This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and molecular subtypes.
Testing the association between copy number variation 66 arm-level events and 10 molecular subtypes across 36 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.
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6q loss cnv correlated to 'CN_CNMF'.
Clinical Features |
CN CNMF |
METHLYATION CNMF |
RPPA CNMF |
RPPA CHIERARCHICAL |
MRNASEQ CNMF |
MRNASEQ CHIERARCHICAL |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
MIRSEQ MATURE CNMF |
MIRSEQ MATURE CHIERARCHICAL |
||
nCNV (%) | nWild-Type | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
6q loss | 20 (56%) | 16 |
0.000242 (0.16) |
0.0126 (0.52) |
0.00683 (0.476) |
0.0221 (0.631) |
0.191 (1.00) |
0.144 (1.00) |
0.208 (1.00) |
0.255 (1.00) |
0.32 (1.00) |
0.407 (1.00) |
1p gain | 10 (28%) | 26 |
0.139 (1.00) |
0.65 (1.00) |
1 (1.00) |
0.79 (1.00) |
0.639 (1.00) |
0.553 (1.00) |
0.108 (1.00) |
0.263 (1.00) |
0.26 (1.00) |
0.688 (1.00) |
1q gain | 21 (58%) | 15 |
0.516 (1.00) |
0.0921 (1.00) |
1 (1.00) |
1 (1.00) |
0.694 (1.00) |
0.236 (1.00) |
0.114 (1.00) |
0.178 (1.00) |
0.736 (1.00) |
0.589 (1.00) |
2p gain | 6 (17%) | 30 |
0.662 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.369 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.599 (1.00) |
2q gain | 6 (17%) | 30 |
0.182 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.714 (1.00) |
0.525 (1.00) |
0.504 (1.00) |
0.367 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.598 (1.00) |
3p gain | 3 (8%) | 33 |
0.231 (1.00) |
0.0972 (1.00) |
1 (1.00) |
0.325 (1.00) |
0.154 (1.00) |
0.336 (1.00) |
0.234 (1.00) |
0.0637 (1.00) |
0.581 (1.00) |
|
3q gain | 8 (22%) | 28 |
0.236 (1.00) |
0.0578 (1.00) |
0.641 (1.00) |
0.716 (1.00) |
0.103 (1.00) |
0.0983 (1.00) |
0.541 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.393 (1.00) |
4p gain | 3 (8%) | 33 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.77 (1.00) |
0.421 (1.00) |
0.559 (1.00) |
1 (1.00) |
|
5p gain | 12 (33%) | 24 |
1 (1.00) |
0.821 (1.00) |
1 (1.00) |
0.2 (1.00) |
0.615 (1.00) |
0.977 (1.00) |
0.764 (1.00) |
1 (1.00) |
1 (1.00) |
0.762 (1.00) |
5q gain | 12 (33%) | 24 |
1 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.199 (1.00) |
0.615 (1.00) |
0.977 (1.00) |
0.765 (1.00) |
1 (1.00) |
1 (1.00) |
0.764 (1.00) |
6p gain | 7 (19%) | 29 |
0.684 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.369 (1.00) |
0.891 (1.00) |
0.187 (1.00) |
0.318 (1.00) |
0.674 (1.00) |
0.238 (1.00) |
7p gain | 7 (19%) | 29 |
0.684 (1.00) |
1 (1.00) |
0.626 (1.00) |
0.302 (1.00) |
0.209 (1.00) |
0.389 (1.00) |
0.375 (1.00) |
0.565 (1.00) |
0.674 (1.00) |
0.0187 (0.602) |
7q gain | 6 (17%) | 30 |
1 (1.00) |
0.628 (1.00) |
1 (1.00) |
0.69 (1.00) |
0.453 (1.00) |
0.538 (1.00) |
0.687 (1.00) |
0.82 (1.00) |
1 (1.00) |
0.00744 (0.476) |
8p gain | 6 (17%) | 30 |
1 (1.00) |
0.239 (1.00) |
0.626 (1.00) |
0.674 (1.00) |
0.331 (1.00) |
0.167 (1.00) |
0.203 (1.00) |
0.364 (1.00) |
0.367 (1.00) |
0.119 (1.00) |
8q gain | 12 (33%) | 24 |
1 (1.00) |
0.205 (1.00) |
0.702 (1.00) |
0.568 (1.00) |
0.173 (1.00) |
0.54 (1.00) |
0.183 (1.00) |
0.167 (1.00) |
0.721 (1.00) |
0.132 (1.00) |
10p gain | 5 (14%) | 31 |
1 (1.00) |
0.399 (1.00) |
0.626 (1.00) |
0.0412 (0.848) |
0.834 (1.00) |
0.0727 (1.00) |
0.789 (1.00) |
0.933 (1.00) |
0.63 (1.00) |
0.863 (1.00) |
11p gain | 4 (11%) | 32 |
0.605 (1.00) |
0.178 (1.00) |
0.537 (1.00) |
0.105 (1.00) |
0.202 (1.00) |
0.00542 (0.476) |
0.74 (1.00) |
0.745 (1.00) |
0.287 (1.00) |
0.185 (1.00) |
11q gain | 4 (11%) | 32 |
0.605 (1.00) |
0.177 (1.00) |
0.537 (1.00) |
0.104 (1.00) |
0.202 (1.00) |
0.00557 (0.476) |
0.741 (1.00) |
0.748 (1.00) |
0.287 (1.00) |
0.186 (1.00) |
12p gain | 9 (25%) | 27 |
1 (1.00) |
0.557 (1.00) |
1 (1.00) |
0.236 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.465 (1.00) |
0.841 (1.00) |
0.443 (1.00) |
0.335 (1.00) |
12q gain | 8 (22%) | 28 |
1 (1.00) |
0.536 (1.00) |
1 (1.00) |
0.536 (1.00) |
0.879 (1.00) |
0.982 (1.00) |
0.436 (1.00) |
0.826 (1.00) |
0.236 (1.00) |
0.629 (1.00) |
13q gain | 3 (8%) | 33 |
0.231 (1.00) |
0.0984 (1.00) |
1 (1.00) |
0.0417 (0.848) |
0.0395 (0.848) |
0.395 (1.00) |
0.887 (1.00) |
1 (1.00) |
0.0246 (0.649) |
|
15q gain | 6 (17%) | 30 |
0.662 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.863 (1.00) |
0.66 (1.00) |
0.193 (1.00) |
0.434 (1.00) |
0.677 (1.00) |
0.00872 (0.48) |
16p gain | 7 (19%) | 29 |
0.0918 (1.00) |
0.571 (1.00) |
0.372 (1.00) |
0.633 (1.00) |
0.664 (1.00) |
0.64 (1.00) |
0.374 (1.00) |
0.915 (1.00) |
0.674 (1.00) |
0.296 (1.00) |
16q gain | 5 (14%) | 31 |
0.342 (1.00) |
1 (1.00) |
1 (1.00) |
0.0922 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.922 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.926 (1.00) |
17p gain | 3 (8%) | 33 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.251 (1.00) |
0.773 (1.00) |
0.215 (1.00) |
0.687 (1.00) |
0.612 (1.00) |
0.559 (1.00) |
0.578 (1.00) |
17q gain | 7 (19%) | 29 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.532 (1.00) |
0.493 (1.00) |
0.253 (1.00) |
0.935 (1.00) |
1 (1.00) |
0.418 (1.00) |
0.523 (1.00) |
18p gain | 7 (19%) | 29 |
1 (1.00) |
0.759 (1.00) |
0.626 (1.00) |
0.303 (1.00) |
0.665 (1.00) |
0.762 (1.00) |
0.488 (1.00) |
0.882 (1.00) |
0.418 (1.00) |
0.847 (1.00) |
18q gain | 6 (17%) | 30 |
0.391 (1.00) |
0.335 (1.00) |
0.626 (1.00) |
0.675 (1.00) |
0.0711 (1.00) |
0.566 (1.00) |
0.194 (1.00) |
0.436 (1.00) |
0.677 (1.00) |
0.393 (1.00) |
19p gain | 6 (17%) | 30 |
0.662 (1.00) |
0.86 (1.00) |
0.626 (1.00) |
0.726 (1.00) |
0.626 (1.00) |
0.657 (1.00) |
0.579 (1.00) |
0.439 (1.00) |
0.0628 (1.00) |
1 (1.00) |
19q gain | 6 (17%) | 30 |
0.662 (1.00) |
0.86 (1.00) |
0.626 (1.00) |
0.724 (1.00) |
0.626 (1.00) |
0.659 (1.00) |
0.583 (1.00) |
0.436 (1.00) |
0.0628 (1.00) |
1 (1.00) |
20p gain | 11 (31%) | 25 |
1 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.482 (1.00) |
0.724 (1.00) |
0.426 (1.00) |
0.238 (1.00) |
0.279 (1.00) |
0.465 (1.00) |
0.338 (1.00) |
20q gain | 12 (33%) | 24 |
0.732 (1.00) |
0.617 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.754 (1.00) |
0.283 (1.00) |
0.141 (1.00) |
0.149 (1.00) |
0.499 (1.00) |
0.225 (1.00) |
21q gain | 3 (8%) | 33 |
1 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.674 (1.00) |
0.455 (1.00) |
0.887 (1.00) |
0.185 (1.00) |
0.707 (1.00) |
0.25 (1.00) |
0.131 (1.00) |
22q gain | 5 (14%) | 31 |
0.342 (1.00) |
0.599 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.0873 (1.00) |
0.287 (1.00) |
0.852 (1.00) |
0.933 (1.00) |
1 (1.00) |
0.928 (1.00) |
1p loss | 4 (11%) | 32 |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.657 (1.00) |
0.613 (1.00) |
0.815 (1.00) |
0.796 (1.00) |
0.626 (1.00) |
0.81 (1.00) |
3p loss | 22 (61%) | 14 |
0.00222 (0.366) |
0.249 (1.00) |
0.696 (1.00) |
0.0607 (1.00) |
0.617 (1.00) |
0.0117 (0.517) |
0.776 (1.00) |
0.589 (1.00) |
0.499 (1.00) |
0.991 (1.00) |
3q loss | 3 (8%) | 33 |
0.593 (1.00) |
0.479 (1.00) |
0.52 (1.00) |
0.166 (1.00) |
0.0229 (0.631) |
0.69 (1.00) |
0.611 (1.00) |
0.559 (1.00) |
0.396 (1.00) |
|
4p loss | 10 (28%) | 26 |
0.274 (1.00) |
0.101 (1.00) |
0.417 (1.00) |
1 (1.00) |
0.224 (1.00) |
0.322 (1.00) |
0.784 (1.00) |
0.648 (1.00) |
0.709 (1.00) |
0.286 (1.00) |
4q loss | 13 (36%) | 23 |
1 (1.00) |
0.388 (1.00) |
1 (1.00) |
0.687 (1.00) |
0.371 (1.00) |
0.389 (1.00) |
0.459 (1.00) |
0.837 (1.00) |
0.736 (1.00) |
0.364 (1.00) |
6p loss | 5 (14%) | 31 |
0.65 (1.00) |
0.0221 (0.631) |
1 (1.00) |
1 (1.00) |
0.704 (1.00) |
0.982 (1.00) |
0.37 (1.00) |
0.241 (1.00) |
0.63 (1.00) |
0.982 (1.00) |
7p loss | 4 (11%) | 32 |
0.605 (1.00) |
0.421 (1.00) |
0.52 (1.00) |
0.43 (1.00) |
0.282 (1.00) |
0.513 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.857 (1.00) |
|
7q loss | 4 (11%) | 32 |
1 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.428 (1.00) |
0.285 (1.00) |
0.321 (1.00) |
0.277 (1.00) |
0.287 (1.00) |
0.391 (1.00) |
|
8p loss | 10 (28%) | 26 |
0.717 (1.00) |
0.127 (1.00) |
1 (1.00) |
0.55 (1.00) |
0.0178 (0.602) |
0.077 (1.00) |
0.0941 (1.00) |
0.0362 (0.824) |
0.26 (1.00) |
0.169 (1.00) |
8q loss | 3 (8%) | 33 |
0.593 (1.00) |
0.26 (1.00) |
0.279 (1.00) |
0.523 (1.00) |
0.245 (1.00) |
0.79 (1.00) |
0.77 (1.00) |
0.0774 (1.00) |
1 (1.00) |
0.133 (1.00) |
9p loss | 18 (50%) | 18 |
1 (1.00) |
0.288 (1.00) |
0.466 (1.00) |
0.00621 (0.476) |
0.692 (1.00) |
0.295 (1.00) |
0.188 (1.00) |
0.128 (1.00) |
0.5 (1.00) |
0.591 (1.00) |
9q loss | 19 (53%) | 17 |
1 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.0112 (0.517) |
0.582 (1.00) |
0.133 (1.00) |
0.708 (1.00) |
0.368 (1.00) |
0.192 (1.00) |
0.607 (1.00) |
10p loss | 6 (17%) | 30 |
1 (1.00) |
0.86 (1.00) |
1 (1.00) |
0.108 (1.00) |
0.732 (1.00) |
0.358 (1.00) |
0.581 (1.00) |
0.777 (1.00) |
0.677 (1.00) |
0.0142 (0.52) |
10q loss | 5 (14%) | 31 |
0.167 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.678 (1.00) |
0.41 (1.00) |
0.983 (1.00) |
0.851 (1.00) |
0.697 (1.00) |
1 (1.00) |
0.554 (1.00) |
11p loss | 8 (22%) | 28 |
0.434 (1.00) |
1 (1.00) |
0.626 (1.00) |
0.487 (1.00) |
0.208 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.839 (1.00) |
0.694 (1.00) |
0.39 (1.00) |
11q loss | 9 (25%) | 27 |
0.255 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.485 (1.00) |
0.0745 (1.00) |
0.472 (1.00) |
0.765 (1.00) |
0.583 (1.00) |
0.705 (1.00) |
0.758 (1.00) |
12q loss | 3 (8%) | 33 |
0.231 (1.00) |
0.478 (1.00) |
0.126 (1.00) |
0.325 (1.00) |
0.156 (1.00) |
0.609 (1.00) |
1 (1.00) |
1 (1.00) |
0.397 (1.00) |
|
13q loss | 15 (42%) | 21 |
1 (1.00) |
1 (1.00) |
0.712 (1.00) |
0.516 (1.00) |
0.63 (1.00) |
0.745 (1.00) |
0.754 (1.00) |
0.314 (1.00) |
0.736 (1.00) |
0.333 (1.00) |
14q loss | 13 (36%) | 23 |
0.014 (0.52) |
0.564 (1.00) |
0.419 (1.00) |
0.00718 (0.476) |
1 (1.00) |
0.0424 (0.848) |
1 (1.00) |
0.909 (1.00) |
0.484 (1.00) |
0.282 (1.00) |
15q loss | 5 (14%) | 31 |
0.342 (1.00) |
0.597 (1.00) |
1 (1.00) |
1 (1.00) |
0.087 (1.00) |
0.289 (1.00) |
0.508 (1.00) |
0.754 (1.00) |
0.63 (1.00) |
0.982 (1.00) |
16p loss | 4 (11%) | 32 |
1 (1.00) |
1 (1.00) |
0.52 (1.00) |
0.808 (1.00) |
1 (1.00) |
0.74 (1.00) |
0.966 (1.00) |
0.626 (1.00) |
0.186 (1.00) |
|
16q loss | 7 (19%) | 29 |
0.684 (1.00) |
0.333 (1.00) |
0.626 (1.00) |
0.431 (1.00) |
0.66 (1.00) |
0.412 (1.00) |
0.661 (1.00) |
0.0192 (0.602) |
1 (1.00) |
0.663 (1.00) |
17p loss | 10 (28%) | 26 |
0.717 (1.00) |
0.519 (1.00) |
1 (1.00) |
1 (1.00) |
0.113 (1.00) |
0.353 (1.00) |
0.255 (1.00) |
0.291 (1.00) |
1 (1.00) |
0.141 (1.00) |
18p loss | 6 (17%) | 30 |
1 (1.00) |
1 (1.00) |
0.126 (1.00) |
0.481 (1.00) |
0.445 (1.00) |
0.603 (1.00) |
0.238 (1.00) |
0.571 (1.00) |
0.367 (1.00) |
0.311 (1.00) |
18q loss | 8 (22%) | 28 |
0.236 (1.00) |
0.701 (1.00) |
0.327 (1.00) |
0.841 (1.00) |
0.101 (1.00) |
0.613 (1.00) |
0.131 (1.00) |
0.253 (1.00) |
0.424 (1.00) |
0.0628 (1.00) |
19p loss | 4 (11%) | 32 |
0.605 (1.00) |
0.299 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.148 (1.00) |
0.682 (1.00) |
0.0498 (0.966) |
0.243 (1.00) |
0.125 (1.00) |
0.00793 (0.476) |
19q loss | 3 (8%) | 33 |
1 (1.00) |
0.479 (1.00) |
0.52 (1.00) |
0.324 (1.00) |
0.734 (1.00) |
0.862 (1.00) |
1 (1.00) |
1 (1.00) |
0.578 (1.00) |
|
20p loss | 5 (14%) | 31 |
1 (1.00) |
0.596 (1.00) |
0.52 (1.00) |
0.0313 (0.739) |
0.522 (1.00) |
0.0954 (1.00) |
0.415 (1.00) |
0.376 (1.00) |
0.0117 (0.517) |
|
21q loss | 15 (42%) | 21 |
0.311 (1.00) |
1 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.136 (1.00) |
0.289 (1.00) |
0.332 (1.00) |
0.629 (1.00) |
0.31 (1.00) |
0.688 (1.00) |
22q loss | 5 (14%) | 31 |
0.65 (1.00) |
0.839 (1.00) |
0.626 (1.00) |
0.378 (1.00) |
0.333 (1.00) |
0.154 (1.00) |
0.677 (1.00) |
0.802 (1.00) |
0.376 (1.00) |
0.399 (1.00) |
xp loss | 15 (42%) | 21 |
0.00185 (0.366) |
0.0271 (0.663) |
0.442 (1.00) |
0.849 (1.00) |
1 (1.00) |
0.266 (1.00) |
0.575 (1.00) |
0.963 (1.00) |
0.501 (1.00) |
0.996 (1.00) |
xq loss | 15 (42%) | 21 |
0.00185 (0.366) |
0.027 (0.663) |
0.442 (1.00) |
0.848 (1.00) |
1 (1.00) |
0.263 (1.00) |
0.572 (1.00) |
0.962 (1.00) |
0.501 (1.00) |
0.996 (1.00) |
P value = 0.000242 (Fisher's exact test), Q value = 0.16
nPatients | CLUS_1 | CLUS_2 |
---|---|---|
ALL | 19 | 17 |
6Q LOSS MUTATED | 5 | 15 |
6Q LOSS WILD-TYPE | 14 | 2 |
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Copy number data file = broad_values_by_arm.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/CHOL-TP/15082092/transformed.cor.cli.txt
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Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/CHOL-TP/15087707/CHOL-TP.transferedmergedcluster.txt
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Number of patients = 36
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Number of significantly arm-level cnvs = 66
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Number of molecular subtypes = 10
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Exclude genes that fewer than K tumors have mutations, K = 3
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.