This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 68 focal events and 8 clinical features across 562 patients, 11 significant findings detected with Q value < 0.25.
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amp_1q21.3 cnv correlated to 'AGE'.
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amp_1q42.2 cnv correlated to 'AGE'.
-
amp_10p15.3 cnv correlated to 'AGE'.
-
amp_12p13.33 cnv correlated to 'AGE'.
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amp_12p12.1 cnv correlated to 'AGE'.
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amp_19q12 cnv correlated to 'AGE'.
-
amp_19q13.2 cnv correlated to 'AGE'.
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amp_20q11.21 cnv correlated to 'AGE'.
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amp_20q13.33 cnv correlated to 'AGE'.
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del_6q27 cnv correlated to 'AGE'.
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del_16q23.1 cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE |
PRIMARY SITE OF DISEASE |
KARNOFSKY PERFORMANCE SCORE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 1q21 3 | 358 (64%) | 204 |
0.246 (1.00) |
4.41e-06 (0.00239) |
0.126 (1.00) |
0.473 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.982 (1.00) |
1 (1.00) |
amp 1q42 2 | 308 (55%) | 254 |
0.196 (1.00) |
0.000447 (0.239) |
0.251 (1.00) |
0.795 (1.00) |
0.592 (1.00) |
0.876 (1.00) |
0.675 (1.00) |
0.533 (1.00) |
amp 10p15 3 | 244 (43%) | 318 |
0.166 (1.00) |
0.00045 (0.241) |
0.156 (1.00) |
0.947 (1.00) |
0.582 (1.00) |
0.759 (1.00) |
0.0231 (1.00) |
0.196 (1.00) |
amp 12p13 33 | 320 (57%) | 242 |
0.63 (1.00) |
3.44e-07 (0.000186) |
0.758 (1.00) |
0.534 (1.00) |
1 (1.00) |
0.343 (1.00) |
0.947 (1.00) |
1 (1.00) |
amp 12p12 1 | 305 (54%) | 257 |
0.0495 (1.00) |
3.9e-08 (2.12e-05) |
0.25 (1.00) |
0.286 (1.00) |
0.595 (1.00) |
1 (1.00) |
0.443 (1.00) |
1 (1.00) |
amp 19q12 | 315 (56%) | 247 |
0.479 (1.00) |
1.57e-05 (0.00843) |
0.158 (1.00) |
0.616 (1.00) |
1 (1.00) |
1 (1.00) |
0.466 (1.00) |
1 (1.00) |
amp 19q13 2 | 238 (42%) | 324 |
0.0118 (1.00) |
7.93e-06 (0.00428) |
0.153 (1.00) |
0.96 (1.00) |
0.577 (1.00) |
0.212 (1.00) |
0.00574 (1.00) |
0.748 (1.00) |
amp 20q11 21 | 335 (60%) | 227 |
0.0825 (1.00) |
4.53e-08 (2.46e-05) |
1 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.582 (1.00) |
0.34 (1.00) |
0.749 (1.00) |
amp 20q13 33 | 389 (69%) | 173 |
0.392 (1.00) |
1.05e-05 (0.00564) |
1 (1.00) |
0.808 (1.00) |
1 (1.00) |
0.0805 (1.00) |
0.101 (1.00) |
0.73 (1.00) |
del 6q27 | 375 (67%) | 187 |
0.339 (1.00) |
0.000444 (0.238) |
1 (1.00) |
0.618 (1.00) |
1 (1.00) |
0.871 (1.00) |
0.954 (1.00) |
1 (1.00) |
del 16q23 1 | 439 (78%) | 123 |
0.238 (1.00) |
0.000273 (0.146) |
0.631 (1.00) |
0.116 (1.00) |
1 (1.00) |
0.0948 (1.00) |
1 (1.00) |
0.244 (1.00) |
amp 1p34 3 | 285 (51%) | 277 |
0.0217 (1.00) |
0.0153 (1.00) |
1 (1.00) |
0.833 (1.00) |
0.249 (1.00) |
0.476 (1.00) |
0.0775 (1.00) |
1 (1.00) |
amp 2p23 2 | 240 (43%) | 322 |
0.735 (1.00) |
0.107 (1.00) |
0.757 (1.00) |
0.901 (1.00) |
1 (1.00) |
0.662 (1.00) |
0.93 (1.00) |
1 (1.00) |
amp 2q31 2 | 256 (46%) | 306 |
0.145 (1.00) |
0.0179 (1.00) |
0.754 (1.00) |
0.621 (1.00) |
0.0939 (1.00) |
0.873 (1.00) |
0.831 (1.00) |
0.338 (1.00) |
amp 3q26 2 | 469 (83%) | 93 |
0.879 (1.00) |
0.00147 (0.782) |
1 (1.00) |
0.0138 (1.00) |
1 (1.00) |
0.778 (1.00) |
0.443 (1.00) |
0.648 (1.00) |
amp 4p16 3 | 156 (28%) | 406 |
0.587 (1.00) |
0.673 (1.00) |
0.725 (1.00) |
0.156 (1.00) |
0.188 (1.00) |
0.53 (1.00) |
0.213 (1.00) |
0.734 (1.00) |
amp 4q13 3 | 110 (20%) | 452 |
0.294 (1.00) |
0.209 (1.00) |
0.584 (1.00) |
0.219 (1.00) |
0.48 (1.00) |
0.412 (1.00) |
0.414 (1.00) |
1 (1.00) |
amp 5p15 33 | 301 (54%) | 261 |
0.0818 (1.00) |
0.00694 (1.00) |
0.749 (1.00) |
0.795 (1.00) |
0.6 (1.00) |
0.0477 (1.00) |
0.873 (1.00) |
0.753 (1.00) |
amp 6p22 3 | 293 (52%) | 269 |
0.119 (1.00) |
0.00585 (1.00) |
1 (1.00) |
0.523 (1.00) |
1 (1.00) |
0.511 (1.00) |
0.591 (1.00) |
0.343 (1.00) |
amp 7q36 3 | 306 (54%) | 256 |
0.134 (1.00) |
0.621 (1.00) |
1 (1.00) |
0.0223 (1.00) |
0.594 (1.00) |
0.213 (1.00) |
0.154 (1.00) |
0.348 (1.00) |
amp 8p11 21 | 206 (37%) | 356 |
0.245 (1.00) |
0.00102 (0.545) |
0.124 (1.00) |
0.884 (1.00) |
0.558 (1.00) |
0.16 (1.00) |
1 (1.00) |
1 (1.00) |
amp 8q24 21 | 444 (79%) | 118 |
0.489 (1.00) |
0.0897 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.508 (1.00) |
0.392 (1.00) |
0.639 (1.00) |
0.437 (1.00) |
amp 10q22 3 | 178 (32%) | 384 |
0.562 (1.00) |
0.157 (1.00) |
0.0975 (1.00) |
0.96 (1.00) |
1 (1.00) |
0.455 (1.00) |
0.267 (1.00) |
1 (1.00) |
amp 11q14 1 | 249 (44%) | 313 |
0.473 (1.00) |
0.503 (1.00) |
0.254 (1.00) |
0.365 (1.00) |
1 (1.00) |
1 (1.00) |
0.829 (1.00) |
0.524 (1.00) |
amp 14q11 2 | 144 (26%) | 418 |
0.738 (1.00) |
0.0588 (1.00) |
0.129 (1.00) |
0.394 (1.00) |
0.163 (1.00) |
0.837 (1.00) |
0.519 (1.00) |
0.139 (1.00) |
amp 14q32 33 | 152 (27%) | 410 |
0.503 (1.00) |
0.0108 (1.00) |
0.717 (1.00) |
0.424 (1.00) |
0.0195 (1.00) |
1 (1.00) |
0.793 (1.00) |
0.717 (1.00) |
amp 15q26 3 | 157 (28%) | 405 |
0.0685 (1.00) |
0.182 (1.00) |
0.735 (1.00) |
0.443 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.521 (1.00) |
0.731 (1.00) |
amp 17q25 3 | 209 (37%) | 353 |
0.0801 (1.00) |
0.657 (1.00) |
0.262 (1.00) |
0.67 (1.00) |
1 (1.00) |
0.0894 (1.00) |
0.655 (1.00) |
1 (1.00) |
amp 18q11 2 | 138 (25%) | 424 |
0.666 (1.00) |
0.0869 (1.00) |
0.117 (1.00) |
0.162 (1.00) |
0.571 (1.00) |
0.836 (1.00) |
0.659 (1.00) |
0.264 (1.00) |
amp 19p13 12 | 306 (54%) | 256 |
0.233 (1.00) |
0.0513 (1.00) |
0.456 (1.00) |
0.576 (1.00) |
0.594 (1.00) |
0.416 (1.00) |
0.961 (1.00) |
1 (1.00) |
amp 20p13 | 311 (55%) | 251 |
0.281 (1.00) |
0.00131 (0.698) |
0.753 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.382 (1.00) |
0.824 (1.00) |
0.522 (1.00) |
amp 22q12 2 | 89 (16%) | 473 |
0.557 (1.00) |
0.0375 (1.00) |
0.506 (1.00) |
0.497 (1.00) |
1 (1.00) |
1 (1.00) |
0.948 (1.00) |
0.167 (1.00) |
amp xp11 23 | 154 (27%) | 408 |
0.247 (1.00) |
0.0894 (1.00) |
0.0686 (1.00) |
0.441 (1.00) |
0.565 (1.00) |
0.33 (1.00) |
0.833 (1.00) |
1 (1.00) |
amp xq28 | 214 (38%) | 348 |
0.481 (1.00) |
0.652 (1.00) |
0.78 (1.00) |
0.598 (1.00) |
0.0547 (1.00) |
0.876 (1.00) |
0.831 (1.00) |
0.329 (1.00) |
del 1p36 11 | 263 (47%) | 299 |
0.183 (1.00) |
0.272 (1.00) |
0.75 (1.00) |
0.323 (1.00) |
1 (1.00) |
1 (1.00) |
0.518 (1.00) |
0.526 (1.00) |
del 1q41 | 92 (16%) | 470 |
0.821 (1.00) |
0.386 (1.00) |
1 (1.00) |
0.628 (1.00) |
0.416 (1.00) |
0.605 (1.00) |
0.0645 (1.00) |
0.373 (1.00) |
del 2p25 3 | 120 (21%) | 442 |
0.922 (1.00) |
0.437 (1.00) |
0.623 (1.00) |
0.971 (1.00) |
0.514 (1.00) |
0.022 (1.00) |
0.496 (1.00) |
0.461 (1.00) |
del 2q22 1 | 133 (24%) | 429 |
0.412 (1.00) |
0.277 (1.00) |
0.664 (1.00) |
0.558 (1.00) |
1 (1.00) |
0.644 (1.00) |
0.495 (1.00) |
0.0673 (1.00) |
del 2q37 3 | 170 (30%) | 392 |
0.472 (1.00) |
0.0259 (1.00) |
0.358 (1.00) |
0.503 (1.00) |
0.219 (1.00) |
0.172 (1.00) |
0.42 (1.00) |
0.492 (1.00) |
del 3p26 2 | 206 (37%) | 356 |
0.764 (1.00) |
0.00327 (1.00) |
0.125 (1.00) |
0.34 (1.00) |
0.0488 (1.00) |
0.287 (1.00) |
0.841 (1.00) |
1 (1.00) |
del 4q22 1 | 384 (68%) | 178 |
0.659 (1.00) |
0.795 (1.00) |
0.79 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.846 (1.00) |
0.815 (1.00) |
0.173 (1.00) |
del 4q34 3 | 410 (73%) | 152 |
0.956 (1.00) |
0.489 (1.00) |
0.718 (1.00) |
0.301 (1.00) |
0.567 (1.00) |
0.571 (1.00) |
0.954 (1.00) |
0.0673 (1.00) |
del 5q11 2 | 341 (61%) | 221 |
0.767 (1.00) |
0.816 (1.00) |
0.771 (1.00) |
0.309 (1.00) |
0.565 (1.00) |
0.209 (1.00) |
0.087 (1.00) |
1 (1.00) |
del 5q13 2 | 406 (72%) | 156 |
0.245 (1.00) |
0.895 (1.00) |
0.732 (1.00) |
0.148 (1.00) |
0.188 (1.00) |
0.24 (1.00) |
0.215 (1.00) |
1 (1.00) |
del 7p22 1 | 245 (44%) | 317 |
0.0696 (1.00) |
0.0108 (1.00) |
0.758 (1.00) |
0.27 (1.00) |
1 (1.00) |
0.18 (1.00) |
0.693 (1.00) |
0.749 (1.00) |
del 8p23 3 | 378 (67%) | 184 |
0.19 (1.00) |
0.0623 (1.00) |
1 (1.00) |
0.91 (1.00) |
1 (1.00) |
0.86 (1.00) |
0.905 (1.00) |
0.176 (1.00) |
del 8p21 2 | 394 (70%) | 168 |
0.712 (1.00) |
0.0634 (1.00) |
1 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.293 (1.00) |
del 9p24 3 | 255 (45%) | 307 |
0.755 (1.00) |
0.0111 (1.00) |
0.453 (1.00) |
0.95 (1.00) |
0.593 (1.00) |
0.75 (1.00) |
0.892 (1.00) |
1 (1.00) |
del 9q34 13 | 336 (60%) | 226 |
0.905 (1.00) |
0.101 (1.00) |
0.769 (1.00) |
0.717 (1.00) |
0.277 (1.00) |
0.5 (1.00) |
0.685 (1.00) |
0.745 (1.00) |
del 10p15 3 | 117 (21%) | 445 |
0.368 (1.00) |
0.92 (1.00) |
0.606 (1.00) |
0.792 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.305 (1.00) |
0.695 (1.00) |
del 10q24 2 | 245 (44%) | 317 |
0.268 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.181 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.0262 (1.00) |
1 (1.00) |
del 11p15 5 | 332 (59%) | 230 |
0.115 (1.00) |
0.383 (1.00) |
0.0271 (1.00) |
0.299 (1.00) |
1 (1.00) |
0.873 (1.00) |
0.852 (1.00) |
1 (1.00) |
del 11q25 | 193 (34%) | 369 |
0.707 (1.00) |
0.0672 (1.00) |
0.225 (1.00) |
0.31 (1.00) |
0.272 (1.00) |
0.252 (1.00) |
0.916 (1.00) |
0.036 (1.00) |
del 12q24 33 | 211 (38%) | 351 |
0.822 (1.00) |
0.081 (1.00) |
0.129 (1.00) |
0.842 (1.00) |
0.295 (1.00) |
0.0412 (1.00) |
0.59 (1.00) |
0.0372 (1.00) |
del 13q14 2 | 352 (63%) | 210 |
0.0842 (1.00) |
0.436 (1.00) |
0.78 (1.00) |
0.771 (1.00) |
0.559 (1.00) |
0.331 (1.00) |
0.157 (1.00) |
0.745 (1.00) |
del 14q23 3 | 296 (53%) | 266 |
0.817 (1.00) |
0.44 (1.00) |
0.473 (1.00) |
0.0469 (1.00) |
0.105 (1.00) |
0.76 (1.00) |
0.276 (1.00) |
0.113 (1.00) |
del 15q15 1 | 356 (63%) | 206 |
0.817 (1.00) |
0.0039 (1.00) |
0.412 (1.00) |
0.318 (1.00) |
0.302 (1.00) |
1 (1.00) |
0.652 (1.00) |
0.328 (1.00) |
del 16p13 3 | 303 (54%) | 259 |
0.949 (1.00) |
0.769 (1.00) |
0.752 (1.00) |
0.399 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.806 (1.00) |
0.521 (1.00) |
del 16q22 1 | 449 (80%) | 113 |
0.765 (1.00) |
0.00983 (1.00) |
0.187 (1.00) |
0.273 (1.00) |
1 (1.00) |
0.167 (1.00) |
0.963 (1.00) |
0.421 (1.00) |
del 17p12 | 477 (85%) | 85 |
0.974 (1.00) |
0.823 (1.00) |
0.485 (1.00) |
0.765 (1.00) |
1 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.657 (1.00) |
del 17q11 2 | 460 (82%) | 102 |
0.542 (1.00) |
0.0115 (1.00) |
0.0673 (1.00) |
0.759 (1.00) |
1 (1.00) |
0.873 (1.00) |
0.481 (1.00) |
1 (1.00) |
del 18q23 | 372 (66%) | 190 |
0.817 (1.00) |
0.426 (1.00) |
0.216 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.452 (1.00) |
0.311 (1.00) |
del 19p13 3 | 495 (88%) | 67 |
0.231 (1.00) |
0.0291 (1.00) |
1 (1.00) |
0.0707 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.186 (1.00) |
1 (1.00) |
del 19q13 33 | 291 (52%) | 271 |
0.527 (1.00) |
0.509 (1.00) |
1 (1.00) |
0.239 (1.00) |
0.25 (1.00) |
0.356 (1.00) |
0.0792 (1.00) |
0.113 (1.00) |
del 19q13 43 | 275 (49%) | 287 |
0.41 (1.00) |
0.0314 (1.00) |
1 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.143 (1.00) |
0.205 (1.00) |
del 21q22 3 | 220 (39%) | 342 |
0.405 (1.00) |
0.408 (1.00) |
0.771 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.662 (1.00) |
0.678 (1.00) |
0.329 (1.00) |
del 22q13 32 | 489 (87%) | 73 |
0.996 (1.00) |
0.997 (1.00) |
0.433 (1.00) |
0.766 (1.00) |
1 (1.00) |
0.673 (1.00) |
0.786 (1.00) |
1 (1.00) |
del xp21 1 | 347 (62%) | 215 |
0.971 (1.00) |
0.39 (1.00) |
1 (1.00) |
0.99 (1.00) |
0.29 (1.00) |
0.761 (1.00) |
0.648 (1.00) |
0.536 (1.00) |
P value = 4.41e-06 (Wilcoxon-test), Q value = 0.0024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 2(1Q21.3) MUTATED | 345 | 61.6 (11.0) |
AMP PEAK 2(1Q21.3) WILD-TYPE | 196 | 56.7 (12.1) |
P value = 0.000447 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 3(1Q42.2) MUTATED | 295 | 61.4 (11.3) |
AMP PEAK 3(1Q42.2) WILD-TYPE | 246 | 57.9 (11.7) |
P value = 0.00045 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 14(10P15.3) MUTATED | 238 | 61.7 (11.2) |
AMP PEAK 14(10P15.3) WILD-TYPE | 303 | 58.3 (11.7) |
P value = 3.44e-07 (Wilcoxon-test), Q value = 0.00019
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 17(12P13.33) MUTATED | 308 | 62.0 (10.9) |
AMP PEAK 17(12P13.33) WILD-TYPE | 233 | 56.8 (11.9) |
P value = 3.9e-08 (Wilcoxon-test), Q value = 2.1e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 18(12P12.1) MUTATED | 291 | 62.4 (11.2) |
AMP PEAK 18(12P12.1) WILD-TYPE | 250 | 56.8 (11.3) |
P value = 1.57e-05 (Wilcoxon-test), Q value = 0.0084
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 25(19Q12) MUTATED | 304 | 61.7 (11.1) |
AMP PEAK 25(19Q12) WILD-TYPE | 237 | 57.3 (11.8) |
P value = 7.93e-06 (Wilcoxon-test), Q value = 0.0043
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 26(19Q13.2) MUTATED | 231 | 62.4 (11.2) |
AMP PEAK 26(19Q13.2) WILD-TYPE | 310 | 57.8 (11.6) |
P value = 4.53e-08 (Wilcoxon-test), Q value = 2.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 28(20Q11.21) MUTATED | 322 | 62.1 (11.5) |
AMP PEAK 28(20Q11.21) WILD-TYPE | 219 | 56.4 (10.9) |
P value = 1.05e-05 (Wilcoxon-test), Q value = 0.0056
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
AMP PEAK 29(20Q13.33) MUTATED | 376 | 61.2 (11.6) |
AMP PEAK 29(20Q13.33) WILD-TYPE | 165 | 56.5 (11.1) |
P value = 0.000444 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
DEL PEAK 11(6Q27) MUTATED | 360 | 58.6 (11.5) |
DEL PEAK 11(6Q27) WILD-TYPE | 181 | 62.2 (11.6) |
P value = 0.000273 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 541 | 59.8 (11.6) |
DEL PEAK 27(16Q23.1) MUTATED | 425 | 60.8 (11.5) |
DEL PEAK 27(16Q23.1) WILD-TYPE | 116 | 56.1 (11.2) |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = OV-TP.merged_data.txt
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Number of patients = 562
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Number of significantly focal cnvs = 68
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Number of selected clinical features = 8
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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 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.