This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 30 focal events and 11 clinical features across 516 patients, 21 significant findings detected with Q value < 0.25.
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amp_3q26.32 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_3p26.3 cnv correlated to 'RACE'.
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del_3p22.2 cnv correlated to 'PATHOLOGY.T.STAGE' and 'RACE'.
-
del_3p12.2 cnv correlated to 'GENDER'.
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del_3q11.2 cnv correlated to 'GENDER'.
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del_4q34.3 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_9p23 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_9p21.3 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', 'PATHOLOGY.M.STAGE', and 'GENDER'.
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del_10q23.31 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_13q14.2 cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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del_14q31.1 cnv correlated to 'NEOPLASM.DISEASESTAGE', 'PATHOLOGY.T.STAGE', and 'PATHOLOGY.N.STAGE'.
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 9p21 3 | 157 (30%) | 359 |
0.241 (1.00) |
0.0442 (1.00) |
1e-05 (0.00311) |
1e-05 (0.00311) |
0.03 (1.00) |
0.00014 (0.0419) |
0.00047 (0.138) |
0.546 (1.00) |
0.797 (1.00) |
0.109 (1.00) |
0.826 (1.00) |
del 14q31 1 | 223 (43%) | 293 |
0.131 (1.00) |
0.112 (1.00) |
2e-05 (0.00608) |
0.00014 (0.0419) |
0.000109 (0.0328) |
0.00109 (0.316) |
0.139 (1.00) |
0.184 (1.00) |
0.251 (1.00) |
0.0173 (1.00) |
1 (1.00) |
amp 3q26 32 | 86 (17%) | 430 |
0.222 (1.00) |
0.983 (1.00) |
0.00011 (0.033) |
0.0002 (0.0594) |
0.0577 (1.00) |
0.00087 (0.253) |
0.807 (1.00) |
0.395 (1.00) |
0.605 (1.00) |
1 (1.00) |
|
del 3p22 2 | 456 (88%) | 60 |
0.8 (1.00) |
0.37 (1.00) |
0.0257 (1.00) |
0.00032 (0.0944) |
1 (1.00) |
0.582 (1.00) |
1 (1.00) |
0.322 (1.00) |
0.4 (1.00) |
2e-05 (0.00608) |
1 (1.00) |
del 4q34 3 | 78 (15%) | 438 |
0.857 (1.00) |
0.566 (1.00) |
2e-05 (0.00608) |
1e-05 (0.00311) |
0.725 (1.00) |
0.0111 (1.00) |
0.309 (1.00) |
0.477 (1.00) |
0.0892 (1.00) |
0.59 (1.00) |
|
del 9p23 | 149 (29%) | 367 |
0.465 (1.00) |
0.0246 (1.00) |
1e-05 (0.00311) |
1e-05 (0.00311) |
0.103 (1.00) |
0.00315 (0.898) |
0.00166 (0.477) |
0.546 (1.00) |
0.797 (1.00) |
0.293 (1.00) |
0.654 (1.00) |
del 13q14 2 | 81 (16%) | 435 |
0.0145 (1.00) |
0.757 (1.00) |
1e-05 (0.00311) |
1e-05 (0.00311) |
0.33 (1.00) |
0.0553 (1.00) |
0.802 (1.00) |
0.949 (1.00) |
0.12 (1.00) |
0.399 (1.00) |
|
del 3p26 3 | 446 (86%) | 70 |
0.205 (1.00) |
0.326 (1.00) |
0.148 (1.00) |
0.0116 (1.00) |
0.731 (1.00) |
0.856 (1.00) |
0.79 (1.00) |
0.169 (1.00) |
0.4 (1.00) |
0.00033 (0.097) |
0.397 (1.00) |
del 3p12 2 | 298 (58%) | 218 |
0.19 (1.00) |
0.741 (1.00) |
0.668 (1.00) |
0.224 (1.00) |
0.623 (1.00) |
0.501 (1.00) |
0.000814 (0.238) |
0.394 (1.00) |
0.517 (1.00) |
0.22 (1.00) |
0.538 (1.00) |
del 3q11 2 | 158 (31%) | 358 |
0.444 (1.00) |
0.0244 (1.00) |
0.356 (1.00) |
0.0863 (1.00) |
0.599 (1.00) |
0.742 (1.00) |
1.8e-07 (5.62e-05) |
0.485 (1.00) |
0.779 (1.00) |
0.186 (1.00) |
0.371 (1.00) |
del 10q23 31 | 94 (18%) | 422 |
0.228 (1.00) |
0.587 (1.00) |
0.00875 (1.00) |
0.00021 (0.0622) |
1 (1.00) |
0.0577 (1.00) |
0.043 (1.00) |
0.589 (1.00) |
0.133 (1.00) |
0.427 (1.00) |
|
amp 1q24 1 | 62 (12%) | 454 |
0.14 (1.00) |
0.0811 (1.00) |
0.173 (1.00) |
0.121 (1.00) |
0.0803 (1.00) |
0.337 (1.00) |
0.574 (1.00) |
0.763 (1.00) |
0.857 (1.00) |
0.529 (1.00) |
|
amp 1q32 1 | 62 (12%) | 454 |
0.155 (1.00) |
0.0215 (1.00) |
0.108 (1.00) |
0.106 (1.00) |
0.711 (1.00) |
0.494 (1.00) |
0.574 (1.00) |
0.763 (1.00) |
0.857 (1.00) |
0.213 (1.00) |
|
amp 4q32 1 | 16 (3%) | 500 |
0.375 (1.00) |
0.295 (1.00) |
0.654 (1.00) |
0.4 (1.00) |
0.57 (1.00) |
0.852 (1.00) |
0.599 (1.00) |
0.104 (1.00) |
1 (1.00) |
1 (1.00) |
|
amp 5q35 1 | 326 (63%) | 190 |
0.0703 (1.00) |
0.152 (1.00) |
0.509 (1.00) |
0.312 (1.00) |
0.31 (1.00) |
0.336 (1.00) |
0.072 (1.00) |
0.819 (1.00) |
0.135 (1.00) |
0.00329 (0.934) |
1 (1.00) |
amp 7q36 3 | 173 (34%) | 343 |
0.475 (1.00) |
0.562 (1.00) |
0.0208 (1.00) |
0.0611 (1.00) |
0.447 (1.00) |
0.0103 (1.00) |
0.0196 (1.00) |
0.108 (1.00) |
0.345 (1.00) |
0.084 (1.00) |
0.27 (1.00) |
amp 8q24 22 | 78 (15%) | 438 |
0.322 (1.00) |
0.00626 (1.00) |
0.00171 (0.489) |
0.0014 (0.403) |
0.737 (1.00) |
0.107 (1.00) |
0.0739 (1.00) |
0.765 (1.00) |
0.331 (1.00) |
0.231 (1.00) |
|
amp 10p14 | 20 (4%) | 496 |
0.926 (1.00) |
0.0427 (1.00) |
0.4 (1.00) |
0.0319 (1.00) |
0.212 (1.00) |
0.69 (1.00) |
0.642 (1.00) |
0.244 (1.00) |
0.45 (1.00) |
1 (1.00) |
|
amp xp22 2 | 30 (6%) | 486 |
0.229 (1.00) |
0.796 (1.00) |
0.05 (1.00) |
0.0953 (1.00) |
1 (1.00) |
0.16 (1.00) |
1 (1.00) |
1 (1.00) |
0.0232 (1.00) |
0.613 (1.00) |
|
amp xp11 4 | 32 (6%) | 484 |
0.284 (1.00) |
0.953 (1.00) |
0.0414 (1.00) |
0.114 (1.00) |
1 (1.00) |
0.099 (1.00) |
1 (1.00) |
1 (1.00) |
0.0717 (1.00) |
0.381 (1.00) |
|
amp xq11 2 | 28 (5%) | 488 |
0.626 (1.00) |
0.301 (1.00) |
0.394 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.577 (1.00) |
1 (1.00) |
1 (1.00) |
0.0737 (1.00) |
0.611 (1.00) |
|
amp xq28 | 36 (7%) | 480 |
0.936 (1.00) |
0.482 (1.00) |
0.616 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.0949 (1.00) |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
0.392 (1.00) |
|
del 1p36 23 | 101 (20%) | 415 |
0.0309 (1.00) |
0.113 (1.00) |
0.321 (1.00) |
0.1 (1.00) |
1 (1.00) |
0.117 (1.00) |
0.105 (1.00) |
0.793 (1.00) |
1 (1.00) |
0.217 (1.00) |
|
del 1p31 1 | 75 (15%) | 441 |
0.264 (1.00) |
0.138 (1.00) |
0.651 (1.00) |
0.0392 (1.00) |
0.492 (1.00) |
0.158 (1.00) |
0.0193 (1.00) |
0.793 (1.00) |
0.575 (1.00) |
0.0902 (1.00) |
|
del 1q43 | 40 (8%) | 476 |
0.387 (1.00) |
0.71 (1.00) |
1 (1.00) |
0.15 (1.00) |
1 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.441 (1.00) |
0.719 (1.00) |
|
del 2q37 3 | 50 (10%) | 466 |
0.0717 (1.00) |
0.712 (1.00) |
0.491 (1.00) |
0.74 (1.00) |
1 (1.00) |
0.653 (1.00) |
0.162 (1.00) |
0.589 (1.00) |
0.492 (1.00) |
||
del 3p14 1 | 365 (71%) | 151 |
0.971 (1.00) |
0.964 (1.00) |
0.261 (1.00) |
0.0531 (1.00) |
0.428 (1.00) |
0.548 (1.00) |
0.00122 (0.351) |
0.899 (1.00) |
0.517 (1.00) |
0.0796 (1.00) |
0.827 (1.00) |
del 6q26 | 150 (29%) | 366 |
0.773 (1.00) |
0.248 (1.00) |
0.454 (1.00) |
0.642 (1.00) |
0.00907 (1.00) |
0.838 (1.00) |
0.0155 (1.00) |
0.36 (1.00) |
0.0591 (1.00) |
0.258 (1.00) |
0.178 (1.00) |
del 6q26 | 150 (29%) | 366 |
0.468 (1.00) |
0.204 (1.00) |
0.453 (1.00) |
0.639 (1.00) |
0.00907 (1.00) |
0.84 (1.00) |
0.00869 (1.00) |
0.36 (1.00) |
0.0591 (1.00) |
0.259 (1.00) |
0.178 (1.00) |
del 8p23 2 | 152 (29%) | 364 |
0.237 (1.00) |
0.177 (1.00) |
0.1 (1.00) |
0.0736 (1.00) |
1 (1.00) |
0.137 (1.00) |
0.191 (1.00) |
0.694 (1.00) |
0.731 (1.00) |
0.0906 (1.00) |
0.0371 (1.00) |
P value = 0.00011 (Fisher's exact test), Q value = 0.033
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
AMP PEAK 3(3Q26.32) MUTATED | 28 | 6 | 27 | 25 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 225 | 51 | 99 | 55 |
P value = 2e-04 (Fisher's exact test), Q value = 0.059
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
AMP PEAK 3(3Q26.32) MUTATED | 29 | 8 | 45 | 4 |
AMP PEAK 3(3Q26.32) WILD-TYPE | 229 | 61 | 133 | 7 |
P value = 0.00033 (Fisher's exact test), Q value = 0.097
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 44 | 457 |
DEL PEAK 5(3P26.3) MUTATED | 6 | 29 | 404 |
DEL PEAK 5(3P26.3) WILD-TYPE | 2 | 15 | 53 |
P value = 0.00032 (Fisher's exact test), Q value = 0.094
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 6(3P22.2) MUTATED | 221 | 61 | 168 | 6 |
DEL PEAK 6(3P22.2) WILD-TYPE | 37 | 8 | 10 | 5 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0061
nPatients | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|
ALL | 8 | 44 | 457 |
DEL PEAK 6(3P22.2) MUTATED | 6 | 29 | 414 |
DEL PEAK 6(3P22.2) WILD-TYPE | 2 | 15 | 43 |
P value = 0.000814 (Fisher's exact test), Q value = 0.24
nPatients | FEMALE | MALE |
---|---|---|
ALL | 186 | 330 |
DEL PEAK 8(3P12.2) MUTATED | 89 | 209 |
DEL PEAK 8(3P12.2) WILD-TYPE | 97 | 121 |
P value = 1.8e-07 (Fisher's exact test), Q value = 5.6e-05
nPatients | FEMALE | MALE |
---|---|---|
ALL | 186 | 330 |
DEL PEAK 9(3Q11.2) MUTATED | 31 | 127 |
DEL PEAK 9(3Q11.2) WILD-TYPE | 155 | 203 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0061
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
DEL PEAK 10(4Q34.3) MUTATED | 19 | 7 | 31 | 21 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 234 | 50 | 95 | 59 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 10(4Q34.3) MUTATED | 20 | 9 | 43 | 6 |
DEL PEAK 10(4Q34.3) WILD-TYPE | 238 | 60 | 135 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
DEL PEAK 14(9P23) MUTATED | 50 | 12 | 51 | 36 |
DEL PEAK 14(9P23) WILD-TYPE | 203 | 45 | 75 | 44 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 14(9P23) MUTATED | 53 | 16 | 75 | 5 |
DEL PEAK 14(9P23) WILD-TYPE | 205 | 53 | 103 | 6 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
DEL PEAK 15(9P21.3) MUTATED | 51 | 11 | 55 | 40 |
DEL PEAK 15(9P21.3) WILD-TYPE | 202 | 46 | 71 | 40 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 15(9P21.3) MUTATED | 54 | 15 | 82 | 6 |
DEL PEAK 15(9P21.3) WILD-TYPE | 204 | 54 | 96 | 5 |
P value = 0.00014 (Fisher's exact test), Q value = 0.042
nPatients | M0 | M1 | MX |
---|---|---|---|
ALL | 417 | 78 | 19 |
DEL PEAK 15(9P21.3) MUTATED | 115 | 39 | 3 |
DEL PEAK 15(9P21.3) WILD-TYPE | 302 | 39 | 16 |
P value = 0.00047 (Fisher's exact test), Q value = 0.14
nPatients | FEMALE | MALE |
---|---|---|
ALL | 186 | 330 |
DEL PEAK 15(9P21.3) MUTATED | 39 | 118 |
DEL PEAK 15(9P21.3) WILD-TYPE | 147 | 212 |
P value = 0.00021 (Fisher's exact test), Q value = 0.062
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 16(10Q23.31) MUTATED | 32 | 12 | 44 | 6 |
DEL PEAK 16(10Q23.31) WILD-TYPE | 226 | 57 | 134 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
DEL PEAK 17(13Q14.2) MUTATED | 26 | 3 | 31 | 21 |
DEL PEAK 17(13Q14.2) WILD-TYPE | 227 | 54 | 95 | 59 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0031
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 17(13Q14.2) MUTATED | 28 | 4 | 42 | 7 |
DEL PEAK 17(13Q14.2) WILD-TYPE | 230 | 65 | 136 | 4 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0061
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 253 | 57 | 126 | 80 |
DEL PEAK 18(14Q31.1) MUTATED | 82 | 27 | 67 | 47 |
DEL PEAK 18(14Q31.1) WILD-TYPE | 171 | 30 | 59 | 33 |
P value = 0.00014 (Fisher's exact test), Q value = 0.042
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 69 | 178 | 11 |
DEL PEAK 18(14Q31.1) MUTATED | 87 | 35 | 97 | 4 |
DEL PEAK 18(14Q31.1) WILD-TYPE | 171 | 34 | 81 | 7 |
P value = 0.000109 (Fisher's exact test), Q value = 0.033
nPatients | 0 | 1 |
---|---|---|
ALL | 231 | 18 |
DEL PEAK 18(14Q31.1) MUTATED | 97 | 16 |
DEL PEAK 18(14Q31.1) WILD-TYPE | 134 | 2 |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = KIRC-TP.merged_data.txt
-
Number of patients = 516
-
Number of significantly focal cnvs = 30
-
Number of selected clinical features = 11
-
Exclude genes that fewer than K tumors have mutations, K = 3
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
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
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.
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.