This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.
Testing the association between copy number variation of 74 peak regions and 6 clinical features across 544 patients, 15 significant findings detected with Q value < 0.25.
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Amp Peak 8(7p11.2) cnvs correlated to 'Time to Death' and 'AGE'.
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Amp Peak 9(7q11.21) cnvs correlated to 'Time to Death' and 'AGE'.
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Amp Peak 10(7q21.2) cnvs correlated to 'AGE'.
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Del Peak 20(9p21.3) cnvs correlated to 'AGE'.
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Del Peak 22(10p15.3) cnvs correlated to 'Time to Death' and 'AGE'.
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Del Peak 23(10p13) cnvs correlated to 'Time to Death' and 'AGE'.
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Del Peak 24(10p11.23) cnvs correlated to 'Time to Death' and 'AGE'.
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Del Peak 25(10q23.31) cnvs correlated to 'Time to Death' and 'AGE'.
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Del Peak 26(10q26.3) cnvs correlated to 'AGE'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 74 regions and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.
|
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
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 | |
| Amp Peak 8(7p11 2) | 478 (88%) | 66 |
2.57e-06 (0.00113) |
5.95e-09 (2.64e-06) |
0.502 (1.00) |
0.0351 (1.00) |
0.0239 (1.00) |
0.514 (1.00) |
| Amp Peak 9(7q11 21) | 439 (81%) | 105 |
0.000152 (0.0656) |
8.05e-08 (3.55e-05) |
0.224 (1.00) |
0.658 (1.00) |
0.0268 (1.00) |
0.516 (1.00) |
| Del Peak 22(10p15 3) | 446 (82%) | 98 |
1.24e-05 (0.00539) |
3.12e-08 (1.38e-05) |
0.0679 (1.00) |
0.615 (1.00) |
0.0429 (1.00) |
0.823 (1.00) |
| Del Peak 23(10p13) | 447 (82%) | 97 |
6.7e-06 (0.00291) |
2.12e-07 (9.32e-05) |
0.0297 (1.00) |
0.884 (1.00) |
0.151 (1.00) |
0.911 (1.00) |
| Del Peak 24(10p11 23) | 451 (83%) | 93 |
9.14e-07 (0.000401) |
1.16e-08 (5.13e-06) |
0.103 (1.00) |
0.232 (1.00) |
0.18 (1.00) |
0.909 (1.00) |
| Del Peak 25(10q23 31) | 486 (89%) | 58 |
2.27e-05 (0.00984) |
2.71e-06 (0.00119) |
0.572 (1.00) |
0.0751 (1.00) |
0.302 (1.00) |
0.781 (1.00) |
| Amp Peak 10(7q21 2) | 454 (83%) | 90 |
0.000634 (0.272) |
4.22e-06 (0.00184) |
0.637 (1.00) |
0.49 (1.00) |
0.0633 (1.00) |
0.357 (1.00) |
| Del Peak 20(9p21 3) | 399 (73%) | 145 |
0.0223 (1.00) |
0.000156 (0.067) |
0.552 (1.00) |
0.0926 (1.00) |
0.255 (1.00) |
0.847 (1.00) |
| Del Peak 26(10q26 3) | 486 (89%) | 58 |
0.00189 (0.807) |
2.89e-05 (0.0125) |
0.572 (1.00) |
0.118 (1.00) |
0.659 (1.00) |
0.578 (1.00) |
| Amp Peak 1(1p36 21) | 87 (16%) | 457 |
0.0861 (1.00) |
0.316 (1.00) |
0.283 (1.00) |
0.653 (1.00) |
0.618 (1.00) |
0.815 (1.00) |
| Amp Peak 2(1q32 1) | 148 (27%) | 396 |
0.373 (1.00) |
0.296 (1.00) |
0.624 (1.00) |
0.279 (1.00) |
0.68 (1.00) |
0.923 (1.00) |
| Amp Peak 3(1q44) | 96 (18%) | 448 |
0.503 (1.00) |
0.929 (1.00) |
0.359 (1.00) |
0.633 (1.00) |
0.81 (1.00) |
0.822 (1.00) |
| Amp Peak 4(2p24 3) | 44 (8%) | 500 |
0.151 (1.00) |
0.268 (1.00) |
0.424 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.118 (1.00) |
| Amp Peak 5(3q26 33) | 105 (19%) | 439 |
0.286 (1.00) |
0.0296 (1.00) |
0.824 (1.00) |
0.688 (1.00) |
0.353 (1.00) |
1 (1.00) |
| Amp Peak 6(4p16 3) | 45 (8%) | 499 |
0.554 (1.00) |
0.539 (1.00) |
0.526 (1.00) |
0.429 (1.00) |
0.0943 (1.00) |
0.212 (1.00) |
| Amp Peak 7(4q12) | 103 (19%) | 441 |
0.619 (1.00) |
0.532 (1.00) |
0.219 (1.00) |
0.597 (1.00) |
0.292 (1.00) |
0.443 (1.00) |
| Amp Peak 11(7q31 2) | 446 (82%) | 98 |
0.0246 (1.00) |
0.00146 (0.623) |
0.362 (1.00) |
0.513 (1.00) |
0.0234 (1.00) |
0.264 (1.00) |
| Amp Peak 12(8q24 21) | 62 (11%) | 482 |
0.351 (1.00) |
0.165 (1.00) |
0.218 (1.00) |
0.602 (1.00) |
0.774 (1.00) |
0.688 (1.00) |
| Amp Peak 13(11p13) | 26 (5%) | 518 |
0.867 (1.00) |
0.308 (1.00) |
0.539 (1.00) |
0.296 (1.00) |
0.392 (1.00) |
1 (1.00) |
| Amp Peak 14(12p13 32) | 78 (14%) | 466 |
0.839 (1.00) |
0.145 (1.00) |
0.901 (1.00) |
0.695 (1.00) |
0.795 (1.00) |
0.714 (1.00) |
| Amp Peak 15(12q14 1) | 127 (23%) | 417 |
0.125 (1.00) |
0.87 (1.00) |
0.468 (1.00) |
0.808 (1.00) |
0.665 (1.00) |
0.92 (1.00) |
| Amp Peak 16(12q15) | 87 (16%) | 457 |
0.945 (1.00) |
0.697 (1.00) |
0.339 (1.00) |
0.911 (1.00) |
0.135 (1.00) |
0.294 (1.00) |
| Amp Peak 17(13q34) | 30 (6%) | 514 |
0.828 (1.00) |
0.847 (1.00) |
0.338 (1.00) |
0.838 (1.00) |
1 (1.00) |
1 (1.00) |
| Amp Peak 18(14q32 33) | 31 (6%) | 513 |
0.0676 (1.00) |
0.00493 (1.00) |
0.453 (1.00) |
0.254 (1.00) |
1 (1.00) |
0.854 (1.00) |
| Amp Peak 19(17p13 2) | 47 (9%) | 497 |
0.573 (1.00) |
0.871 (1.00) |
0.164 (1.00) |
0.165 (1.00) |
0.414 (1.00) |
0.0476 (1.00) |
| Amp Peak 20(17q25 1) | 75 (14%) | 469 |
0.06 (1.00) |
0.03 (1.00) |
0.255 (1.00) |
0.837 (1.00) |
0.69 (1.00) |
0.535 (1.00) |
| Amp Peak 21(19p13 2) | 231 (42%) | 313 |
0.143 (1.00) |
0.658 (1.00) |
0.859 (1.00) |
0.441 (1.00) |
0.853 (1.00) |
0.863 (1.00) |
| Amp Peak 22(19q12) | 196 (36%) | 348 |
0.333 (1.00) |
0.397 (1.00) |
0.649 (1.00) |
0.996 (1.00) |
0.849 (1.00) |
0.326 (1.00) |
| Amp Peak 23(21q21 1) | 62 (11%) | 482 |
0.582 (1.00) |
0.0125 (1.00) |
0.681 (1.00) |
0.549 (1.00) |
0.565 (1.00) |
0.688 (1.00) |
| Del Peak 1(1p36 32) | 97 (18%) | 447 |
0.444 (1.00) |
0.615 (1.00) |
0.0666 (1.00) |
0.985 (1.00) |
1 (1.00) |
0.737 (1.00) |
| Del Peak 2(1p36 23) | 132 (24%) | 412 |
0.912 (1.00) |
0.0122 (1.00) |
0.014 (1.00) |
0.193 (1.00) |
0.749 (1.00) |
0.11 (1.00) |
| Del Peak 3(1p32 3) | 59 (11%) | 485 |
0.761 (1.00) |
0.06 (1.00) |
0.159 (1.00) |
0.687 (1.00) |
0.0786 (1.00) |
1 (1.00) |
| Del Peak 4(1p22 1) | 46 (8%) | 498 |
0.272 (1.00) |
0.321 (1.00) |
1 (1.00) |
0.585 (1.00) |
1 (1.00) |
0.54 (1.00) |
| Del Peak 5(1q42 11) | 45 (8%) | 499 |
0.0871 (1.00) |
0.0607 (1.00) |
1 (1.00) |
0.0102 (1.00) |
0.137 (1.00) |
0.279 (1.00) |
| Del Peak 6(1q44) | 31 (6%) | 513 |
0.3 (1.00) |
0.286 (1.00) |
0.851 (1.00) |
0.0669 (1.00) |
0.695 (1.00) |
0.854 (1.00) |
| Del Peak 7(2q22 1) | 43 (8%) | 501 |
0.311 (1.00) |
0.0941 (1.00) |
0.198 (1.00) |
0.686 (1.00) |
0.174 (1.00) |
0.431 (1.00) |
| Del Peak 8(2q37 1) | 55 (10%) | 489 |
0.76 (1.00) |
0.345 (1.00) |
0.146 (1.00) |
0.657 (1.00) |
0.361 (1.00) |
1 (1.00) |
| Del Peak 9(3p21 1) | 52 (10%) | 492 |
0.0237 (1.00) |
0.0119 (1.00) |
0.883 (1.00) |
0.698 (1.00) |
0.086 (1.00) |
0.19 (1.00) |
| Del Peak 10(3q13 31) | 55 (10%) | 489 |
0.528 (1.00) |
0.063 (1.00) |
0.383 (1.00) |
0.306 (1.00) |
0.29 (1.00) |
0.571 (1.00) |
| Del Peak 11(3q22 1) | 55 (10%) | 489 |
0.656 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.49 (1.00) |
0.29 (1.00) |
0.777 (1.00) |
| Del Peak 12(3q29) | 62 (11%) | 482 |
0.26 (1.00) |
0.194 (1.00) |
0.891 (1.00) |
0.459 (1.00) |
0.193 (1.00) |
0.349 (1.00) |
| Del Peak 13(4p16 3) | 79 (15%) | 465 |
0.405 (1.00) |
0.0747 (1.00) |
0.214 (1.00) |
0.146 (1.00) |
0.603 (1.00) |
0.465 (1.00) |
| Del Peak 14(4q34 3) | 89 (16%) | 455 |
0.165 (1.00) |
0.0944 (1.00) |
0.0581 (1.00) |
0.66 (1.00) |
0.174 (1.00) |
0.246 (1.00) |
| Del Peak 15(5q35 2) | 54 (10%) | 490 |
0.0355 (1.00) |
0.118 (1.00) |
0.77 (1.00) |
0.367 (1.00) |
0.541 (1.00) |
0.668 (1.00) |
| Del Peak 16(6q22 31) | 153 (28%) | 391 |
0.0359 (1.00) |
0.268 (1.00) |
0.0648 (1.00) |
0.454 (1.00) |
0.76 (1.00) |
0.568 (1.00) |
| Del Peak 17(6q26) | 172 (32%) | 372 |
0.188 (1.00) |
0.734 (1.00) |
0.133 (1.00) |
0.702 (1.00) |
0.693 (1.00) |
0.854 (1.00) |
| Del Peak 18(8p23 2) | 65 (12%) | 479 |
0.181 (1.00) |
0.0441 (1.00) |
0.589 (1.00) |
0.634 (1.00) |
0.48 (1.00) |
0.43 (1.00) |
| Del Peak 19(8q24 3) | 57 (10%) | 487 |
0.866 (1.00) |
0.659 (1.00) |
0.887 (1.00) |
0.366 (1.00) |
0.551 (1.00) |
0.484 (1.00) |
| Del Peak 21(9q34 2) | 71 (13%) | 473 |
0.529 (1.00) |
0.999 (1.00) |
1 (1.00) |
0.644 (1.00) |
0.892 (1.00) |
0.204 (1.00) |
| Del Peak 27(11p15 5) | 127 (23%) | 417 |
0.0634 (1.00) |
0.0125 (1.00) |
0.12 (1.00) |
0.242 (1.00) |
0.665 (1.00) |
0.614 (1.00) |
| Del Peak 28(11p11 2) | 100 (18%) | 444 |
0.0895 (1.00) |
0.671 (1.00) |
0.113 (1.00) |
0.796 (1.00) |
0.407 (1.00) |
0.912 (1.00) |
| Del Peak 29(11q14 1) | 94 (17%) | 450 |
0.818 (1.00) |
0.781 (1.00) |
0.202 (1.00) |
0.538 (1.00) |
0.021 (1.00) |
0.174 (1.00) |
| Del Peak 30(12p13 1) | 75 (14%) | 469 |
0.44 (1.00) |
0.91 (1.00) |
0.446 (1.00) |
0.825 (1.00) |
0.792 (1.00) |
0.901 (1.00) |
| Del Peak 31(12q12) | 75 (14%) | 469 |
0.718 (1.00) |
0.711 (1.00) |
0.799 (1.00) |
0.81 (1.00) |
0.351 (1.00) |
0.71 (1.00) |
| Del Peak 32(12q15) | 75 (14%) | 469 |
0.587 (1.00) |
0.861 (1.00) |
0.309 (1.00) |
0.186 (1.00) |
0.351 (1.00) |
1 (1.00) |
| Del Peak 33(13q12 11) | 177 (33%) | 367 |
0.946 (1.00) |
0.847 (1.00) |
0.779 (1.00) |
0.855 (1.00) |
0.241 (1.00) |
0.17 (1.00) |
| Del Peak 34(13q14 2) | 230 (42%) | 314 |
0.586 (1.00) |
0.538 (1.00) |
0.929 (1.00) |
0.828 (1.00) |
0.355 (1.00) |
0.0558 (1.00) |
| Del Peak 35(14q13 1) | 173 (32%) | 371 |
0.741 (1.00) |
0.488 (1.00) |
0.159 (1.00) |
0.27 (1.00) |
0.694 (1.00) |
0.357 (1.00) |
| Del Peak 36(14q24 2) | 169 (31%) | 375 |
0.929 (1.00) |
0.497 (1.00) |
0.344 (1.00) |
0.605 (1.00) |
0.921 (1.00) |
0.138 (1.00) |
| Del Peak 37(15q14) | 146 (27%) | 398 |
0.446 (1.00) |
0.0672 (1.00) |
0.767 (1.00) |
0.826 (1.00) |
0.149 (1.00) |
0.081 (1.00) |
| Del Peak 38(16p12 2) | 90 (17%) | 454 |
0.285 (1.00) |
0.262 (1.00) |
0.291 (1.00) |
0.808 (1.00) |
0.806 (1.00) |
0.818 (1.00) |
| Del Peak 39(16q23 3) | 94 (17%) | 450 |
0.184 (1.00) |
0.956 (1.00) |
0.417 (1.00) |
0.266 (1.00) |
0.039 (1.00) |
0.734 (1.00) |
| Del Peak 40(17p13 2) | 81 (15%) | 463 |
0.601 (1.00) |
0.554 (1.00) |
0.221 (1.00) |
0.189 (1.00) |
0.609 (1.00) |
0.549 (1.00) |
| Del Peak 41(17p13 1) | 91 (17%) | 453 |
0.826 (1.00) |
0.183 (1.00) |
0.0613 (1.00) |
0.797 (1.00) |
0.11 (1.00) |
0.909 (1.00) |
| Del Peak 42(17q11 2) | 67 (12%) | 477 |
0.605 (1.00) |
0.583 (1.00) |
1 (1.00) |
0.245 (1.00) |
0.0498 (1.00) |
0.795 (1.00) |
| Del Peak 43(18q22 3) | 79 (15%) | 465 |
0.999 (1.00) |
0.383 (1.00) |
0.804 (1.00) |
0.128 (1.00) |
0.697 (1.00) |
0.626 (1.00) |
| Del Peak 44(19q13 41) | 99 (18%) | 445 |
0.0808 (1.00) |
0.517 (1.00) |
0.91 (1.00) |
0.264 (1.00) |
0.476 (1.00) |
0.317 (1.00) |
| Del Peak 45(21q22 3) | 60 (11%) | 484 |
0.961 (1.00) |
0.154 (1.00) |
0.263 (1.00) |
0.296 (1.00) |
1 (1.00) |
0.411 (1.00) |
| Del Peak 46(22q12 2) | 188 (35%) | 356 |
0.842 (1.00) |
0.142 (1.00) |
0.927 (1.00) |
0.397 (1.00) |
0.773 (1.00) |
0.857 (1.00) |
| Del Peak 47(22q13 31) | 204 (38%) | 340 |
0.976 (1.00) |
0.255 (1.00) |
0.717 (1.00) |
0.223 (1.00) |
0.57 (1.00) |
0.249 (1.00) |
| Del Peak 48(22q13 31) | 203 (37%) | 341 |
0.964 (1.00) |
0.252 (1.00) |
0.928 (1.00) |
0.211 (1.00) |
0.507 (1.00) |
0.595 (1.00) |
| Del Peak 49(22q13 32) | 207 (38%) | 337 |
0.735 (1.00) |
0.267 (1.00) |
0.718 (1.00) |
0.599 (1.00) |
0.571 (1.00) |
0.479 (1.00) |
| Del Peak 50(Xp22 2) | 124 (23%) | 420 |
0.359 (1.00) |
0.498 (1.00) |
0.754 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.474 (1.00) |
| Del Peak 51(Xq23) | 119 (22%) | 425 |
0.234 (1.00) |
0.832 (1.00) |
0.916 (1.00) |
0.553 (1.00) |
0.658 (1.00) |
0.213 (1.00) |
P value = 2.57e-06 (logrank test), Q value = 0.0011
Table S1. Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| AMP PEAK 8(7P11.2) MUTATED | 478 | 367 | 0.1 - 127.6 (9.2) |
| AMP PEAK 8(7P11.2) WILD-TYPE | 66 | 44 | 0.2 - 108.8 (13.5) |
Figure S1. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 5.95e-09 (t-test), Q value = 2.6e-06
Table S2. Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| AMP PEAK 8(7P11.2) MUTATED | 478 | 59.7 (12.4) |
| AMP PEAK 8(7P11.2) WILD-TYPE | 66 | 43.9 (19.0) |
Figure S2. Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 0.000152 (logrank test), Q value = 0.066
Table S3. Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| AMP PEAK 9(7Q11.21) MUTATED | 439 | 333 | 0.1 - 127.6 (9.2) |
| AMP PEAK 9(7Q11.21) WILD-TYPE | 105 | 78 | 0.2 - 108.8 (12.4) |
Figure S3. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 8.05e-08 (t-test), Q value = 3.5e-05
Table S4. Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| AMP PEAK 9(7Q11.21) MUTATED | 439 | 59.9 (12.3) |
| AMP PEAK 9(7Q11.21) WILD-TYPE | 105 | 49.2 (18.3) |
Figure S4. Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 4.22e-06 (t-test), Q value = 0.0018
Table S5. Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| AMP PEAK 10(7Q21.2) MUTATED | 454 | 59.5 (12.3) |
| AMP PEAK 10(7Q21.2) WILD-TYPE | 90 | 49.1 (19.7) |
Figure S5. Get High-res Image Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 0.000156 (t-test), Q value = 0.067
Table S6. Gene #43: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 20(9P21.3) MUTATED | 399 | 59.3 (13.5) |
| DEL PEAK 20(9P21.3) WILD-TYPE | 145 | 53.7 (15.7) |
Figure S6. Get High-res Image Gene #43: 'Del Peak 20(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 1.24e-05 (logrank test), Q value = 0.0054
Table S7. Gene #45: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| DEL PEAK 22(10P15.3) MUTATED | 446 | 343 | 0.1 - 92.6 (9.4) |
| DEL PEAK 22(10P15.3) WILD-TYPE | 98 | 68 | 0.1 - 127.6 (10.5) |
Figure S7. Get High-res Image Gene #45: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 3.12e-08 (t-test), Q value = 1.4e-05
Table S8. Gene #45: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 22(10P15.3) MUTATED | 446 | 59.9 (12.3) |
| DEL PEAK 22(10P15.3) WILD-TYPE | 98 | 48.3 (18.4) |
Figure S8. Get High-res Image Gene #45: 'Del Peak 22(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 6.7e-06 (logrank test), Q value = 0.0029
Table S9. Gene #46: 'Del Peak 23(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| DEL PEAK 23(10P13) MUTATED | 447 | 343 | 0.1 - 92.6 (9.4) |
| DEL PEAK 23(10P13) WILD-TYPE | 97 | 68 | 0.1 - 127.6 (9.8) |
Figure S9. Get High-res Image Gene #46: 'Del Peak 23(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 2.12e-07 (t-test), Q value = 9.3e-05
Table S10. Gene #46: 'Del Peak 23(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 23(10P13) MUTATED | 447 | 59.8 (12.2) |
| DEL PEAK 23(10P13) WILD-TYPE | 97 | 48.7 (18.9) |
Figure S10. Get High-res Image Gene #46: 'Del Peak 23(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 9.14e-07 (logrank test), Q value = 4e-04
Table S11. Gene #47: 'Del Peak 24(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| DEL PEAK 24(10P11.23) MUTATED | 451 | 345 | 0.1 - 92.6 (9.4) |
| DEL PEAK 24(10P11.23) WILD-TYPE | 93 | 66 | 0.1 - 127.6 (12.4) |
Figure S11. Get High-res Image Gene #47: 'Del Peak 24(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 1.16e-08 (t-test), Q value = 5.1e-06
Table S12. Gene #47: 'Del Peak 24(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 24(10P11.23) MUTATED | 451 | 60.0 (12.1) |
| DEL PEAK 24(10P11.23) WILD-TYPE | 93 | 47.4 (18.8) |
Figure S12. Get High-res Image Gene #47: 'Del Peak 24(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 2.27e-05 (logrank test), Q value = 0.0098
Table S13. Gene #48: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 544 | 411 | 0.1 - 127.6 (9.6) |
| DEL PEAK 25(10Q23.31) MUTATED | 486 | 372 | 0.1 - 127.6 (9.6) |
| DEL PEAK 25(10Q23.31) WILD-TYPE | 58 | 39 | 0.2 - 108.8 (10.9) |
Figure S13. Get High-res Image Gene #48: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'
P value = 2.71e-06 (t-test), Q value = 0.0012
Table S14. Gene #48: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 25(10Q23.31) MUTATED | 486 | 59.2 (13.0) |
| DEL PEAK 25(10Q23.31) WILD-TYPE | 58 | 46.2 (18.7) |
Figure S14. Get High-res Image Gene #48: 'Del Peak 25(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'
P value = 2.89e-05 (t-test), Q value = 0.012
Table S15. Gene #49: 'Del Peak 26(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 544 | 57.8 (14.3) |
| DEL PEAK 26(10Q26.3) MUTATED | 486 | 59.0 (13.1) |
| DEL PEAK 26(10Q26.3) WILD-TYPE | 58 | 47.6 (18.9) |
Figure S15. Get High-res Image Gene #49: 'Del Peak 26(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'
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Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
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Clinical data file = GBM.clin.merged.picked.txt
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Number of patients = 544
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Number of copy number variation regions = 74
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Number of selected clinical features = 6
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Exclude regions that fewer than K tumors have alterations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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.