This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 71 focal events and 8 clinical features across 573 patients, 26 significant findings detected with Q value < 0.25.
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amp_1p34.3 cnv correlated to 'Time to Death'.
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amp_1q21.3 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_1q42.2 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_3q26.2 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_5p15.33 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_6p22.3 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_8p11.21 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_10p15.3 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_12p13.33 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_12p12.1 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_12q15 cnv correlated to 'YEARS_TO_BIRTH' and 'TUMOR_TISSUE_SITE'.
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amp_19q12 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_19q13.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'RACE'.
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amp_20p13 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_20q11.21 cnv correlated to 'YEARS_TO_BIRTH'.
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amp_20q13.33 cnv correlated to 'YEARS_TO_BIRTH'.
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del_3p26.2 cnv correlated to 'YEARS_TO_BIRTH'.
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del_6q27 cnv correlated to 'YEARS_TO_BIRTH'.
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del_7p22.1 cnv correlated to 'YEARS_TO_BIRTH'.
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del_11p15.5 cnv correlated to 'TUMOR_TISSUE_SITE'.
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del_15q11.2 cnv correlated to 'YEARS_TO_BIRTH'.
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del_15q15.1 cnv correlated to 'YEARS_TO_BIRTH'.
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del_16q23.1 cnv correlated to 'YEARS_TO_BIRTH'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
RESIDUAL TUMOR |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 19q13 2 | 242 (42%) | 331 |
0.00598 (0.17) |
3.06e-06 (0.000348) |
0.0739 (0.594) |
1 (1.00) |
0.845 (1.00) |
0.736 (1.00) |
0.0111 (0.247) |
0.747 (1.00) |
amp 12q15 | 221 (39%) | 352 |
0.245 (0.903) |
4.56e-07 (6.48e-05) |
0.00764 (0.207) |
0.377 (0.974) |
0.343 (0.964) |
0.4 (0.978) |
0.762 (1.00) |
0.739 (1.00) |
amp 1p34 3 | 291 (51%) | 282 |
0.0108 (0.247) |
0.0164 (0.31) |
1 (1.00) |
0.686 (1.00) |
0.654 (1.00) |
0.399 (0.978) |
0.12 (0.692) |
1 (1.00) |
amp 1q21 3 | 364 (64%) | 209 |
0.293 (0.931) |
8.07e-06 (0.000655) |
0.379 (0.975) |
0.363 (0.974) |
0.364 (0.974) |
0.0878 (0.648) |
0.956 (1.00) |
1 (1.00) |
amp 1q42 2 | 317 (55%) | 256 |
0.317 (0.954) |
0.000784 (0.0342) |
0.174 (0.81) |
0.183 (0.83) |
0.749 (1.00) |
0.883 (1.00) |
0.957 (1.00) |
0.53 (1.00) |
amp 3q26 2 | 479 (84%) | 94 |
0.784 (1.00) |
0.00206 (0.0835) |
1 (1.00) |
0.187 (0.845) |
0.0256 (0.415) |
0.828 (1.00) |
0.54 (1.00) |
0.648 (1.00) |
amp 5p15 33 | 306 (53%) | 267 |
0.0568 (0.566) |
0.0113 (0.247) |
0.514 (1.00) |
0.189 (0.845) |
0.735 (1.00) |
0.165 (0.81) |
0.825 (1.00) |
0.753 (1.00) |
amp 6p22 3 | 300 (52%) | 273 |
0.0303 (0.465) |
0.00267 (0.101) |
1 (1.00) |
1 (1.00) |
0.289 (0.927) |
0.87 (1.00) |
0.754 (1.00) |
0.342 (0.964) |
amp 8p11 21 | 210 (37%) | 363 |
0.269 (0.91) |
0.000568 (0.0269) |
0.113 (0.69) |
1 (1.00) |
0.941 (1.00) |
0.785 (1.00) |
0.978 (1.00) |
1 (1.00) |
amp 10p15 3 | 250 (44%) | 323 |
0.132 (0.74) |
0.000468 (0.0242) |
0.317 (0.954) |
0.664 (1.00) |
0.979 (1.00) |
0.65 (1.00) |
0.272 (0.91) |
0.197 (0.846) |
amp 12p13 33 | 328 (57%) | 245 |
0.839 (1.00) |
1.86e-07 (3.53e-05) |
0.4 (0.978) |
0.0759 (0.599) |
0.79 (1.00) |
0.274 (0.91) |
1 (1.00) |
1 (1.00) |
amp 12p12 1 | 312 (54%) | 261 |
0.158 (0.81) |
1.83e-08 (5.89e-06) |
0.128 (0.728) |
1 (1.00) |
0.495 (1.00) |
1 (1.00) |
0.514 (1.00) |
1 (1.00) |
amp 19q12 | 318 (55%) | 255 |
0.233 (0.889) |
1.75e-05 (0.00124) |
0.043 (0.499) |
0.658 (1.00) |
0.715 (1.00) |
0.23 (0.886) |
0.377 (0.974) |
1 (1.00) |
amp 20p13 | 315 (55%) | 258 |
0.252 (0.91) |
0.00526 (0.166) |
0.323 (0.954) |
0.657 (1.00) |
0.169 (0.81) |
0.752 (1.00) |
0.0742 (0.594) |
0.524 (1.00) |
amp 20q11 21 | 344 (60%) | 229 |
0.159 (0.81) |
2.07e-08 (5.89e-06) |
1 (1.00) |
1 (1.00) |
0.361 (0.974) |
0.695 (1.00) |
0.432 (1.00) |
0.748 (1.00) |
amp 20q13 33 | 399 (70%) | 174 |
0.405 (0.978) |
6.57e-06 (0.000622) |
0.597 (1.00) |
0.641 (1.00) |
0.475 (1.00) |
0.0632 (0.592) |
0.0964 (0.677) |
0.731 (1.00) |
del 3p26 2 | 207 (36%) | 366 |
0.492 (1.00) |
0.00367 (0.13) |
0.273 (0.91) |
1 (1.00) |
0.405 (0.978) |
0.532 (1.00) |
0.355 (0.974) |
1 (1.00) |
del 6q27 | 375 (65%) | 198 |
0.115 (0.69) |
0.000102 (0.00643) |
0.371 (0.974) |
0.658 (1.00) |
0.968 (1.00) |
0.782 (1.00) |
0.88 (1.00) |
1 (1.00) |
del 7p22 1 | 250 (44%) | 323 |
0.154 (0.81) |
0.00824 (0.213) |
0.402 (0.978) |
0.661 (1.00) |
0.486 (1.00) |
0.572 (1.00) |
0.803 (1.00) |
0.75 (1.00) |
del 11p15 5 | 340 (59%) | 233 |
0.0644 (0.592) |
0.363 (0.974) |
0.011 (0.247) |
0.653 (1.00) |
0.539 (1.00) |
0.753 (1.00) |
0.84 (1.00) |
1 (1.00) |
del 15q11 2 | 295 (51%) | 278 |
0.924 (1.00) |
0.00427 (0.143) |
0.624 (1.00) |
1 (1.00) |
0.557 (1.00) |
0.601 (1.00) |
0.195 (0.846) |
0.752 (1.00) |
del 15q15 1 | 359 (63%) | 214 |
0.956 (1.00) |
0.00571 (0.17) |
0.793 (1.00) |
1 (1.00) |
0.708 (1.00) |
1 (1.00) |
0.516 (1.00) |
0.327 (0.954) |
del 16q23 1 | 447 (78%) | 126 |
0.202 (0.846) |
0.000464 (0.0242) |
0.708 (1.00) |
0.59 (1.00) |
0.0657 (0.592) |
0.0499 (0.534) |
0.934 (1.00) |
0.249 (0.91) |
amp 2p23 2 | 247 (43%) | 326 |
0.439 (1.00) |
0.0926 (0.674) |
1 (1.00) |
1 (1.00) |
0.843 (1.00) |
0.783 (1.00) |
0.776 (1.00) |
1 (1.00) |
amp 2q31 2 | 259 (45%) | 314 |
0.231 (0.886) |
0.0245 (0.409) |
0.321 (0.954) |
0.661 (1.00) |
0.903 (1.00) |
0.848 (1.00) |
0.652 (1.00) |
0.338 (0.963) |
amp 4p16 3 | 159 (28%) | 414 |
0.21 (0.846) |
0.647 (1.00) |
0.572 (1.00) |
0.625 (1.00) |
0.236 (0.893) |
0.747 (1.00) |
0.305 (0.952) |
0.727 (1.00) |
amp 4q13 3 | 113 (20%) | 460 |
0.1 (0.686) |
0.198 (0.846) |
0.259 (0.91) |
0.275 (0.91) |
0.555 (1.00) |
0.104 (0.689) |
0.526 (1.00) |
1 (1.00) |
amp 7q36 3 | 316 (55%) | 257 |
0.0783 (0.609) |
0.715 (1.00) |
1 (1.00) |
1 (1.00) |
0.0805 (0.618) |
0.849 (1.00) |
0.0724 (0.594) |
0.342 (0.964) |
amp 8q24 21 | 455 (79%) | 118 |
0.462 (1.00) |
0.0981 (0.679) |
1 (1.00) |
0.266 (0.91) |
0.801 (1.00) |
0.923 (1.00) |
0.665 (1.00) |
0.428 (1.00) |
amp 10q22 3 | 182 (32%) | 391 |
0.446 (1.00) |
0.111 (0.69) |
0.0548 (0.556) |
0.658 (1.00) |
0.852 (1.00) |
0.46 (1.00) |
0.272 (0.91) |
1 (1.00) |
amp 11q14 1 | 253 (44%) | 320 |
0.399 (0.978) |
0.574 (1.00) |
0.634 (1.00) |
0.387 (0.978) |
0.76 (1.00) |
0.773 (1.00) |
0.842 (1.00) |
0.524 (1.00) |
amp 14q11 2 | 147 (26%) | 426 |
0.871 (1.00) |
0.0416 (0.492) |
0.0824 (0.624) |
1 (1.00) |
0.469 (1.00) |
0.741 (1.00) |
0.488 (1.00) |
0.141 (0.779) |
amp 14q32 33 | 156 (27%) | 417 |
0.31 (0.954) |
0.0187 (0.339) |
0.394 (0.978) |
0.119 (0.692) |
0.991 (1.00) |
0.956 (1.00) |
0.773 (1.00) |
0.72 (1.00) |
amp 15q26 3 | 160 (28%) | 413 |
0.0468 (0.511) |
0.204 (0.846) |
1 (1.00) |
1 (1.00) |
0.833 (1.00) |
0.868 (1.00) |
0.506 (1.00) |
0.733 (1.00) |
amp 17q25 3 | 212 (37%) | 361 |
0.16 (0.81) |
0.768 (1.00) |
0.619 (1.00) |
0.656 (1.00) |
0.925 (1.00) |
0.0522 (0.539) |
0.763 (1.00) |
1 (1.00) |
amp 18q11 2 | 139 (24%) | 434 |
0.413 (0.989) |
0.11 (0.69) |
0.0716 (0.594) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.553 (1.00) |
0.26 (0.91) |
amp 19p13 12 | 314 (55%) | 259 |
0.552 (1.00) |
0.0414 (0.492) |
0.8 (1.00) |
1 (1.00) |
0.318 (0.954) |
0.265 (0.91) |
0.892 (1.00) |
1 (1.00) |
amp 22q12 2 | 91 (16%) | 482 |
0.427 (1.00) |
0.0413 (0.492) |
0.0945 (0.677) |
1 (1.00) |
0.302 (0.947) |
0.625 (1.00) |
0.936 (1.00) |
0.173 (0.81) |
amp xp11 23 | 159 (28%) | 414 |
0.202 (0.846) |
0.104 (0.689) |
0.0343 (0.492) |
1 (1.00) |
0.554 (1.00) |
0.191 (0.846) |
0.931 (1.00) |
1 (1.00) |
amp xq28 | 217 (38%) | 356 |
0.441 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.372 (0.974) |
0.245 (0.903) |
0.528 (1.00) |
0.821 (1.00) |
0.327 (0.954) |
del 1p36 11 | 266 (46%) | 307 |
0.121 (0.692) |
0.289 (0.927) |
0.627 (1.00) |
1 (1.00) |
0.815 (1.00) |
0.759 (1.00) |
0.268 (0.91) |
0.525 (1.00) |
del 1q41 | 95 (17%) | 478 |
0.473 (1.00) |
0.442 (1.00) |
1 (1.00) |
0.195 (0.846) |
0.979 (1.00) |
0.588 (1.00) |
0.112 (0.69) |
0.377 (0.974) |
del 2p25 3 | 120 (21%) | 453 |
0.783 (1.00) |
0.467 (1.00) |
0.696 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.0395 (0.492) |
0.12 (0.692) |
0.45 (1.00) |
del 2q22 1 | 134 (23%) | 439 |
0.198 (0.846) |
0.296 (0.933) |
0.496 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.666 (1.00) |
0.417 (0.995) |
0.0614 (0.592) |
del 2q37 3 | 172 (30%) | 401 |
0.348 (0.969) |
0.0191 (0.339) |
0.783 (1.00) |
0.163 (0.81) |
0.166 (0.81) |
0.675 (1.00) |
0.802 (1.00) |
1 (1.00) |
del 3q13 31 | 84 (15%) | 489 |
0.42 (0.999) |
0.811 (1.00) |
1 (1.00) |
1 (1.00) |
0.225 (0.881) |
0.437 (1.00) |
0.808 (1.00) |
1 (1.00) |
del 4q22 1 | 390 (68%) | 183 |
0.156 (0.81) |
0.879 (1.00) |
0.799 (1.00) |
0.664 (1.00) |
0.736 (1.00) |
0.853 (1.00) |
0.734 (1.00) |
0.174 (0.81) |
del 4q34 3 | 416 (73%) | 157 |
0.649 (1.00) |
0.46 (1.00) |
0.571 (1.00) |
0.33 (0.954) |
0.152 (0.81) |
0.406 (0.978) |
0.829 (1.00) |
0.0674 (0.594) |
del 5q12 1 | 350 (61%) | 223 |
0.951 (1.00) |
0.678 (1.00) |
0.496 (1.00) |
1 (1.00) |
0.243 (0.903) |
0.376 (0.974) |
0.108 (0.69) |
1 (1.00) |
del 5q13 2 | 414 (72%) | 159 |
0.159 (0.81) |
0.998 (1.00) |
0.401 (0.978) |
0.628 (1.00) |
0.177 (0.81) |
0.213 (0.847) |
0.23 (0.886) |
0.733 (1.00) |
del 8p23 3 | 384 (67%) | 189 |
0.261 (0.91) |
0.0691 (0.594) |
1 (1.00) |
0.666 (1.00) |
0.555 (1.00) |
0.52 (1.00) |
0.862 (1.00) |
0.175 (0.81) |
del 8p21 2 | 401 (70%) | 172 |
0.824 (1.00) |
0.0738 (0.594) |
1 (1.00) |
0.633 (1.00) |
0.894 (1.00) |
0.561 (1.00) |
0.981 (1.00) |
0.293 (0.931) |
del 9p24 3 | 259 (45%) | 314 |
0.915 (1.00) |
0.0153 (0.299) |
0.321 (0.954) |
1 (1.00) |
0.554 (1.00) |
0.816 (1.00) |
0.85 (1.00) |
1 (1.00) |
del 9q34 13 | 341 (60%) | 232 |
0.694 (1.00) |
0.0614 (0.592) |
0.497 (1.00) |
1 (1.00) |
0.962 (1.00) |
0.676 (1.00) |
0.386 (0.978) |
1 (1.00) |
del 10p15 3 | 117 (20%) | 456 |
0.335 (0.961) |
0.881 (1.00) |
0.68 (1.00) |
0.588 (1.00) |
0.831 (1.00) |
1 (1.00) |
0.222 (0.875) |
0.697 (1.00) |
del 10q24 2 | 250 (44%) | 323 |
0.163 (0.81) |
0.0508 (0.535) |
1 (1.00) |
0.656 (1.00) |
0.646 (1.00) |
1 (1.00) |
0.243 (0.903) |
1 (1.00) |
del 11q25 | 200 (35%) | 373 |
0.862 (1.00) |
0.041 (0.492) |
0.158 (0.81) |
1 (1.00) |
0.322 (0.954) |
0.706 (1.00) |
0.9 (1.00) |
0.0382 (0.492) |
del 12q24 33 | 214 (37%) | 359 |
0.849 (1.00) |
0.0741 (0.594) |
0.383 (0.976) |
0.655 (1.00) |
0.636 (1.00) |
0.0449 (0.5) |
0.757 (1.00) |
0.0368 (0.492) |
del 13q14 2 | 359 (63%) | 214 |
0.0356 (0.492) |
0.403 (0.978) |
0.383 (0.976) |
0.37 (0.974) |
0.843 (1.00) |
0.257 (0.91) |
0.276 (0.91) |
0.746 (1.00) |
del 14q23 3 | 303 (53%) | 270 |
0.937 (1.00) |
0.498 (1.00) |
0.177 (0.81) |
0.667 (1.00) |
0.0965 (0.677) |
0.377 (0.974) |
0.348 (0.969) |
0.115 (0.69) |
del 16p13 3 | 309 (54%) | 264 |
0.751 (1.00) |
0.688 (1.00) |
1 (1.00) |
0.669 (1.00) |
0.501 (1.00) |
0.906 (1.00) |
0.87 (1.00) |
0.521 (1.00) |
del 16q22 1 | 457 (80%) | 116 |
0.839 (1.00) |
0.0145 (0.294) |
0.274 (0.91) |
0.588 (1.00) |
0.133 (0.74) |
0.0442 (0.5) |
0.913 (1.00) |
0.428 (1.00) |
del 17p12 | 486 (85%) | 87 |
0.464 (1.00) |
0.772 (1.00) |
0.168 (0.81) |
1 (1.00) |
0.831 (1.00) |
0.491 (1.00) |
0.975 (1.00) |
0.656 (1.00) |
del 17q11 2 | 467 (82%) | 106 |
0.797 (1.00) |
0.0125 (0.263) |
0.0222 (0.383) |
1 (1.00) |
0.994 (1.00) |
1 (1.00) |
0.703 (1.00) |
0.697 (1.00) |
del 18q23 | 377 (66%) | 196 |
0.966 (1.00) |
0.615 (1.00) |
0.154 (0.81) |
1 (1.00) |
0.653 (1.00) |
0.106 (0.69) |
0.287 (0.927) |
1 (1.00) |
del 19p13 3 | 506 (88%) | 67 |
0.329 (0.954) |
0.0263 (0.415) |
1 (1.00) |
1 (1.00) |
0.102 (0.688) |
1 (1.00) |
0.0649 (0.592) |
1 (1.00) |
del 19q13 33 | 296 (52%) | 277 |
0.253 (0.91) |
0.548 (1.00) |
0.806 (1.00) |
1 (1.00) |
0.0847 (0.633) |
0.328 (0.954) |
0.208 (0.846) |
0.114 (0.69) |
del 19q13 43 | 282 (49%) | 291 |
0.205 (0.846) |
0.0336 (0.492) |
1 (1.00) |
0.209 (0.846) |
0.0408 (0.492) |
0.372 (0.974) |
0.213 (0.847) |
0.209 (0.846) |
del 21q22 3 | 224 (39%) | 349 |
0.288 (0.927) |
0.426 (1.00) |
0.792 (1.00) |
1 (1.00) |
0.329 (0.954) |
0.355 (0.974) |
0.642 (1.00) |
0.331 (0.954) |
del 22q13 32 | 498 (87%) | 75 |
0.984 (1.00) |
0.847 (1.00) |
0.285 (0.927) |
1 (1.00) |
0.432 (1.00) |
0.819 (1.00) |
0.799 (1.00) |
1 (1.00) |
del xp21 1 | 352 (61%) | 221 |
0.867 (1.00) |
0.354 (0.974) |
1 (1.00) |
0.654 (1.00) |
0.948 (1.00) |
0.756 (1.00) |
0.913 (1.00) |
0.747 (1.00) |
P value = 0.0108 (logrank test), Q value = 0.25
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 298 | 0.3 - 180.2 (29.4) |
AMP PEAK 1(1P34.3) MUTATED | 286 | 138 | 0.4 - 180.2 (29.6) |
AMP PEAK 1(1P34.3) WILD-TYPE | 273 | 160 | 0.3 - 118.4 (29.4) |
P value = 8.07e-06 (Wilcoxon-test), Q value = 0.00065
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 2(1Q21.3) MUTATED | 351 | 61.5 (10.9) |
AMP PEAK 2(1Q21.3) WILD-TYPE | 201 | 56.9 (12.1) |
P value = 0.000784 (Wilcoxon-test), Q value = 0.034
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 3(1Q42.2) MUTATED | 304 | 61.3 (11.2) |
AMP PEAK 3(1Q42.2) WILD-TYPE | 248 | 58.1 (11.8) |
P value = 0.00206 (Wilcoxon-test), Q value = 0.083
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 6(3Q26.2) MUTATED | 462 | 60.5 (11.3) |
AMP PEAK 6(3Q26.2) WILD-TYPE | 90 | 56.2 (12.3) |
P value = 0.0113 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 9(5P15.33) MUTATED | 297 | 61.0 (11.4) |
AMP PEAK 9(5P15.33) WILD-TYPE | 255 | 58.5 (11.6) |
P value = 0.00267 (Wilcoxon-test), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 10(6P22.3) MUTATED | 290 | 61.2 (11.8) |
AMP PEAK 10(6P22.3) WILD-TYPE | 262 | 58.3 (11.2) |
P value = 0.000568 (Wilcoxon-test), Q value = 0.027
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 12(8P11.21) MUTATED | 200 | 62.1 (10.9) |
AMP PEAK 12(8P11.21) WILD-TYPE | 352 | 58.5 (11.8) |
P value = 0.000468 (Wilcoxon-test), Q value = 0.024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 14(10P15.3) MUTATED | 244 | 61.7 (11.2) |
AMP PEAK 14(10P15.3) WILD-TYPE | 308 | 58.4 (11.7) |
P value = 1.86e-07 (Wilcoxon-test), Q value = 3.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 17(12P13.33) MUTATED | 316 | 62.1 (10.8) |
AMP PEAK 17(12P13.33) WILD-TYPE | 236 | 56.8 (11.9) |
P value = 1.83e-08 (Wilcoxon-test), Q value = 5.9e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 18(12P12.1) MUTATED | 298 | 62.4 (11.2) |
AMP PEAK 18(12P12.1) WILD-TYPE | 254 | 56.8 (11.3) |
P value = 4.56e-07 (Wilcoxon-test), Q value = 6.5e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 19(12Q15) MUTATED | 207 | 63.0 (11.2) |
AMP PEAK 19(12Q15) WILD-TYPE | 345 | 57.9 (11.4) |
P value = 0.00764 (Fisher's exact test), Q value = 0.21
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 3 | 558 | 2 |
AMP PEAK 19(12Q15) MUTATED | 3 | 209 | 2 |
AMP PEAK 19(12Q15) WILD-TYPE | 0 | 349 | 0 |
P value = 1.75e-05 (Wilcoxon-test), Q value = 0.0012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 26(19Q12) MUTATED | 307 | 61.8 (11.1) |
AMP PEAK 26(19Q12) WILD-TYPE | 245 | 57.4 (11.7) |
P value = 0.00598 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 559 | 298 | 0.3 - 180.2 (29.4) |
AMP PEAK 27(19Q13.2) MUTATED | 237 | 135 | 0.3 - 180.2 (24.9) |
AMP PEAK 27(19Q13.2) WILD-TYPE | 322 | 163 | 0.4 - 130.0 (31.4) |
P value = 3.06e-06 (Wilcoxon-test), Q value = 0.00035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 27(19Q13.2) MUTATED | 235 | 62.5 (11.2) |
AMP PEAK 27(19Q13.2) WILD-TYPE | 317 | 57.8 (11.5) |
P value = 0.0111 (Fisher's exact test), Q value = 0.25
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER | WHITE |
---|---|---|---|---|---|
ALL | 3 | 19 | 34 | 1 | 476 |
AMP PEAK 27(19Q13.2) MUTATED | 2 | 4 | 8 | 1 | 210 |
AMP PEAK 27(19Q13.2) WILD-TYPE | 1 | 15 | 26 | 0 | 266 |
P value = 0.00526 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 28(20P13) MUTATED | 305 | 61.1 (11.7) |
AMP PEAK 28(20P13) WILD-TYPE | 247 | 58.2 (11.2) |
P value = 2.07e-08 (Wilcoxon-test), Q value = 5.9e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 29(20Q11.21) MUTATED | 331 | 62.1 (11.5) |
AMP PEAK 29(20Q11.21) WILD-TYPE | 221 | 56.4 (10.9) |
P value = 6.57e-06 (Wilcoxon-test), Q value = 0.00062
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
AMP PEAK 30(20Q13.33) MUTATED | 386 | 61.3 (11.5) |
AMP PEAK 30(20Q13.33) WILD-TYPE | 166 | 56.5 (11.1) |
P value = 0.00367 (Wilcoxon-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 6(3P26.2) MUTATED | 199 | 61.8 (11.6) |
DEL PEAK 6(3P26.2) WILD-TYPE | 353 | 58.7 (11.4) |
P value = 0.000102 (Wilcoxon-test), Q value = 0.0064
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 12(6Q27) MUTATED | 360 | 58.5 (11.4) |
DEL PEAK 12(6Q27) WILD-TYPE | 192 | 62.4 (11.5) |
P value = 0.00824 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 13(7P22.1) MUTATED | 240 | 58.5 (11.4) |
DEL PEAK 13(7P22.1) WILD-TYPE | 312 | 60.9 (11.6) |
P value = 0.011 (Fisher's exact test), Q value = 0.25
nPatients | OMENTUM | OVARY | PERITONEUM OVARY |
---|---|---|---|
ALL | 3 | 558 | 2 |
DEL PEAK 20(11P15.5) MUTATED | 0 | 336 | 0 |
DEL PEAK 20(11P15.5) WILD-TYPE | 3 | 222 | 2 |
P value = 0.00427 (Wilcoxon-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 25(15Q11.2) MUTATED | 284 | 61.2 (11.4) |
DEL PEAK 25(15Q11.2) WILD-TYPE | 268 | 58.4 (11.6) |
P value = 0.00571 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 26(15Q15.1) MUTATED | 346 | 60.9 (11.1) |
DEL PEAK 26(15Q15.1) WILD-TYPE | 206 | 58.1 (12.1) |
P value = 0.000464 (Wilcoxon-test), Q value = 0.024
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 552 | 59.8 (11.6) |
DEL PEAK 29(16Q23.1) MUTATED | 433 | 60.8 (11.5) |
DEL PEAK 29(16Q23.1) WILD-TYPE | 119 | 56.4 (11.3) |
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/19783383/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/19775421/OV-TP.merged_data.txt
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Number of patients = 573
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Number of significantly focal cnvs = 71
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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.