILD-TYPE 226 46 95 61

Figure S53.  Get High-res Image Gene #28: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0068

Table S54.  Gene #28: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 16(10Q23.31) MUTATED 34 12 44 6
DEL PEAK 16(10Q23.31) WILD-TYPE 231 57 135 5

Figure S54.  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 = 0.000433 (logrank test), Q value = 0.0068

Table S55.  Gene #29: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 17(13Q14.2) MUTATED 81 37 0.2 - 89.4 (30.6)
DEL PEAK 17(13Q14.2) WILD-TYPE 441 131 0.1 - 120.6 (37.1)

Figure S55.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'NEOPLASM_DISEASESTAGE'

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

Table S56.  Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 17(13Q14.2) MUTATED 27 3 31 21
DEL PEAK 17(13Q14.2) WILD-TYPE 233 54 96 59

Figure S56.  Get High-res Image Gene #29: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

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

Table S57.  Gene #29: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 17(13Q14.2) MUTATED 29 4 42 7
DEL PEAK 17(13Q14.2) WILD-TYPE 236 65 137 4

Figure S57.  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 = 0.25

Table S58.  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 S58.  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 = 0.000743 (logrank test), Q value = 0.01

Table S59.  Gene #30: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 522 168 0.1 - 120.6 (36.4)
DEL PEAK 18(14Q31.1) MUTATED 225 92 0.2 - 96.4 (35.9)
DEL PEAK 18(14Q31.1) WILD-TYPE 297 76 0.1 - 120.6 (37.0)

Figure S59.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00065

Table S60.  Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 260 57 127 80
DEL PEAK 18(14Q31.1) MUTATED 85 27 67 47
DEL PEAK 18(14Q31.1) WILD-TYPE 175 30 60 33

Figure S60.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0034

Table S61.  Gene #30: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 265 69 179 11
DEL PEAK 18(14Q31.1) MUTATED 90 35 97 4
DEL PEAK 18(14Q31.1) WILD-TYPE 175 34 82 7

Figure S61.  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 = 0.000116 (Fisher's exact test), Q value = 0.0028

Table S62.  Gene #30: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 232 18
DEL PEAK 18(14Q31.1) MUTATED 98 16
DEL PEAK 18(14Q31.1) WILD-TYPE 134 2

Figure S62.  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 S63.  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 S63.  Get High-res Image Gene #30: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'RACE'

P value = 0.0217 (Fisher's exact test), Q value = 0.17

Table S64.  Gene #30: 'del_14q31.1' versus Clinical Feature #11: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 8 52 457
DEL PEAK 18(14Q31.1) MUTATED 2 14 206
DEL PEAK 18(14Q31.1) WILD-TYPE 6 38 251

Figure S64.  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/15087097/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/15081616/KIRC-TP.merged_data.txt

  • Number of patients = 524

  • 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.

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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