(primary solid tumor cohort)
This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 63 arm-level results and 11 clinical features across 131 patients, 2 significant findings detected with Q value < 0.25.
-
Amp Peak 7(4q13.3) cnv correlated to 'KARNOFSKY.PERFORMANCE.SCORE'.
-
Del Peak 14(6q21) cnv correlated to 'NEOPLASM.DISEASESTAGE'.
Clinical Features |
Time to Death |
AGE | GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | t-test | t-test | Fisher's exact test | Chi-square test | t-test | t-test | Fisher's exact test | |
Amp Peak 7(4q13 3) | 17 (13%) | 114 |
0.522 (1.00) |
0.112 (1.00) |
0.0363 (1.00) |
7.05e-05 (0.0444) |
0.886 (1.00) |
0.84 (1.00) |
0.834 (1.00) |
0.761 (1.00) |
0.902 (1.00) |
0.626 (1.00) |
|
Del Peak 14(6q21) | 55 (42%) | 76 |
0.107 (1.00) |
0.175 (1.00) |
0.839 (1.00) |
0.966 (1.00) |
0.826 (1.00) |
0.514 (1.00) |
0.654 (1.00) |
0.00842 (1.00) |
0.0031 (1.00) |
0.000244 (0.154) |
|
Amp Peak 1(1p34 2) | 41 (31%) | 90 |
0.762 (1.00) |
0.246 (1.00) |
0.518 (1.00) |
0.193 (1.00) |
0.237 (1.00) |
0.917 (1.00) |
0.614 (1.00) |
0.538 (1.00) |
0.463 (1.00) |
0.486 (1.00) |
|
Amp Peak 2(1q21 3) | 68 (52%) | 63 |
0.432 (1.00) |
0.401 (1.00) |
0.691 (1.00) |
0.366 (1.00) |
0.0467 (1.00) |
0.472 (1.00) |
0.325 (1.00) |
0.0299 (1.00) |
0.0852 (1.00) |
0.0782 (1.00) |
|
Amp Peak 3(1q23 3) | 72 (55%) | 59 |
0.638 (1.00) |
0.42 (1.00) |
0.423 (1.00) |
0.301 (1.00) |
0.242 (1.00) |
0.619 (1.00) |
0.0307 (1.00) |
0.101 (1.00) |
0.0745 (1.00) |
0.0918 (1.00) |
|
Amp Peak 4(3p25 2) | 65 (50%) | 66 |
0.0512 (1.00) |
0.427 (1.00) |
0.0435 (1.00) |
0.263 (1.00) |
0.759 (1.00) |
0.331 (1.00) |
0.758 (1.00) |
0.759 (1.00) |
0.488 (1.00) |
0.521 (1.00) |
|
Amp Peak 5(3q26 32) | 75 (57%) | 56 |
0.0481 (1.00) |
0.624 (1.00) |
0.839 (1.00) |
0.751 (1.00) |
0.871 (1.00) |
0.802 (1.00) |
0.648 (1.00) |
0.242 (1.00) |
0.921 (1.00) |
0.638 (1.00) |
|
Amp Peak 6(4p16 3) | 27 (21%) | 104 |
0.0532 (1.00) |
0.61 (1.00) |
0.0805 (1.00) |
0.391 (1.00) |
0.444 (1.00) |
0.818 (1.00) |
0.0101 (1.00) |
0.163 (1.00) |
0.953 (1.00) |
0.0359 (1.00) |
|
Amp Peak 8(5p15 1) | 63 (48%) | 68 |
0.761 (1.00) |
0.47 (1.00) |
0.315 (1.00) |
0.595 (1.00) |
0.501 (1.00) |
0.128 (1.00) |
0.627 (1.00) |
0.00171 (1.00) |
0.106 (1.00) |
0.876 (1.00) |
|
Amp Peak 9(6p22 3) | 55 (42%) | 76 |
0.302 (1.00) |
0.367 (1.00) |
0.686 (1.00) |
0.703 (1.00) |
0.644 (1.00) |
0.187 (1.00) |
0.813 (1.00) |
0.38 (1.00) |
0.0136 (1.00) |
0.588 (1.00) |
|
Amp Peak 10(6q12) | 22 (17%) | 109 |
0.409 (1.00) |
0.101 (1.00) |
0.28 (1.00) |
0.256 (1.00) |
0.126 (1.00) |
0.145 (1.00) |
1 (1.00) |
0.907 (1.00) |
0.0806 (1.00) |
0.643 (1.00) |
|
Amp Peak 11(6q21) | 15 (11%) | 116 |
0.878 (1.00) |
0.384 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.299 (1.00) |
0.798 (1.00) |
0.734 (1.00) |
0.467 (1.00) |
0.903 (1.00) |
0.894 (1.00) |
|
Amp Peak 12(7p11 2) | 68 (52%) | 63 |
0.623 (1.00) |
0.0509 (1.00) |
0.841 (1.00) |
0.524 (1.00) |
0.389 (1.00) |
0.0783 (1.00) |
0.609 (1.00) |
0.187 (1.00) |
0.948 (1.00) |
0.897 (1.00) |
|
Amp Peak 13(8p11 23) | 44 (34%) | 87 |
0.493 (1.00) |
0.902 (1.00) |
0.404 (1.00) |
0.943 (1.00) |
0.178 (1.00) |
0.275 (1.00) |
0.515 (1.00) |
0.786 (1.00) |
0.829 (1.00) |
0.565 (1.00) |
|
Amp Peak 14(8p11 21) | 43 (33%) | 88 |
0.00533 (1.00) |
0.598 (1.00) |
0.134 (1.00) |
0.578 (1.00) |
0.09 (1.00) |
0.0893 (1.00) |
0.266 (1.00) |
0.875 (1.00) |
0.752 (1.00) |
1 (1.00) |
|
Amp Peak 15(8q22 3) | 81 (62%) | 50 |
0.159 (1.00) |
0.963 (1.00) |
0.0374 (1.00) |
0.398 (1.00) |
0.261 (1.00) |
0.318 (1.00) |
0.545 (1.00) |
0.176 (1.00) |
0.11 (1.00) |
1 (1.00) |
|
Amp Peak 16(8q24 21) | 79 (60%) | 52 |
0.0842 (1.00) |
0.714 (1.00) |
0.0633 (1.00) |
0.41 (1.00) |
0.816 (1.00) |
0.688 (1.00) |
0.515 (1.00) |
0.44 (1.00) |
0.136 (1.00) |
0.816 (1.00) |
|
Amp Peak 17(10p15 1) | 56 (43%) | 75 |
0.629 (1.00) |
0.0715 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.7 (1.00) |
0.35 (1.00) |
0.718 (1.00) |
0.0761 (1.00) |
0.539 (1.00) |
0.51 (1.00) |
|
Amp Peak 18(11q13 3) | 50 (38%) | 81 |
0.835 (1.00) |
0.335 (1.00) |
0.679 (1.00) |
0.752 (1.00) |
0.787 (1.00) |
0.0687 (1.00) |
0.112 (1.00) |
0.0554 (1.00) |
0.328 (1.00) |
0.478 (1.00) |
|
Amp Peak 19(12q15) | 44 (34%) | 87 |
0.721 (1.00) |
0.971 (1.00) |
0.677 (1.00) |
0.592 (1.00) |
0.0724 (1.00) |
0.481 (1.00) |
0.52 (1.00) |
0.208 (1.00) |
0.501 (1.00) |
0.222 (1.00) |
|
Amp Peak 20(13q22 1) | 45 (34%) | 86 |
0.503 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.862 (1.00) |
0.182 (1.00) |
0.921 (1.00) |
0.902 (1.00) |
0.873 (1.00) |
0.607 (1.00) |
0.281 (1.00) |
|
Amp Peak 21(16p12 1) | 35 (27%) | 96 |
0.564 (1.00) |
0.655 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.991 (1.00) |
0.687 (1.00) |
0.563 (1.00) |
0.235 (1.00) |
0.99 (1.00) |
0.272 (1.00) |
|
Amp Peak 22(17q11 2) | 62 (47%) | 69 |
0.747 (1.00) |
0.396 (1.00) |
0.842 (1.00) |
0.0164 (1.00) |
0.967 (1.00) |
0.804 (1.00) |
0.0648 (1.00) |
0.0637 (1.00) |
0.68 (1.00) |
0.0302 (1.00) |
|
Amp Peak 23(17q12) | 56 (43%) | 75 |
0.281 (1.00) |
0.512 (1.00) |
1 (1.00) |
0.0578 (1.00) |
0.156 (1.00) |
0.321 (1.00) |
0.137 (1.00) |
0.154 (1.00) |
0.871 (1.00) |
0.0567 (1.00) |
|
Amp Peak 24(19q12) | 58 (44%) | 73 |
0.16 (1.00) |
0.421 (1.00) |
0.842 (1.00) |
0.498 (1.00) |
0.34 (1.00) |
0.258 (1.00) |
0.564 (1.00) |
0.283 (1.00) |
0.154 (1.00) |
0.259 (1.00) |
|
Amp Peak 25(19q13 43) | 56 (43%) | 75 |
0.088 (1.00) |
0.5 (1.00) |
0.839 (1.00) |
0.479 (1.00) |
0.626 (1.00) |
0.417 (1.00) |
0.173 (1.00) |
0.126 (1.00) |
0.0772 (1.00) |
0.136 (1.00) |
|
Amp Peak 26(20q11 21) | 92 (70%) | 39 |
0.793 (1.00) |
0.406 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.0297 (1.00) |
0.645 (1.00) |
0.828 (1.00) |
0.601 (1.00) |
0.622 (1.00) |
0.631 (1.00) |
|
Amp Peak 27(22q11 23) | 32 (24%) | 99 |
0.113 (1.00) |
0.397 (1.00) |
0.169 (1.00) |
0.684 (1.00) |
0.379 (1.00) |
0.1 (1.00) |
0.795 (1.00) |
0.825 (1.00) |
0.747 (1.00) |
0.379 (1.00) |
|
Del Peak 1(1p36 11) | 23 (18%) | 108 |
0.134 (1.00) |
0.144 (1.00) |
1 (1.00) |
0.942 (1.00) |
0.679 (1.00) |
0.318 (1.00) |
0.866 (1.00) |
0.00606 (1.00) |
0.38 (1.00) |
0.626 (1.00) |
|
Del Peak 2(1q32 1) | 25 (19%) | 106 |
0.663 (1.00) |
0.119 (1.00) |
0.0382 (1.00) |
0.666 (1.00) |
0.00608 (1.00) |
0.524 (1.00) |
0.713 (1.00) |
0.367 (1.00) |
0.304 (1.00) |
0.267 (1.00) |
|
Del Peak 3(2q22 1) | 40 (31%) | 91 |
0.204 (1.00) |
0.681 (1.00) |
0.125 (1.00) |
0.534 (1.00) |
0.992 (1.00) |
0.202 (1.00) |
0.197 (1.00) |
0.838 (1.00) |
0.624 (1.00) |
0.509 (1.00) |
|
Del Peak 4(2q34) | 55 (42%) | 76 |
0.232 (1.00) |
0.293 (1.00) |
0.839 (1.00) |
0.632 (1.00) |
0.565 (1.00) |
0.266 (1.00) |
0.548 (1.00) |
0.894 (1.00) |
0.439 (1.00) |
0.597 (1.00) |
|
Del Peak 5(2q37 1) | 67 (51%) | 64 |
0.355 (1.00) |
0.602 (1.00) |
0.0694 (1.00) |
0.433 (1.00) |
0.297 (1.00) |
0.363 (1.00) |
0.387 (1.00) |
0.606 (1.00) |
0.952 (1.00) |
0.332 (1.00) |
|
Del Peak 6(3p21 31) | 42 (32%) | 89 |
0.76 (1.00) |
0.673 (1.00) |
0.667 (1.00) |
0.63 (1.00) |
0.684 (1.00) |
0.0159 (1.00) |
0.668 (1.00) |
0.903 (1.00) |
0.257 (1.00) |
0.702 (1.00) |
|
Del Peak 7(3p14 2) | 43 (33%) | 88 |
0.543 (1.00) |
0.392 (1.00) |
0.67 (1.00) |
0.63 (1.00) |
0.48 (1.00) |
0.0709 (1.00) |
0.761 (1.00) |
0.552 (1.00) |
0.0772 (1.00) |
0.763 (1.00) |
|
Del Peak 8(3p12 3) | 37 (28%) | 94 |
0.798 (1.00) |
0.0607 (1.00) |
0.505 (1.00) |
0.105 (1.00) |
0.993 (1.00) |
0.125 (1.00) |
0.445 (1.00) |
0.509 (1.00) |
0.234 (1.00) |
0.811 (1.00) |
|
Del Peak 9(4q22 1) | 52 (40%) | 79 |
0.825 (1.00) |
0.121 (1.00) |
0.304 (1.00) |
0.861 (1.00) |
1 (1.00) |
0.051 (1.00) |
0.108 (1.00) |
0.805 (1.00) |
0.171 (1.00) |
0.693 (1.00) |
|
Del Peak 10(4q34 2) | 59 (45%) | 72 |
0.338 (1.00) |
0.0777 (1.00) |
0.84 (1.00) |
0.631 (1.00) |
0.476 (1.00) |
0.8 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.486 (1.00) |
0.147 (1.00) |
|
Del Peak 11(5q11 2) | 68 (52%) | 63 |
0.743 (1.00) |
0.00609 (1.00) |
0.232 (1.00) |
0.549 (1.00) |
0.258 (1.00) |
0.472 (1.00) |
0.467 (1.00) |
0.125 (1.00) |
0.262 (1.00) |
0.00443 (1.00) |
|
Del Peak 12(5q35 1) | 66 (50%) | 65 |
0.516 (1.00) |
0.0448 (1.00) |
0.0724 (1.00) |
0.414 (1.00) |
0.667 (1.00) |
0.363 (1.00) |
0.127 (1.00) |
0.306 (1.00) |
0.171 (1.00) |
0.00436 (1.00) |
|
Del Peak 13(6p25 3) | 37 (28%) | 94 |
0.144 (1.00) |
0.901 (1.00) |
0.266 (1.00) |
0.154 (1.00) |
0.497 (1.00) |
0.258 (1.00) |
0.382 (1.00) |
0.0226 (1.00) |
0.05 (1.00) |
0.0533 (1.00) |
|
Del Peak 15(6q27) | 56 (43%) | 75 |
0.0427 (1.00) |
0.374 (1.00) |
0.423 (1.00) |
0.364 (1.00) |
0.526 (1.00) |
0.077 (1.00) |
0.571 (1.00) |
0.0255 (1.00) |
0.00745 (1.00) |
0.00718 (1.00) |
|
Del Peak 16(8p23 3) | 70 (53%) | 61 |
0.862 (1.00) |
0.47 (1.00) |
0.318 (1.00) |
0.906 (1.00) |
0.767 (1.00) |
0.951 (1.00) |
0.121 (1.00) |
0.193 (1.00) |
0.626 (1.00) |
0.2 (1.00) |
|
Del Peak 17(8p21 1) | 74 (56%) | 57 |
0.705 (1.00) |
0.252 (1.00) |
0.159 (1.00) |
0.729 (1.00) |
0.744 (1.00) |
0.434 (1.00) |
0.0302 (1.00) |
0.211 (1.00) |
0.356 (1.00) |
0.0582 (1.00) |
|
Del Peak 18(9p23) | 58 (44%) | 73 |
0.651 (1.00) |
0.788 (1.00) |
0.549 (1.00) |
0.753 (1.00) |
0.661 (1.00) |
0.379 (1.00) |
0.867 (1.00) |
0.438 (1.00) |
0.57 (1.00) |
0.808 (1.00) |
|
Del Peak 19(9p21 3) | 76 (58%) | 55 |
0.334 (1.00) |
0.771 (1.00) |
0.419 (1.00) |
0.975 (1.00) |
0.214 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.063 (1.00) |
0.533 (1.00) |
0.639 (1.00) |
|
Del Peak 20(10p12 1) | 27 (21%) | 104 |
0.966 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.932 (1.00) |
0.121 (1.00) |
0.626 (1.00) |
0.65 (1.00) |
0.328 (1.00) |
0.907 (1.00) |
|
Del Peak 21(10q23 31) | 57 (44%) | 74 |
0.688 (1.00) |
0.00687 (1.00) |
1 (1.00) |
0.0916 (1.00) |
0.606 (1.00) |
0.504 (1.00) |
0.629 (1.00) |
0.0482 (1.00) |
0.186 (1.00) |
0.0917 (1.00) |
|
Del Peak 22(11p15 5) | 66 (50%) | 65 |
0.409 (1.00) |
0.00881 (1.00) |
0.842 (1.00) |
0.00871 (1.00) |
0.869 (1.00) |
0.198 (1.00) |
0.58 (1.00) |
0.128 (1.00) |
0.182 (1.00) |
0.0489 (1.00) |
|
Del Peak 23(11q25) | 42 (32%) | 89 |
0.538 (1.00) |
0.537 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.256 (1.00) |
0.0851 (1.00) |
0.431 (1.00) |
0.262 (1.00) |
0.0475 (1.00) |
0.257 (1.00) |
|
Del Peak 24(13q14 2) | 51 (39%) | 80 |
0.353 (1.00) |
0.0997 (1.00) |
0.303 (1.00) |
0.753 (1.00) |
0.696 (1.00) |
0.0358 (1.00) |
0.763 (1.00) |
0.188 (1.00) |
0.221 (1.00) |
0.0522 (1.00) |
|
Del Peak 25(14q12) | 37 (28%) | 94 |
0.378 (1.00) |
0.258 (1.00) |
0.181 (1.00) |
0.487 (1.00) |
0.0496 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.143 (1.00) |
0.16 (1.00) |
0.0779 (1.00) |
|
Del Peak 26(14q32 31) | 38 (29%) | 93 |
0.676 (1.00) |
0.113 (1.00) |
0.0478 (1.00) |
0.312 (1.00) |
0.55 (1.00) |
0.558 (1.00) |
0.427 (1.00) |
0.981 (1.00) |
0.696 (1.00) |
0.722 (1.00) |
|
Del Peak 27(15q13 1) | 49 (37%) | 82 |
0.205 (1.00) |
0.123 (1.00) |
0.407 (1.00) |
0.285 (1.00) |
0.62 (1.00) |
0.0608 (1.00) |
0.0809 (1.00) |
0.323 (1.00) |
0.452 (1.00) |
0.326 (1.00) |
|
Del Peak 28(16p13 3) | 48 (37%) | 83 |
0.487 (1.00) |
0.258 (1.00) |
0.682 (1.00) |
0.862 (1.00) |
0.627 (1.00) |
0.212 (1.00) |
0.654 (1.00) |
0.63 (1.00) |
0.688 (1.00) |
0.502 (1.00) |
|
Del Peak 29(16q23 1) | 37 (28%) | 94 |
0.213 (1.00) |
0.847 (1.00) |
0.658 (1.00) |
0.127 (1.00) |
0.823 (1.00) |
0.0137 (1.00) |
0.715 (1.00) |
0.048 (1.00) |
0.213 (1.00) |
0.254 (1.00) |
|
Del Peak 30(17p12) | 68 (52%) | 63 |
0.124 (1.00) |
0.478 (1.00) |
0.426 (1.00) |
0.827 (1.00) |
0.969 (1.00) |
0.876 (1.00) |
1 (1.00) |
0.205 (1.00) |
0.522 (1.00) |
0.00843 (1.00) |
|
Del Peak 31(18q23) | 57 (44%) | 74 |
0.215 (1.00) |
0.088 (1.00) |
0.841 (1.00) |
0.125 (1.00) |
0.406 (1.00) |
0.799 (1.00) |
0.759 (1.00) |
0.941 (1.00) |
0.457 (1.00) |
0.874 (1.00) |
|
Del Peak 32(19p13 3) | 52 (40%) | 79 |
0.609 (1.00) |
0.447 (1.00) |
0.837 (1.00) |
0.517 (1.00) |
0.187 (1.00) |
0.695 (1.00) |
0.0415 (1.00) |
0.196 (1.00) |
0.605 (1.00) |
0.198 (1.00) |
|
Del Peak 33(22q13 32) | 53 (40%) | 78 |
0.912 (1.00) |
0.35 (1.00) |
0.839 (1.00) |
0.0926 (1.00) |
0.868 (1.00) |
0.248 (1.00) |
0.0183 (1.00) |
0.824 (1.00) |
0.429 (1.00) |
0.387 (1.00) |
|
Del Peak 34(Xp11 3) | 36 (27%) | 95 |
0.824 (1.00) |
0.177 (1.00) |
0.499 (1.00) |
0.607 (1.00) |
0.18 (1.00) |
0.331 (1.00) |
0.847 (1.00) |
0.174 (1.00) |
0.96 (1.00) |
0.468 (1.00) |
|
Del Peak 35(Xq21 33) | 31 (24%) | 100 |
0.446 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.508 (1.00) |
0.634 (1.00) |
0.09 (1.00) |
0.444 (1.00) |
0.307 (1.00) |
0.929 (1.00) |
0.595 (1.00) |
|
Del Peak 36(Xq22 3) | 29 (22%) | 102 |
0.0907 (1.00) |
0.762 (1.00) |
0.809 (1.00) |
0.683 (1.00) |
0.739 (1.00) |
0.322 (1.00) |
0.431 (1.00) |
0.653 (1.00) |
0.981 (1.00) |
0.907 (1.00) |
P value = 7.05e-05 (t-test), Q value = 0.044
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 37 | 78.1 (16.3) |
AMP PEAK 7(4Q13.3) MUTATED | 3 | 90.0 (0.0) |
AMP PEAK 7(4Q13.3) WILD-TYPE | 34 | 77.1 (16.6) |
P value = 0.000244 (Fisher's exact test), Q value = 0.15
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 1 | 36 | 43 | 46 |
DEL PEAK 14(6Q21) MUTATED | 0 | 16 | 8 | 28 |
DEL PEAK 14(6Q21) WILD-TYPE | 1 | 20 | 35 | 18 |
-
Mutation data file = all_lesions.conf_99.cnv.cluster.txt
-
Clinical data file = BLCA-TP.clin.merged.picked.txt
-
Number of patients = 131
-
Number of significantly arm-level cnvs = 63
-
Number of selected clinical features = 11
-
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 multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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.