This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level results and 7 clinical features across 554 patients, 8 significant findings detected with Q value < 0.25.
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2p gain cnv correlated to 'AGE'.
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3q gain cnv correlated to 'AGE'.
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10p gain cnv correlated to 'AGE'.
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12p gain cnv correlated to 'AGE'.
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12q gain cnv correlated to 'AGE'.
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20p gain cnv correlated to 'AGE'.
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20q gain cnv correlated to 'AGE'.
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9q loss cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
KARNOFSKY PERFORMANCE SCORE |
TUMOR STAGE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
2p gain | 124 (22%) | 430 |
0.0314 (1.00) |
2.19e-07 (0.000121) |
1 (1.00) |
0.956 (1.00) |
0.966 (1.00) |
0.533 (1.00) |
0.696 (1.00) |
3q gain | 203 (37%) | 351 |
0.513 (1.00) |
7.09e-07 (0.000392) |
0.126 (1.00) |
0.671 (1.00) |
0.523 (1.00) |
0.302 (1.00) |
0.214 (1.00) |
10p gain | 133 (24%) | 421 |
0.163 (1.00) |
3.74e-05 (0.0205) |
0.111 (1.00) |
0.152 (1.00) |
0.794 (1.00) |
1 (1.00) |
0.128 (1.00) |
12p gain | 201 (36%) | 353 |
0.277 (1.00) |
3e-08 (1.67e-05) |
0.124 (1.00) |
0.0302 (1.00) |
0.00495 (1.00) |
1 (1.00) |
0.0416 (1.00) |
12q gain | 116 (21%) | 438 |
0.137 (1.00) |
3.23e-06 (0.00177) |
0.61 (1.00) |
0.0312 (1.00) |
0.0712 (1.00) |
0.507 (1.00) |
0.285 (1.00) |
20p gain | 229 (41%) | 325 |
0.157 (1.00) |
2.5e-06 (0.00138) |
1 (1.00) |
0.105 (1.00) |
0.196 (1.00) |
0.572 (1.00) |
0.272 (1.00) |
20q gain | 266 (48%) | 288 |
0.114 (1.00) |
7.92e-07 (0.000437) |
1 (1.00) |
0.229 (1.00) |
0.0879 (1.00) |
0.61 (1.00) |
0.515 (1.00) |
9q loss | 234 (42%) | 320 |
0.599 (1.00) |
3.22e-06 (0.00177) |
0.151 (1.00) |
0.779 (1.00) |
0.346 (1.00) |
0.576 (1.00) |
0.661 (1.00) |
1p gain | 103 (19%) | 451 |
0.0912 (1.00) |
0.62 (1.00) |
0.159 (1.00) |
0.126 (1.00) |
0.261 (1.00) |
0.0903 (1.00) |
0.889 (1.00) |
1q gain | 156 (28%) | 398 |
0.293 (1.00) |
0.0194 (1.00) |
0.0697 (1.00) |
0.0331 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.904 (1.00) |
2q gain | 98 (18%) | 456 |
0.11 (1.00) |
0.000479 (0.262) |
1 (1.00) |
0.69 (1.00) |
0.66 (1.00) |
0.0823 (1.00) |
0.477 (1.00) |
3p gain | 108 (19%) | 446 |
0.462 (1.00) |
0.0555 (1.00) |
0.581 (1.00) |
0.73 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.216 (1.00) |
4p gain | 30 (5%) | 524 |
0.28 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.781 (1.00) |
1 (1.00) |
0.145 (1.00) |
4q gain | 17 (3%) | 537 |
0.528 (1.00) |
0.0825 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.0254 (1.00) |
5p gain | 139 (25%) | 415 |
0.384 (1.00) |
0.294 (1.00) |
0.121 (1.00) |
0.791 (1.00) |
0.871 (1.00) |
1 (1.00) |
0.707 (1.00) |
5q gain | 31 (6%) | 523 |
0.307 (1.00) |
0.927 (1.00) |
0.206 (1.00) |
0.137 (1.00) |
0.852 (1.00) |
1 (1.00) |
1 (1.00) |
6p gain | 121 (22%) | 433 |
0.399 (1.00) |
0.00541 (1.00) |
0.628 (1.00) |
0.0337 (1.00) |
0.0697 (1.00) |
1 (1.00) |
0.598 (1.00) |
6q gain | 62 (11%) | 492 |
0.492 (1.00) |
0.0555 (1.00) |
1 (1.00) |
0.195 (1.00) |
0.014 (1.00) |
1 (1.00) |
0.864 (1.00) |
7p gain | 121 (22%) | 433 |
0.175 (1.00) |
0.00094 (0.513) |
1 (1.00) |
0.292 (1.00) |
0.41 (1.00) |
1 (1.00) |
0.188 (1.00) |
7q gain | 142 (26%) | 412 |
0.145 (1.00) |
0.00518 (1.00) |
0.695 (1.00) |
0.276 (1.00) |
0.238 (1.00) |
0.573 (1.00) |
0.0807 (1.00) |
8p gain | 85 (15%) | 469 |
0.0767 (1.00) |
0.813 (1.00) |
1 (1.00) |
0.894 (1.00) |
0.383 (1.00) |
0.394 (1.00) |
0.366 (1.00) |
8q gain | 202 (36%) | 352 |
0.162 (1.00) |
0.519 (1.00) |
0.248 (1.00) |
0.946 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.0426 (1.00) |
9p gain | 61 (11%) | 493 |
0.921 (1.00) |
0.72 (1.00) |
1 (1.00) |
0.95 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.488 (1.00) |
9q gain | 28 (5%) | 526 |
0.675 (1.00) |
0.642 (1.00) |
1 (1.00) |
0.254 (1.00) |
1 (1.00) |
1 (1.00) |
|
10q gain | 69 (12%) | 485 |
0.383 (1.00) |
0.0268 (1.00) |
0.414 (1.00) |
0.32 (1.00) |
0.37 (1.00) |
1 (1.00) |
0.0308 (1.00) |
11p gain | 41 (7%) | 513 |
0.612 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.852 (1.00) |
0.141 (1.00) |
1 (1.00) |
0.0366 (1.00) |
11q gain | 59 (11%) | 495 |
0.374 (1.00) |
0.305 (1.00) |
1 (1.00) |
0.566 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.163 (1.00) |
13q gain | 38 (7%) | 516 |
0.719 (1.00) |
0.0339 (1.00) |
1 (1.00) |
0.333 (1.00) |
0.192 (1.00) |
0.279 (1.00) |
|
14q gain | 33 (6%) | 521 |
0.311 (1.00) |
0.78 (1.00) |
1 (1.00) |
0.497 (1.00) |
0.537 (1.00) |
0.169 (1.00) |
0.818 (1.00) |
15q gain | 24 (4%) | 530 |
0.855 (1.00) |
0.348 (1.00) |
1 (1.00) |
0.0315 (1.00) |
1 (1.00) |
0.424 (1.00) |
|
16p gain | 32 (6%) | 522 |
0.61 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.485 (1.00) |
16q gain | 16 (3%) | 538 |
0.666 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.748 (1.00) |
|
17p gain | 10 (2%) | 544 |
0.161 (1.00) |
0.0805 (1.00) |
1 (1.00) |
0.767 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.221 (1.00) |
17q gain | 23 (4%) | 531 |
0.0947 (1.00) |
0.182 (1.00) |
1 (1.00) |
0.614 (1.00) |
0.574 (1.00) |
1 (1.00) |
0.28 (1.00) |
18p gain | 75 (14%) | 479 |
0.165 (1.00) |
0.16 (1.00) |
1 (1.00) |
0.341 (1.00) |
0.0077 (1.00) |
1 (1.00) |
0.114 (1.00) |
18q gain | 42 (8%) | 512 |
0.617 (1.00) |
0.446 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.067 (1.00) |
0.211 (1.00) |
0.0613 (1.00) |
19p gain | 97 (18%) | 457 |
0.33 (1.00) |
0.0138 (1.00) |
1 (1.00) |
0.996 (1.00) |
0.26 (1.00) |
0.439 (1.00) |
0.474 (1.00) |
19q gain | 90 (16%) | 464 |
0.146 (1.00) |
0.0138 (1.00) |
1 (1.00) |
0.649 (1.00) |
0.282 (1.00) |
0.413 (1.00) |
0.768 (1.00) |
21q gain | 68 (12%) | 486 |
0.00788 (1.00) |
0.0129 (1.00) |
0.409 (1.00) |
0.566 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.74 (1.00) |
22q gain | 10 (2%) | 544 |
0.778 (1.00) |
0.3 (1.00) |
1 (1.00) |
0.721 (1.00) |
1 (1.00) |
0.407 (1.00) |
|
Xq gain | 34 (6%) | 520 |
0.0973 (1.00) |
0.514 (1.00) |
1 (1.00) |
0.137 (1.00) |
1 (1.00) |
1 (1.00) |
0.82 (1.00) |
1p loss | 34 (6%) | 520 |
0.8 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.296 (1.00) |
0.817 (1.00) |
0.173 (1.00) |
0.496 (1.00) |
1q loss | 23 (4%) | 531 |
0.312 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.387 (1.00) |
0.12 (1.00) |
0.0557 (1.00) |
2p loss | 26 (5%) | 528 |
0.579 (1.00) |
0.847 (1.00) |
1 (1.00) |
0.0731 (1.00) |
0.472 (1.00) |
1 (1.00) |
0.8 (1.00) |
2q loss | 30 (5%) | 524 |
0.72 (1.00) |
0.452 (1.00) |
0.2 (1.00) |
0.0731 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.477 (1.00) |
3p loss | 58 (10%) | 496 |
0.178 (1.00) |
0.162 (1.00) |
0.358 (1.00) |
0.321 (1.00) |
0.682 (1.00) |
0.283 (1.00) |
0.286 (1.00) |
3q loss | 23 (4%) | 531 |
0.136 (1.00) |
0.847 (1.00) |
0.156 (1.00) |
0.607 (1.00) |
0.171 (1.00) |
0.12 (1.00) |
0.784 (1.00) |
4p loss | 251 (45%) | 303 |
0.248 (1.00) |
0.302 (1.00) |
0.165 (1.00) |
0.106 (1.00) |
0.469 (1.00) |
0.593 (1.00) |
1 (1.00) |
4q loss | 293 (53%) | 261 |
0.419 (1.00) |
0.163 (1.00) |
0.751 (1.00) |
0.952 (1.00) |
0.324 (1.00) |
1 (1.00) |
0.516 (1.00) |
5p loss | 82 (15%) | 472 |
0.229 (1.00) |
0.0152 (1.00) |
0.474 (1.00) |
0.227 (1.00) |
0.334 (1.00) |
1 (1.00) |
0.878 (1.00) |
5q loss | 166 (30%) | 388 |
0.576 (1.00) |
0.0603 (1.00) |
0.348 (1.00) |
0.42 (1.00) |
0.305 (1.00) |
1 (1.00) |
0.0746 (1.00) |
6p loss | 121 (22%) | 433 |
0.108 (1.00) |
0.00239 (1.00) |
0.628 (1.00) |
0.647 (1.00) |
0.455 (1.00) |
0.523 (1.00) |
1 (1.00) |
6q loss | 189 (34%) | 365 |
0.408 (1.00) |
0.00534 (1.00) |
0.115 (1.00) |
0.309 (1.00) |
0.373 (1.00) |
1 (1.00) |
1 (1.00) |
7p loss | 90 (16%) | 464 |
0.098 (1.00) |
0.999 (1.00) |
0.509 (1.00) |
0.0336 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.659 (1.00) |
7q loss | 49 (9%) | 505 |
0.0253 (1.00) |
0.248 (1.00) |
0.31 (1.00) |
0.00339 (1.00) |
0.953 (1.00) |
0.243 (1.00) |
0.565 (1.00) |
8p loss | 227 (41%) | 327 |
0.395 (1.00) |
0.0313 (1.00) |
0.145 (1.00) |
0.031 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.741 (1.00) |
8q loss | 61 (11%) | 493 |
0.634 (1.00) |
0.0342 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.0235 (1.00) |
1 (1.00) |
0.729 (1.00) |
9p loss | 205 (37%) | 349 |
0.562 (1.00) |
0.0319 (1.00) |
0.127 (1.00) |
0.53 (1.00) |
0.662 (1.00) |
0.558 (1.00) |
0.0925 (1.00) |
10p loss | 60 (11%) | 494 |
0.724 (1.00) |
0.0826 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.89 (1.00) |
0.291 (1.00) |
0.73 (1.00) |
10q loss | 86 (16%) | 468 |
0.899 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.412 (1.00) |
0.00363 (1.00) |
0.233 (1.00) |
11p loss | 139 (25%) | 415 |
0.656 (1.00) |
0.0256 (1.00) |
1 (1.00) |
0.537 (1.00) |
0.49 (1.00) |
1 (1.00) |
0.53 (1.00) |
11q loss | 103 (19%) | 451 |
0.904 (1.00) |
0.0755 (1.00) |
0.562 (1.00) |
0.395 (1.00) |
0.372 (1.00) |
0.461 (1.00) |
0.781 (1.00) |
12p loss | 49 (9%) | 505 |
0.813 (1.00) |
0.12 (1.00) |
1 (1.00) |
0.113 (1.00) |
0.0214 (1.00) |
1 (1.00) |
0.126 (1.00) |
12q loss | 72 (13%) | 482 |
0.294 (1.00) |
0.446 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.0055 (1.00) |
1 (1.00) |
0.194 (1.00) |
13q loss | 251 (45%) | 303 |
0.307 (1.00) |
0.84 (1.00) |
0.457 (1.00) |
0.496 (1.00) |
0.207 (1.00) |
1 (1.00) |
0.444 (1.00) |
14q loss | 160 (29%) | 394 |
0.413 (1.00) |
0.0967 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.0456 (1.00) |
0.561 (1.00) |
0.633 (1.00) |
15q loss | 213 (38%) | 341 |
0.89 (1.00) |
0.0447 (1.00) |
0.273 (1.00) |
0.65 (1.00) |
0.113 (1.00) |
0.562 (1.00) |
0.182 (1.00) |
16p loss | 257 (46%) | 297 |
0.12 (1.00) |
0.959 (1.00) |
0.466 (1.00) |
0.259 (1.00) |
0.222 (1.00) |
0.599 (1.00) |
0.231 (1.00) |
16q loss | 346 (62%) | 208 |
0.192 (1.00) |
0.00304 (1.00) |
0.779 (1.00) |
0.0536 (1.00) |
0.391 (1.00) |
1 (1.00) |
0.18 (1.00) |
17p loss | 416 (75%) | 138 |
0.919 (1.00) |
0.0213 (1.00) |
0.26 (1.00) |
0.883 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.802 (1.00) |
17q loss | 319 (58%) | 235 |
0.377 (1.00) |
0.0484 (1.00) |
1 (1.00) |
0.0547 (1.00) |
0.702 (1.00) |
0.266 (1.00) |
0.061 (1.00) |
18p loss | 179 (32%) | 375 |
0.533 (1.00) |
0.815 (1.00) |
0.791 (1.00) |
0.752 (1.00) |
0.108 (1.00) |
0.245 (1.00) |
0.0271 (1.00) |
18q loss | 225 (41%) | 329 |
0.53 (1.00) |
0.838 (1.00) |
0.767 (1.00) |
0.65 (1.00) |
0.386 (1.00) |
0.569 (1.00) |
0.0461 (1.00) |
19p loss | 137 (25%) | 417 |
0.68 (1.00) |
0.124 (1.00) |
0.68 (1.00) |
0.549 (1.00) |
0.537 (1.00) |
0.574 (1.00) |
0.614 (1.00) |
19q loss | 137 (25%) | 417 |
0.954 (1.00) |
0.756 (1.00) |
0.68 (1.00) |
0.482 (1.00) |
0.69 (1.00) |
1 (1.00) |
0.449 (1.00) |
20p loss | 35 (6%) | 519 |
0.0308 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.00339 (1.00) |
0.765 (1.00) |
0.178 (1.00) |
0.122 (1.00) |
20q loss | 21 (4%) | 533 |
0.0397 (1.00) |
0.796 (1.00) |
1 (1.00) |
0.00339 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.779 (1.00) |
21q loss | 145 (26%) | 409 |
0.654 (1.00) |
0.955 (1.00) |
1 (1.00) |
0.508 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.265 (1.00) |
22q loss | 376 (68%) | 178 |
0.281 (1.00) |
0.179 (1.00) |
0.386 (1.00) |
0.954 (1.00) |
0.188 (1.00) |
0.555 (1.00) |
1 (1.00) |
Xq loss | 99 (18%) | 455 |
0.353 (1.00) |
0.655 (1.00) |
0.546 (1.00) |
0.485 (1.00) |
0.885 (1.00) |
1 (1.00) |
0.776 (1.00) |
P value = 2.19e-07 (t-test), Q value = 0.00012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
2P GAIN MUTATED | 122 | 64.5 (11.0) |
2P GAIN WILD-TYPE | 421 | 58.4 (11.4) |
P value = 7.09e-07 (t-test), Q value = 0.00039
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
3Q GAIN MUTATED | 200 | 62.9 (11.0) |
3Q GAIN WILD-TYPE | 343 | 57.9 (11.6) |
P value = 3.74e-05 (t-test), Q value = 0.02
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
10P GAIN MUTATED | 129 | 63.3 (10.7) |
10P GAIN WILD-TYPE | 414 | 58.7 (11.7) |
P value = 3e-08 (t-test), Q value = 1.7e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
12P GAIN MUTATED | 196 | 63.4 (11.2) |
12P GAIN WILD-TYPE | 347 | 57.7 (11.4) |
P value = 3.23e-06 (t-test), Q value = 0.0018
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
12Q GAIN MUTATED | 112 | 64.1 (10.5) |
12Q GAIN WILD-TYPE | 431 | 58.6 (11.6) |
P value = 2.5e-06 (t-test), Q value = 0.0014
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
20P GAIN MUTATED | 225 | 62.5 (11.4) |
20P GAIN WILD-TYPE | 318 | 57.8 (11.4) |
P value = 7.92e-07 (t-test), Q value = 0.00044
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
20Q GAIN MUTATED | 261 | 62.3 (11.7) |
20Q GAIN WILD-TYPE | 282 | 57.4 (11.0) |
P value = 3.22e-06 (t-test), Q value = 0.0018
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 543 | 59.8 (11.6) |
9Q LOSS MUTATED | 228 | 62.5 (11.3) |
9Q LOSS WILD-TYPE | 315 | 57.8 (11.5) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = OV.clin.merged.picked.txt
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Number of patients = 554
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Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 7
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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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.