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 31 focal events and 11 clinical features across 221 patients, 39 significant findings detected with Q value < 0.25.

  • amp_7q31.2 cnv correlated to 'NEOPLASM.DISEASESTAGE'.

  • del_1p36.31 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_3p22.1 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_5q35.2 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_6q22.31 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • del_6q25.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_9p21.3 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_10q21.1 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_11q22.3 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_11q23.3 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_15q13.3 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE',  'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.

  • del_16q24.1 cnv correlated to 'Time to Death'.

  • del_19p13.3 cnv correlated to 'Time to Death' and 'PATHOLOGY.T.STAGE'.

  • del_19q13.42 cnv correlated to 'Time to Death'.

  • del_22q12.2 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.

  • del_xp11.4 cnv correlated to 'Time to Death',  'NEOPLASM.DISEASESTAGE', and 'PATHOLOGY.T.STAGE'.

  • del_xq28 cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 31 focal events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 39 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED 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 Fisher's exact test Fisher's exact test
del 15q13 3 28 (13%) 193 8.62e-05
(0.0259) 		0.144
(1.00) 		0.00034
(0.1) 		0.00013
(0.0387) 		0.00084
(0.242) 		0.119
(1.00) 		0.376
(1.00) 		0.0107
(1.00) 		0.248
(1.00) 		0.523
(1.00) 		1
(1.00)
del 1p36 31 42 (19%) 179 0.000239
(0.0708) 		0.471
(1.00) 		1e-05
(0.00319) 		1e-05
(0.00319) 		0.00531
(1.00) 		0.324
(1.00) 		0.0354
(1.00) 		0.00653
(1.00) 		0.852
(1.00) 		0.632
(1.00) 		1
(1.00)
del 3p22 1 19 (9%) 202 2.53e-05
(0.00784) 		0.187
(1.00) 		5e-05
(0.0152) 		0.00018
(0.0535) 		0.171
(1.00) 		0.074
(1.00) 		0.792
(1.00) 		0.0791
(1.00) 		0.95
(1.00) 		0.613
(1.00) 		1
(1.00)
del 9p21 3 30 (14%) 191 0.00079
(0.228) 		0.424
(1.00) 		1e-05
(0.00319) 		1e-05
(0.00319) 		0.0014
(0.395) 		0.02
(1.00) 		0.0021
(0.589) 		0.0224
(1.00) 		0.0234
(1.00) 		0.0736
(1.00) 		0.612
(1.00)
del 11q22 3 22 (10%) 199 1.36e-06
(0.000441) 		0.084
(1.00) 		7e-05
(0.0211) 		4e-05
(0.0123) 		0.019
(1.00) 		0.288
(1.00) 		0.456
(1.00) 		0.181
(1.00) 		0.619
(1.00) 		0.119
(1.00) 		1
(1.00)
del 11q23 3 21 (10%) 200 3.42e-07
(0.000111) 		0.0856
(1.00) 		1e-05
(0.00319) 		2e-05
(0.00622) 		0.018
(1.00) 		0.298
(1.00) 		0.616
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.126
(1.00) 		1
(1.00)
del xp11 4 23 (10%) 198 3.61e-06
(0.00116) 		0.286
(1.00) 		1e-05
(0.00319) 		4e-05
(0.0123) 		0.112
(1.00) 		0.766
(1.00) 		0.0132
(1.00) 		0.681
(1.00) 		0.322
(1.00) 		0.0119
(1.00) 		1
(1.00)
del 4q34 3 26 (12%) 195 0.122
(1.00) 		0.612
(1.00) 		3e-05
(0.00927) 		8e-05
(0.0241) 		0.0839
(1.00) 		0.315
(1.00) 		0.0186
(1.00) 		0.403
(1.00) 		0.522
(1.00) 		0.0317
(1.00) 		1
(1.00)
del 5q35 2 11 (5%) 210 0.148
(1.00) 		0.0064
(1.00) 		0.00054
(0.157) 		5e-05
(0.0152) 		0.0855
(1.00) 		0.386
(1.00) 		0.0139
(1.00) 		0.601
(1.00) 		0.3
(1.00)
del 6q25 3 23 (10%) 198 0.679
(1.00) 		0.927
(1.00) 		0.00053
(0.154) 		4e-05
(0.0123) 		0.109
(1.00) 		0.581
(1.00) 		0.00302
(0.831) 		0.361
(1.00) 		0.981
(1.00) 		0.056
(1.00) 		1
(1.00)
del 10q21 1 15 (7%) 206 0.0384
(1.00) 		0.622
(1.00) 		3e-05
(0.00927) 		0.00047
(0.138) 		0.0385
(1.00) 		0.439
(1.00) 		0.137
(1.00) 		0.181
(1.00) 		0.332
(1.00) 		1
(1.00)
del 19p13 3 17 (8%) 204 9.48e-06
(0.00303) 		0.902
(1.00) 		0.00108
(0.308) 		0.00039
(0.115) 		0.0376
(1.00) 		0.319
(1.00) 		0.578
(1.00) 		0.00728
(1.00) 		0.496
(1.00) 		0.591
(1.00) 		1
(1.00)
del 22q12 2 53 (24%) 168 0.00414
(1.00) 		0.172
(1.00) 		1e-05
(0.00319) 		1e-05
(0.00319) 		0.00367
(1.00) 		0.0413
(1.00) 		0.000874
(0.251) 		0.297
(1.00) 		0.595
(1.00) 		0.185
(1.00) 		0.411
(1.00)
amp 7q31 2 133 (60%) 88 0.409
(1.00) 		0.0811
(1.00) 		0.00052
(0.152) 		0.0422
(1.00) 		0.349
(1.00) 		0.7
(1.00) 		0.0937
(1.00) 		0.0286
(1.00) 		0.678
(1.00) 		0.867
(1.00) 		0.304
(1.00)
del 6q22 31 21 (10%) 200 0.657
(1.00) 		0.87
(1.00) 		0.00475
(1.00) 		0.0001
(0.0299) 		0.0874
(1.00) 		0.391
(1.00) 		0.0196
(1.00) 		0.5
(1.00) 		0.981
(1.00) 		0.06
(1.00) 		1
(1.00)
del 16q24 1 10 (5%) 211 1.94e-06
(0.000624) 		0.106
(1.00) 		0.0143
(1.00) 		0.0312
(1.00) 		0.192
(1.00) 		0.383
(1.00) 		0.476
(1.00) 		0.532
(1.00) 		0.268
(1.00) 		1
(1.00)
del 19q13 42 16 (7%) 205 1.68e-06
(0.000544) 		0.754
(1.00) 		0.00148
(0.416) 		0.00128
(0.364) 		0.239
(1.00) 		0.302
(1.00) 		0.401
(1.00) 		0.12
(1.00) 		0.266
(1.00) 		1
(1.00)
del xq28 19 (9%) 202 1.22e-06
(0.000397) 		0.0646
(1.00) 		0.00097
(0.277) 		0.00213
(0.594) 		0.0226
(1.00) 		0.666
(1.00) 		0.00611
(1.00) 		0.27
(1.00) 		0.0991
(1.00) 		1
(1.00)
amp 2p23 2 40 (18%) 181 0.482
(1.00) 		0.339
(1.00) 		0.32
(1.00) 		0.503
(1.00) 		0.0211
(1.00) 		0.0236
(1.00) 		0.336
(1.00) 		0.606
(1.00) 		0.544
(1.00) 		0.683
(1.00) 		0.681
(1.00)
amp 2q32 1 47 (21%) 174 0.559
(1.00) 		0.643
(1.00) 		0.0322
(1.00) 		0.12
(1.00) 		0.251
(1.00) 		0.017
(1.00) 		0.587
(1.00) 		0.463
(1.00) 		0.741
(1.00) 		0.29
(1.00) 		1
(1.00)
amp 3q27 1 77 (35%) 144 0.236
(1.00) 		0.68
(1.00) 		0.355
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.0858
(1.00) 		0.435
(1.00) 		0.155
(1.00) 		0.56
(1.00) 		0.253
(1.00) 		0.5
(1.00)
amp 5q35 2 32 (14%) 189 0.89
(1.00) 		0.728
(1.00) 		0.147
(1.00) 		0.184
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.832
(1.00) 		0.305
(1.00) 		0.895
(1.00) 		0.327
(1.00) 		0.361
(1.00)
amp 17q25 2 158 (71%) 63 0.963
(1.00) 		0.0517
(1.00) 		0.289
(1.00) 		0.418
(1.00) 		0.91
(1.00) 		0.00851
(1.00) 		0.102
(1.00) 		0.897
(1.00) 		0.918
(1.00) 		0.398
(1.00) 		0.702
(1.00)
amp 19p13 2 23 (10%) 198 0.64
(1.00) 		0.00821
(1.00) 		0.836
(1.00) 		0.102
(1.00) 		0.769
(1.00) 		0.582
(1.00) 		0.473
(1.00) 		0.969
(1.00) 		0.24
(1.00) 		1
(1.00)
del 2p12 4 (2%) 217 0.53
(1.00) 		0.683
(1.00) 		0.0962
(1.00) 		0.135
(1.00) 		0.118
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
del 2q22 1 7 (3%) 214 0.0265
(1.00) 		0.146
(1.00) 		0.00442
(1.00) 		0.018
(1.00) 		0.217
(1.00) 		0.217
(1.00) 		0.104
(1.00) 		1
(1.00) 		1
(1.00)
del 2q37 3 10 (5%) 211 0.651
(1.00) 		0.51
(1.00) 		0.00942
(1.00) 		0.00301
(0.831) 		1
(1.00) 		0.807
(1.00) 		0.0338
(1.00) 		0.221
(1.00) 		0.782
(1.00) 		1
(1.00)
del 5p15 33 10 (5%) 211 0.216
(1.00) 		0.126
(1.00) 		0.00651
(1.00) 		0.00232
(0.643) 		0.004
(1.00) 		0.359
(1.00) 		0.153
(1.00) 		1
(1.00) 		0.263
(1.00)
del 6p12 3 19 (9%) 202 0.394
(1.00) 		0.813
(1.00) 		0.00131
(0.371) 		0.00223
(0.62) 		0.0471
(1.00) 		0.307
(1.00) 		0.429
(1.00) 		0.934
(1.00) 		0.477
(1.00) 		0.167
(1.00) 		1
(1.00)
del 14q11 2 44 (20%) 177 0.00931
(1.00) 		0.762
(1.00) 		0.0195
(1.00) 		0.0101
(1.00) 		0.0356
(1.00) 		0.438
(1.00) 		0.0608
(1.00) 		0.0995
(1.00) 		0.129
(1.00) 		0.916
(1.00) 		0.69
(1.00)
del 14q24 2 42 (19%) 179 0.00699
(1.00) 		0.433
(1.00) 		0.00875
(1.00) 		0.00443
(1.00) 		0.0177
(1.00) 		0.238
(1.00) 		0.0354
(1.00) 		0.0445
(1.00) 		0.0822
(1.00) 		1
(1.00) 		1
(1.00)
'amp_7q31.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.15

Table S1.  Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
AMP PEAK 5(7Q31.2) MUTATED 92 7 15 10
AMP PEAK 5(7Q31.2) WILD-TYPE 45 9 28 3

Figure S1.  Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.31' versus 'Time to Death'

P value = 0.000239 (logrank test), Q value = 0.071

Table S2.  Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 1(1P36.31) MUTATED 38 5 2.0 - 3760.0 (288.5)
DEL PEAK 1(1P36.31) WILD-TYPE 156 2 2.0 - 5925.0 (590.5)

Figure S2.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S3.  Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 1(1P36.31) MUTATED 13 3 19 4
DEL PEAK 1(1P36.31) WILD-TYPE 124 13 24 9

Figure S3.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_1p36.31' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S4.  Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 1(1P36.31) MUTATED 16 4 22
DEL PEAK 1(1P36.31) WILD-TYPE 130 18 29

Figure S4.  Get High-res Image Gene #8: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_3p22.1' versus 'Time to Death'

P value = 2.53e-05 (logrank test), Q value = 0.0078

Table S5.  Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 5(3P22.1) MUTATED 18 4 4.0 - 2429.0 (317.0)
DEL PEAK 5(3P22.1) WILD-TYPE 176 3 2.0 - 5925.0 (578.0)

Figure S5.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #1: 'Time to Death'

'del_3p22.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.015

Table S6.  Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 5(3P22.1) MUTATED 4 1 11 3
DEL PEAK 5(3P22.1) WILD-TYPE 133 15 32 10

Figure S6.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_3p22.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.053

Table S7.  Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 5(3P22.1) MUTATED 5 2 12
DEL PEAK 5(3P22.1) WILD-TYPE 141 20 39

Figure S7.  Get High-res Image Gene #12: 'del_3p22.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_4q34.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0093

Table S8.  Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 6(4Q34.3) MUTATED 6 2 15 2
DEL PEAK 6(4Q34.3) WILD-TYPE 131 14 28 11

Figure S8.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY.T.STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.024

Table S9.  Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 6(4Q34.3) MUTATED 8 4 14
DEL PEAK 6(4Q34.3) WILD-TYPE 138 18 37

Figure S9.  Get High-res Image Gene #13: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_5q35.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00054 (Fisher's exact test), Q value = 0.16

Table S10.  Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 8(5Q35.2) MUTATED 1 1 7 1
DEL PEAK 8(5Q35.2) WILD-TYPE 136 15 36 12

Figure S10.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_5q35.2' versus 'PATHOLOGY.T.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.015

Table S11.  Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 8(5Q35.2) MUTATED 1 1 9
DEL PEAK 8(5Q35.2) WILD-TYPE 145 21 42

Figure S11.  Get High-res Image Gene #15: 'del_5q35.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q22.31' versus 'PATHOLOGY.T.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.03

Table S12.  Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 10(6Q22.31) MUTATED 8 0 13
DEL PEAK 10(6Q22.31) WILD-TYPE 138 22 38

Figure S12.  Get High-res Image Gene #17: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_6q25.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.15

Table S13.  Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 11(6Q25.3) MUTATED 8 0 12 2
DEL PEAK 11(6Q25.3) WILD-TYPE 129 16 31 11

Figure S13.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_6q25.3' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S14.  Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 11(6Q25.3) MUTATED 8 0 15
DEL PEAK 11(6Q25.3) WILD-TYPE 138 22 36

Figure S14.  Get High-res Image Gene #18: 'del_6q25.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_9p21.3' versus 'Time to Death'

P value = 0.00079 (logrank test), Q value = 0.23

Table S15.  Gene #19: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 12(9P21.3) MUTATED 24 4 4.0 - 2839.0 (355.0)
DEL PEAK 12(9P21.3) WILD-TYPE 170 3 2.0 - 5925.0 (578.0)

Figure S15.  Get High-res Image Gene #19: '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 = 0.0032

Table S16.  Gene #19: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 12(9P21.3) MUTATED 7 0 15 6
DEL PEAK 12(9P21.3) WILD-TYPE 130 16 28 7

Figure S16.  Get High-res Image Gene #19: '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 = 0.0032

Table S17.  Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 12(9P21.3) MUTATED 8 2 20
DEL PEAK 12(9P21.3) WILD-TYPE 138 20 31

Figure S17.  Get High-res Image Gene #19: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_10q21.1' versus 'NEOPLASM.DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.0093

Table S18.  Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 13(10Q21.1) MUTATED 3 0 11 1
DEL PEAK 13(10Q21.1) WILD-TYPE 134 16 32 12

Figure S18.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_10q21.1' versus 'PATHOLOGY.T.STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.14

Table S19.  Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 13(10Q21.1) MUTATED 5 0 10
DEL PEAK 13(10Q21.1) WILD-TYPE 141 22 41

Figure S19.  Get High-res Image Gene #20: 'del_10q21.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'Time to Death'

P value = 1.36e-06 (logrank test), Q value = 0.00044

Table S20.  Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 14(11Q22.3) MUTATED 18 4 4.0 - 3760.0 (223.5)
DEL PEAK 14(11Q22.3) WILD-TYPE 176 3 2.0 - 5925.0 (578.0)

Figure S20.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #1: 'Time to Death'

'del_11q22.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.021

Table S21.  Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 14(11Q22.3) MUTATED 5 2 11 4
DEL PEAK 14(11Q22.3) WILD-TYPE 132 14 32 9

Figure S21.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q22.3' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S22.  Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 14(11Q22.3) MUTATED 6 2 14
DEL PEAK 14(11Q22.3) WILD-TYPE 140 20 37

Figure S22.  Get High-res Image Gene #21: 'del_11q22.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_11q23.3' versus 'Time to Death'

P value = 3.42e-07 (logrank test), Q value = 0.00011

Table S23.  Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 15(11Q23.3) MUTATED 17 4 4.0 - 3760.0 (208.0)
DEL PEAK 15(11Q23.3) WILD-TYPE 177 3 2.0 - 5925.0 (578.0)

Figure S23.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #1: 'Time to Death'

'del_11q23.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S24.  Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 15(11Q23.3) MUTATED 3 2 12 4
DEL PEAK 15(11Q23.3) WILD-TYPE 134 14 31 9

Figure S24.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_11q23.3' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.0062

Table S25.  Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 15(11Q23.3) MUTATED 4 2 15
DEL PEAK 15(11Q23.3) WILD-TYPE 142 20 36

Figure S25.  Get High-res Image Gene #22: 'del_11q23.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q13.3' versus 'Time to Death'

P value = 8.62e-05 (logrank test), Q value = 0.026

Table S26.  Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 18(15Q13.3) MUTATED 22 4 3.0 - 5925.0 (207.5)
DEL PEAK 18(15Q13.3) WILD-TYPE 172 3 2.0 - 3950.0 (578.5)

Figure S26.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #1: 'Time to Death'

'del_15q13.3' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00034 (Fisher's exact test), Q value = 0.1

Table S27.  Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 18(15Q13.3) MUTATED 9 1 11 5
DEL PEAK 18(15Q13.3) WILD-TYPE 128 15 32 8

Figure S27.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_15q13.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.039

Table S28.  Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 18(15Q13.3) MUTATED 11 1 16
DEL PEAK 18(15Q13.3) WILD-TYPE 135 21 35

Figure S28.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_15q13.3' versus 'PATHOLOGY.N.STAGE'

P value = 0.00084 (Fisher's exact test), Q value = 0.24

Table S29.  Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1 N2
ALL 39 20 4
DEL PEAK 18(15Q13.3) MUTATED 3 10 1
DEL PEAK 18(15Q13.3) WILD-TYPE 36 10 3

Figure S29.  Get High-res Image Gene #25: 'del_15q13.3' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'del_16q24.1' versus 'Time to Death'

P value = 1.94e-06 (logrank test), Q value = 0.00062

Table S30.  Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 19(16Q24.1) MUTATED 6 2 13.0 - 1967.0 (69.5)
DEL PEAK 19(16Q24.1) WILD-TYPE 188 5 2.0 - 5925.0 (543.5)

Figure S30.  Get High-res Image Gene #26: 'del_16q24.1' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'Time to Death'

P value = 9.48e-06 (logrank test), Q value = 0.003

Table S31.  Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 20(19P13.3) MUTATED 16 3 4.0 - 1967.0 (330.5)
DEL PEAK 20(19P13.3) WILD-TYPE 178 4 2.0 - 5925.0 (543.5)

Figure S31.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.11

Table S32.  Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 20(19P13.3) MUTATED 5 1 11
DEL PEAK 20(19P13.3) WILD-TYPE 141 21 40

Figure S32.  Get High-res Image Gene #27: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_19q13.42' versus 'Time to Death'

P value = 1.68e-06 (logrank test), Q value = 0.00054

Table S33.  Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 21(19Q13.42) MUTATED 16 4 29.0 - 2839.0 (325.5)
DEL PEAK 21(19Q13.42) WILD-TYPE 178 3 2.0 - 5925.0 (543.5)

Figure S33.  Get High-res Image Gene #28: 'del_19q13.42' versus Clinical Feature #1: 'Time to Death'

'del_22q12.2' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S34.  Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 22(22Q12.2) MUTATED 19 3 22 7
DEL PEAK 22(22Q12.2) WILD-TYPE 118 13 21 6

Figure S34.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_22q12.2' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S35.  Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 22(22Q12.2) MUTATED 21 5 27
DEL PEAK 22(22Q12.2) WILD-TYPE 125 17 24

Figure S35.  Get High-res Image Gene #29: 'del_22q12.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xp11.4' versus 'Time to Death'

P value = 3.61e-06 (logrank test), Q value = 0.0012

Table S36.  Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 23(XP11.4) MUTATED 19 4 4.0 - 2429.0 (307.0)
DEL PEAK 23(XP11.4) WILD-TYPE 175 3 2.0 - 5925.0 (578.0)

Figure S36.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #1: 'Time to Death'

'del_xp11.4' versus 'NEOPLASM.DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0032

Table S37.  Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 137 16 43 13
DEL PEAK 23(XP11.4) MUTATED 4 1 14 2
DEL PEAK 23(XP11.4) WILD-TYPE 133 15 29 11

Figure S37.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'del_xp11.4' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.012

Table S38.  Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

nPatients T1 T2 T3+T4
ALL 146 22 51
DEL PEAK 23(XP11.4) MUTATED 6 2 15
DEL PEAK 23(XP11.4) WILD-TYPE 140 20 36

Figure S38.  Get High-res Image Gene #30: 'del_xp11.4' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'

'del_xq28' versus 'Time to Death'

P value = 1.22e-06 (logrank test), Q value = 4e-04

Table S39.  Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Year
ALL 194 7 2.0 - 5925.0 (540.5)
DEL PEAK 24(XQ28) MUTATED 14 3 3.0 - 1967.0 (265.0)
DEL PEAK 24(XQ28) WILD-TYPE 180 4 2.0 - 5925.0 (578.0)

Figure S39.  Get High-res Image Gene #31: 'del_xq28' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = KIRP-TP.merged_data.txt

  • Number of patients = 221

  • Number of significantly focal cnvs = 31

  • Number of selected clinical features = 11

  • 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)
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