This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 61 arm-level events and 11 clinical features across 66 patients, 3 significant findings detected with Q value < 0.25.
-
16p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.
-
16q loss cnv correlated to '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 | |
16p loss | 4 (6%) | 62 |
0.519 (1.00) |
0.00031 (0.184) |
0.0065 (1.00) |
3.36e-05 (0.02) |
0.639 (1.00) |
1 (1.00) |
1 (1.00) |
||||
16q loss | 5 (8%) | 61 |
0.221 (1.00) |
0.00466 (1.00) |
0.0481 (1.00) |
0.000165 (0.0979) |
0.641 (1.00) |
1 (1.00) |
1 (1.00) |
||||
3p gain | 8 (12%) | 58 |
100 (1.00) |
0.0837 (1.00) |
0.016 (1.00) |
0.466 (1.00) |
0.0327 (1.00) |
0.256 (1.00) |
0.128 (1.00) |
0.295 (1.00) |
1 (1.00) |
||
3q gain | 8 (12%) | 58 |
100 (1.00) |
0.0837 (1.00) |
0.0155 (1.00) |
0.465 (1.00) |
0.0327 (1.00) |
0.253 (1.00) |
0.128 (1.00) |
0.294 (1.00) |
1 (1.00) |
||
4p gain | 24 (36%) | 42 |
100 (1.00) |
0.265 (1.00) |
0.14 (1.00) |
0.805 (1.00) |
1 (1.00) |
0.111 (1.00) |
1 (1.00) |
1 (1.00) |
0.0467 (1.00) |
1 (1.00) |
0.287 (1.00) |
4q gain | 24 (36%) | 42 |
100 (1.00) |
0.265 (1.00) |
0.14 (1.00) |
0.81 (1.00) |
1 (1.00) |
0.113 (1.00) |
1 (1.00) |
1 (1.00) |
0.0467 (1.00) |
1 (1.00) |
0.287 (1.00) |
5p gain | 8 (12%) | 58 |
100 (1.00) |
0.0661 (1.00) |
0.00141 (0.836) |
0.364 (1.00) |
0.0874 (1.00) |
0.00769 (1.00) |
0.455 (1.00) |
1 (1.00) |
1 (1.00) |
||
5q gain | 8 (12%) | 58 |
100 (1.00) |
0.0661 (1.00) |
0.00167 (0.989) |
0.364 (1.00) |
0.0874 (1.00) |
0.00745 (1.00) |
0.455 (1.00) |
1 (1.00) |
1 (1.00) |
||
7p gain | 24 (36%) | 42 |
100 (1.00) |
0.172 (1.00) |
0.36 (1.00) |
0.69 (1.00) |
0.636 (1.00) |
0.111 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.303 (1.00) |
7q gain | 24 (36%) | 42 |
100 (1.00) |
0.172 (1.00) |
0.362 (1.00) |
0.689 (1.00) |
0.636 (1.00) |
0.113 (1.00) |
0.195 (1.00) |
1 (1.00) |
0.784 (1.00) |
1 (1.00) |
0.303 (1.00) |
8p gain | 17 (26%) | 49 |
100 (1.00) |
0.142 (1.00) |
0.389 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.776 (1.00) |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.588 (1.00) |
8q gain | 18 (27%) | 48 |
100 (1.00) |
0.15 (1.00) |
0.227 (1.00) |
0.451 (1.00) |
1 (1.00) |
0.122 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.588 (1.00) |
9p gain | 10 (15%) | 56 |
100 (1.00) |
0.979 (1.00) |
0.121 (1.00) |
0.192 (1.00) |
0.306 (1.00) |
1 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.376 (1.00) |
0.535 (1.00) |
|
9q gain | 10 (15%) | 56 |
100 (1.00) |
0.979 (1.00) |
0.122 (1.00) |
0.193 (1.00) |
0.306 (1.00) |
1 (1.00) |
1 (1.00) |
0.759 (1.00) |
0.373 (1.00) |
0.535 (1.00) |
|
10p gain | 4 (6%) | 62 |
100 (1.00) |
0.34 (1.00) |
0.269 (1.00) |
0.455 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
11p gain | 15 (23%) | 51 |
100 (1.00) |
0.812 (1.00) |
0.741 (1.00) |
0.81 (1.00) |
0.617 (1.00) |
0.385 (1.00) |
1 (1.00) |
0.0467 (1.00) |
0.559 (1.00) |
0.0756 (1.00) |
|
11q gain | 15 (23%) | 51 |
100 (1.00) |
0.945 (1.00) |
0.741 (1.00) |
0.81 (1.00) |
1 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.0467 (1.00) |
0.561 (1.00) |
0.0756 (1.00) |
|
12p gain | 19 (29%) | 47 |
100 (1.00) |
0.0137 (1.00) |
0.0779 (1.00) |
0.316 (1.00) |
1 (1.00) |
0.136 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.357 (1.00) |
1 (1.00) |
1 (1.00) |
12q gain | 20 (30%) | 46 |
100 (1.00) |
0.0696 (1.00) |
0.112 (1.00) |
0.71 (1.00) |
0.33 (1.00) |
0.136 (1.00) |
0.593 (1.00) |
1 (1.00) |
0.234 (1.00) |
0.808 (1.00) |
1 (1.00) |
14q gain | 21 (32%) | 45 |
100 (1.00) |
0.144 (1.00) |
0.0968 (1.00) |
0.381 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.794 (1.00) |
1 (1.00) |
0.234 (1.00) |
1 (1.00) |
0.609 (1.00) |
15q gain | 21 (32%) | 45 |
100 (1.00) |
0.283 (1.00) |
0.412 (1.00) |
0.477 (1.00) |
0.35 (1.00) |
0.155 (1.00) |
0.794 (1.00) |
1 (1.00) |
1 (1.00) |
0.814 (1.00) |
0.124 (1.00) |
16p gain | 21 (32%) | 45 |
100 (1.00) |
0.995 (1.00) |
0.475 (1.00) |
0.406 (1.00) |
0.635 (1.00) |
0.723 (1.00) |
1 (1.00) |
1 (1.00) |
0.0467 (1.00) |
1 (1.00) |
0.124 (1.00) |
16q gain | 21 (32%) | 45 |
100 (1.00) |
0.995 (1.00) |
0.474 (1.00) |
0.405 (1.00) |
0.635 (1.00) |
0.726 (1.00) |
1 (1.00) |
1 (1.00) |
0.0467 (1.00) |
1 (1.00) |
0.124 (1.00) |
18p gain | 17 (26%) | 49 |
100 (1.00) |
0.278 (1.00) |
0.29 (1.00) |
0.433 (1.00) |
0.303 (1.00) |
0.504 (1.00) |
0.776 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.57 (1.00) |
|
18q gain | 16 (24%) | 50 |
100 (1.00) |
0.525 (1.00) |
0.312 (1.00) |
0.198 (1.00) |
0.303 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.298 (1.00) |
1 (1.00) |
0.305 (1.00) |
|
19p gain | 19 (29%) | 47 |
100 (1.00) |
0.0291 (1.00) |
0.0148 (1.00) |
0.518 (1.00) |
0.00246 (1.00) |
0.0834 (1.00) |
0.412 (1.00) |
0.784 (1.00) |
0.259 (1.00) |
0.29 (1.00) |
|
19q gain | 17 (26%) | 49 |
100 (1.00) |
0.0137 (1.00) |
0.296 (1.00) |
0.644 (1.00) |
0.136 (1.00) |
0.0613 (1.00) |
0.776 (1.00) |
1 (1.00) |
0.593 (1.00) |
0.29 (1.00) |
|
20p gain | 20 (30%) | 46 |
100 (1.00) |
0.128 (1.00) |
0.37 (1.00) |
0.792 (1.00) |
0.35 (1.00) |
0.708 (1.00) |
0.593 (1.00) |
1 (1.00) |
0.234 (1.00) |
0.367 (1.00) |
0.588 (1.00) |
20q gain | 21 (32%) | 45 |
100 (1.00) |
0.053 (1.00) |
0.138 (1.00) |
0.846 (1.00) |
0.35 (1.00) |
0.708 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.234 (1.00) |
0.369 (1.00) |
0.609 (1.00) |
21q gain | 4 (6%) | 62 |
100 (1.00) |
0.591 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
22q gain | 19 (29%) | 47 |
100 (1.00) |
0.415 (1.00) |
0.488 (1.00) |
0.52 (1.00) |
0.166 (1.00) |
0.355 (1.00) |
0.412 (1.00) |
0.784 (1.00) |
0.794 (1.00) |
0.588 (1.00) |
|
xq gain | 6 (9%) | 60 |
100 (1.00) |
0.815 (1.00) |
0.382 (1.00) |
0.662 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.388 (1.00) |
0.458 (1.00) |
0.39 (1.00) |
||
1p loss | 53 (80%) | 13 |
100 (1.00) |
0.478 (1.00) |
0.0278 (1.00) |
0.0408 (1.00) |
1 (1.00) |
0.00663 (1.00) |
0.534 (1.00) |
0.438 (1.00) |
0.609 (1.00) |
1 (1.00) |
1 (1.00) |
1q loss | 52 (79%) | 14 |
100 (1.00) |
0.456 (1.00) |
0.00625 (1.00) |
0.0132 (1.00) |
0.529 (1.00) |
0.0203 (1.00) |
0.367 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
2p loss | 46 (70%) | 20 |
100 (1.00) |
0.241 (1.00) |
0.144 (1.00) |
0.113 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.284 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
2q loss | 46 (70%) | 20 |
100 (1.00) |
0.241 (1.00) |
0.144 (1.00) |
0.114 (1.00) |
1 (1.00) |
0.194 (1.00) |
0.284 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
3p loss | 9 (14%) | 57 |
100 (1.00) |
0.0465 (1.00) |
0.076 (1.00) |
0.0231 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.535 (1.00) |
||
3q loss | 8 (12%) | 58 |
100 (1.00) |
0.107 (1.00) |
0.141 (1.00) |
0.0522 (1.00) |
1 (1.00) |
0.638 (1.00) |
0.256 (1.00) |
1 (1.00) |
0.535 (1.00) |
||
5p loss | 10 (15%) | 56 |
100 (1.00) |
0.642 (1.00) |
0.132 (1.00) |
0.0847 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.155 (1.00) |
0.159 (1.00) |
0.121 (1.00) |
|
5q loss | 10 (15%) | 56 |
100 (1.00) |
0.642 (1.00) |
0.134 (1.00) |
0.0855 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.155 (1.00) |
0.158 (1.00) |
0.121 (1.00) |
|
6p loss | 51 (77%) | 15 |
100 (1.00) |
0.379 (1.00) |
0.0834 (1.00) |
0.0563 (1.00) |
0.568 (1.00) |
0.169 (1.00) |
0.244 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
6q loss | 51 (77%) | 15 |
100 (1.00) |
0.379 (1.00) |
0.0833 (1.00) |
0.0559 (1.00) |
0.568 (1.00) |
0.17 (1.00) |
0.244 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
8p loss | 9 (14%) | 57 |
100 (1.00) |
0.779 (1.00) |
0.741 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
0.727 (1.00) |
0.613 (1.00) |
0.566 (1.00) |
||
8q loss | 8 (12%) | 58 |
100 (1.00) |
0.575 (1.00) |
0.702 (1.00) |
0.412 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.567 (1.00) |
1 (1.00) |
||
9p loss | 10 (15%) | 56 |
100 (1.00) |
0.0116 (1.00) |
1 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.492 (1.00) |
0.508 (1.00) |
1 (1.00) |
0.535 (1.00) |
||
9q loss | 10 (15%) | 56 |
100 (1.00) |
0.0116 (1.00) |
1 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.488 (1.00) |
0.508 (1.00) |
1 (1.00) |
0.535 (1.00) |
||
10p loss | 48 (73%) | 18 |
100 (1.00) |
0.762 (1.00) |
0.545 (1.00) |
0.393 (1.00) |
1 (1.00) |
0.0197 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
10q loss | 49 (74%) | 17 |
100 (1.00) |
0.953 (1.00) |
0.347 (1.00) |
0.209 (1.00) |
1 (1.00) |
0.0189 (1.00) |
1 (1.00) |
0.146 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
11p loss | 7 (11%) | 59 |
100 (1.00) |
0.0527 (1.00) |
0.096 (1.00) |
0.0799 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.691 (1.00) |
1 (1.00) |
1 (1.00) |
||
11q loss | 7 (11%) | 59 |
100 (1.00) |
0.0527 (1.00) |
0.0967 (1.00) |
0.0786 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.691 (1.00) |
1 (1.00) |
1 (1.00) |
||
13q loss | 43 (65%) | 23 |
100 (1.00) |
0.0641 (1.00) |
0.447 (1.00) |
0.359 (1.00) |
0.301 (1.00) |
0.535 (1.00) |
0.294 (1.00) |
1 (1.00) |
0.474 (1.00) |
0.817 (1.00) |
1 (1.00) |
17p loss | 50 (76%) | 16 |
100 (1.00) |
0.149 (1.00) |
0.0749 (1.00) |
0.0418 (1.00) |
0.568 (1.00) |
0.171 (1.00) |
0.158 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
17q loss | 50 (76%) | 16 |
100 (1.00) |
0.149 (1.00) |
0.0737 (1.00) |
0.0419 (1.00) |
0.568 (1.00) |
0.169 (1.00) |
0.158 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
|
18p loss | 8 (12%) | 58 |
100 (1.00) |
0.455 (1.00) |
0.443 (1.00) |
0.898 (1.00) |
0.211 (1.00) |
0.66 (1.00) |
0.256 (1.00) |
0.296 (1.00) |
1 (1.00) |
||
18q loss | 10 (15%) | 56 |
100 (1.00) |
0.343 (1.00) |
0.14 (1.00) |
0.835 (1.00) |
0.258 (1.00) |
0.66 (1.00) |
0.295 (1.00) |
0.375 (1.00) |
1 (1.00) |
||
19q loss | 3 (5%) | 63 |
100 (1.00) |
0.423 (1.00) |
0.012 (1.00) |
0.191 (1.00) |
0.0289 (1.00) |
1 (1.00) |
0.1 (1.00) |
0.111 (1.00) |
|||
20p loss | 4 (6%) | 62 |
100 (1.00) |
0.237 (1.00) |
0.138 (1.00) |
0.142 (1.00) |
0.304 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
20q loss | 3 (5%) | 63 |
0.432 (1.00) |
0.041 (1.00) |
0.026 (1.00) |
0.304 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
21q loss | 35 (53%) | 31 |
100 (1.00) |
0.375 (1.00) |
0.905 (1.00) |
0.781 (1.00) |
0.0731 (1.00) |
0.0779 (1.00) |
0.805 (1.00) |
0.448 (1.00) |
0.705 (1.00) |
0.544 (1.00) |
0.613 (1.00) |
22q loss | 8 (12%) | 58 |
100 (1.00) |
0.783 (1.00) |
0.179 (1.00) |
1 (1.00) |
0.211 (1.00) |
0.321 (1.00) |
0.0553 (1.00) |
0.565 (1.00) |
0.39 (1.00) |
||
xq loss | 39 (59%) | 27 |
100 (1.00) |
0.0923 (1.00) |
0.304 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.136 (1.00) |
0.132 (1.00) |
0.17 (1.00) |
0.819 (1.00) |
1 (1.00) |
P value = 0.00031 (Fisher's exact test), Q value = 0.18
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 21 | 25 | 14 | 6 |
16P LOSS MUTATED | 0 | 0 | 1 | 3 |
16P LOSS WILD-TYPE | 21 | 25 | 13 | 3 |
P value = 3.36e-05 (Fisher's exact test), Q value = 0.02
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
16P LOSS MUTATED | 0 | 4 |
16P LOSS WILD-TYPE | 40 | 1 |
P value = 0.000165 (Fisher's exact test), Q value = 0.098
nPatients | N0 | N1+N2 |
---|---|---|
ALL | 40 | 5 |
16Q LOSS MUTATED | 1 | 4 |
16Q LOSS WILD-TYPE | 39 | 1 |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = KICH-TP.merged_data.txt
-
Number of patients = 66
-
Number of significantly arm-level cnvs = 61
-
Number of selected clinical features = 11
-
Exclude regions 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.