This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 80 arm-level events and 12 clinical features across 995 patients, 28 significant findings detected with Q value < 0.25.
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2p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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3q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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6p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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8q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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10p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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21q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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xq gain cnv correlated to 'HISTOLOGICAL.TYPE'.
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1p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.T.STAGE'.
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4p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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4q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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5p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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5q loss cnv correlated to 'AGE', 'HISTOLOGICAL.TYPE', and 'RACE'.
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8p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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9p loss cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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9q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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13q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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14q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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15q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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16q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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18p loss cnv correlated to 'Time to Death'.
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19p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
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19q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-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 | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
5q loss | 212 (21%) | 783 |
0.348 (1.00) |
0.000261 (0.244) |
0.273 (1.00) |
0.00553 (1.00) |
0.253 (1.00) |
0.554 (1.00) |
0.134 (1.00) |
1e-05 (0.00959) |
0.493 (1.00) |
0.0672 (1.00) |
9e-05 (0.0845) |
0.304 (1.00) |
1p loss | 226 (23%) | 769 |
0.0301 (1.00) |
0.000588 (0.546) |
6e-05 (0.0565) |
3e-05 (0.0283) |
0.00596 (1.00) |
0.43 (1.00) |
1 (1.00) |
0.503 (1.00) |
0.675 (1.00) |
0.001 (0.922) |
0.799 (1.00) |
0.677 (1.00) |
9p loss | 296 (30%) | 699 |
0.0226 (1.00) |
0.872 (1.00) |
0.00113 (1.00) |
0.00014 (0.131) |
0.0372 (1.00) |
0.0459 (1.00) |
0.0944 (1.00) |
1e-05 (0.00959) |
0.0909 (1.00) |
0.354 (1.00) |
0.203 (1.00) |
0.575 (1.00) |
2p gain | 113 (11%) | 882 |
0.275 (1.00) |
0.536 (1.00) |
0.705 (1.00) |
0.604 (1.00) |
0.993 (1.00) |
0.974 (1.00) |
0.624 (1.00) |
1e-05 (0.00959) |
0.377 (1.00) |
0.645 (1.00) |
0.00344 (1.00) |
0.0161 (1.00) |
3q gain | 197 (20%) | 798 |
0.572 (1.00) |
0.385 (1.00) |
0.721 (1.00) |
0.163 (1.00) |
0.536 (1.00) |
0.227 (1.00) |
0.703 (1.00) |
1e-05 (0.00959) |
0.217 (1.00) |
0.0158 (1.00) |
0.0226 (1.00) |
0.83 (1.00) |
6p gain | 190 (19%) | 805 |
0.308 (1.00) |
0.927 (1.00) |
0.76 (1.00) |
0.128 (1.00) |
0.458 (1.00) |
0.864 (1.00) |
0.701 (1.00) |
0.00021 (0.196) |
0.153 (1.00) |
0.172 (1.00) |
0.0572 (1.00) |
0.382 (1.00) |
8q gain | 494 (50%) | 501 |
0.55 (1.00) |
0.755 (1.00) |
0.359 (1.00) |
0.707 (1.00) |
0.447 (1.00) |
0.0892 (1.00) |
0.382 (1.00) |
1e-05 (0.00959) |
0.0291 (1.00) |
0.539 (1.00) |
0.0263 (1.00) |
0.172 (1.00) |
10p gain | 200 (20%) | 795 |
0.991 (1.00) |
0.492 (1.00) |
0.128 (1.00) |
0.277 (1.00) |
0.225 (1.00) |
0.11 (1.00) |
1 (1.00) |
6e-05 (0.0565) |
0.0534 (1.00) |
0.437 (1.00) |
0.00346 (1.00) |
1 (1.00) |
20p gain | 383 (38%) | 612 |
0.172 (1.00) |
0.281 (1.00) |
0.0871 (1.00) |
0.606 (1.00) |
0.00852 (1.00) |
0.00596 (1.00) |
0.0269 (1.00) |
1e-05 (0.00959) |
0.0206 (1.00) |
0.476 (1.00) |
0.914 (1.00) |
0.383 (1.00) |
20q gain | 417 (42%) | 578 |
0.32 (1.00) |
0.798 (1.00) |
0.287 (1.00) |
0.0566 (1.00) |
0.0495 (1.00) |
0.0405 (1.00) |
0.218 (1.00) |
1e-05 (0.00959) |
0.134 (1.00) |
0.257 (1.00) |
0.615 (1.00) |
0.171 (1.00) |
21q gain | 187 (19%) | 808 |
0.00378 (1.00) |
0.0767 (1.00) |
0.768 (1.00) |
0.738 (1.00) |
0.806 (1.00) |
0.476 (1.00) |
1 (1.00) |
3e-05 (0.0283) |
0.0583 (1.00) |
0.801 (1.00) |
0.0204 (1.00) |
0.274 (1.00) |
xq gain | 130 (13%) | 865 |
0.3 (1.00) |
0.0968 (1.00) |
0.573 (1.00) |
0.435 (1.00) |
0.716 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.00018 (0.169) |
0.0606 (1.00) |
0.569 (1.00) |
0.249 (1.00) |
0.609 (1.00) |
4p loss | 324 (33%) | 671 |
0.302 (1.00) |
0.298 (1.00) |
0.45 (1.00) |
0.0353 (1.00) |
0.675 (1.00) |
0.468 (1.00) |
0.755 (1.00) |
1e-05 (0.00959) |
0.764 (1.00) |
0.816 (1.00) |
0.0187 (1.00) |
0.589 (1.00) |
4q loss | 288 (29%) | 707 |
0.819 (1.00) |
0.871 (1.00) |
0.598 (1.00) |
0.0713 (1.00) |
0.784 (1.00) |
0.389 (1.00) |
0.739 (1.00) |
1e-05 (0.00959) |
0.535 (1.00) |
0.99 (1.00) |
0.0171 (1.00) |
0.71 (1.00) |
5p loss | 130 (13%) | 865 |
0.348 (1.00) |
0.00579 (1.00) |
0.929 (1.00) |
0.0565 (1.00) |
0.941 (1.00) |
0.91 (1.00) |
1 (1.00) |
1e-05 (0.00959) |
0.144 (1.00) |
0.552 (1.00) |
0.104 (1.00) |
0.461 (1.00) |
8p loss | 362 (36%) | 633 |
0.0283 (1.00) |
0.238 (1.00) |
0.959 (1.00) |
0.249 (1.00) |
0.684 (1.00) |
0.329 (1.00) |
0.755 (1.00) |
2e-05 (0.0189) |
0.559 (1.00) |
0.385 (1.00) |
0.0351 (1.00) |
0.482 (1.00) |
9q loss | 268 (27%) | 727 |
0.276 (1.00) |
0.829 (1.00) |
0.142 (1.00) |
0.00311 (1.00) |
0.133 (1.00) |
0.477 (1.00) |
0.0785 (1.00) |
1e-05 (0.00959) |
0.0576 (1.00) |
0.929 (1.00) |
0.0111 (1.00) |
0.562 (1.00) |
13q loss | 408 (41%) | 587 |
0.0462 (1.00) |
0.369 (1.00) |
0.766 (1.00) |
0.0711 (1.00) |
0.855 (1.00) |
0.986 (1.00) |
0.767 (1.00) |
0.00025 (0.233) |
0.567 (1.00) |
0.694 (1.00) |
0.0122 (1.00) |
0.3 (1.00) |
14q loss | 240 (24%) | 755 |
0.0286 (1.00) |
0.619 (1.00) |
0.875 (1.00) |
0.0328 (1.00) |
0.0595 (1.00) |
0.936 (1.00) |
0.476 (1.00) |
4e-05 (0.0377) |
0.251 (1.00) |
0.0505 (1.00) |
0.00055 (0.511) |
0.326 (1.00) |
15q loss | 296 (30%) | 699 |
0.113 (1.00) |
0.658 (1.00) |
0.541 (1.00) |
0.0106 (1.00) |
0.0462 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.00018 (0.169) |
0.0909 (1.00) |
0.185 (1.00) |
0.181 (1.00) |
0.356 (1.00) |
16q loss | 546 (55%) | 449 |
0.0592 (1.00) |
0.000784 (0.726) |
0.321 (1.00) |
0.451 (1.00) |
0.0651 (1.00) |
0.113 (1.00) |
0.238 (1.00) |
1e-05 (0.00959) |
0.0564 (1.00) |
0.0997 (1.00) |
0.703 (1.00) |
0.734 (1.00) |
18p loss | 293 (29%) | 702 |
9.48e-07 (0.00091) |
0.00479 (1.00) |
0.0572 (1.00) |
0.0132 (1.00) |
0.436 (1.00) |
0.93 (1.00) |
1 (1.00) |
0.0104 (1.00) |
0.878 (1.00) |
0.171 (1.00) |
0.0256 (1.00) |
0.71 (1.00) |
19p loss | 176 (18%) | 819 |
0.105 (1.00) |
0.0885 (1.00) |
0.858 (1.00) |
0.585 (1.00) |
0.409 (1.00) |
0.183 (1.00) |
1 (1.00) |
1e-05 (0.00959) |
0.461 (1.00) |
0.721 (1.00) |
0.00939 (1.00) |
0.371 (1.00) |
19q loss | 149 (15%) | 846 |
0.162 (1.00) |
0.998 (1.00) |
0.665 (1.00) |
0.499 (1.00) |
0.15 (1.00) |
0.285 (1.00) |
0.674 (1.00) |
1e-05 (0.00959) |
0.0937 (1.00) |
0.436 (1.00) |
0.146 (1.00) |
1 (1.00) |
1p gain | 188 (19%) | 807 |
0.392 (1.00) |
0.0977 (1.00) |
0.851 (1.00) |
0.0719 (1.00) |
0.309 (1.00) |
0.941 (1.00) |
1 (1.00) |
0.0196 (1.00) |
0.0388 (1.00) |
0.11 (1.00) |
0.215 (1.00) |
0.519 (1.00) |
1q gain | 649 (65%) | 346 |
0.314 (1.00) |
0.478 (1.00) |
0.0324 (1.00) |
0.00379 (1.00) |
0.596 (1.00) |
0.635 (1.00) |
0.528 (1.00) |
0.0032 (1.00) |
1 (1.00) |
0.847 (1.00) |
0.0791 (1.00) |
0.0746 (1.00) |
2q gain | 71 (7%) | 924 |
0.857 (1.00) |
0.882 (1.00) |
0.886 (1.00) |
0.463 (1.00) |
0.885 (1.00) |
1 (1.00) |
1 (1.00) |
0.0112 (1.00) |
0.786 (1.00) |
0.653 (1.00) |
0.0503 (1.00) |
0.102 (1.00) |
3p gain | 131 (13%) | 864 |
0.335 (1.00) |
0.313 (1.00) |
0.0864 (1.00) |
0.0396 (1.00) |
0.431 (1.00) |
0.00072 (0.667) |
1 (1.00) |
0.00125 (1.00) |
0.535 (1.00) |
0.38 (1.00) |
0.457 (1.00) |
0.795 (1.00) |
4p gain | 74 (7%) | 921 |
0.105 (1.00) |
0.765 (1.00) |
0.18 (1.00) |
0.0745 (1.00) |
0.698 (1.00) |
0.262 (1.00) |
0.575 (1.00) |
0.00586 (1.00) |
0.688 (1.00) |
0.664 (1.00) |
0.656 (1.00) |
0.739 (1.00) |
4q gain | 70 (7%) | 925 |
0.0554 (1.00) |
0.884 (1.00) |
0.242 (1.00) |
0.193 (1.00) |
0.499 (1.00) |
0.275 (1.00) |
0.554 (1.00) |
0.00276 (1.00) |
1 (1.00) |
0.813 (1.00) |
0.471 (1.00) |
0.731 (1.00) |
5p gain | 290 (29%) | 705 |
0.0768 (1.00) |
0.123 (1.00) |
0.384 (1.00) |
0.613 (1.00) |
0.00123 (1.00) |
0.0219 (1.00) |
0.314 (1.00) |
0.514 (1.00) |
0.395 (1.00) |
0.414 (1.00) |
0.379 (1.00) |
1 (1.00) |
5q gain | 194 (19%) | 801 |
0.561 (1.00) |
0.00823 (1.00) |
0.475 (1.00) |
0.35 (1.00) |
0.179 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.75 (1.00) |
0.479 (1.00) |
0.957 (1.00) |
0.0149 (1.00) |
1 (1.00) |
6q gain | 136 (14%) | 859 |
0.268 (1.00) |
0.989 (1.00) |
0.579 (1.00) |
0.0992 (1.00) |
0.0955 (1.00) |
0.977 (1.00) |
1 (1.00) |
0.00067 (0.622) |
0.358 (1.00) |
0.02 (1.00) |
0.26 (1.00) |
0.314 (1.00) |
7p gain | 283 (28%) | 712 |
0.531 (1.00) |
0.14 (1.00) |
0.903 (1.00) |
0.832 (1.00) |
0.926 (1.00) |
0.511 (1.00) |
0.0155 (1.00) |
0.124 (1.00) |
0.242 (1.00) |
0.989 (1.00) |
0.554 (1.00) |
0.85 (1.00) |
7q gain | 239 (24%) | 756 |
0.729 (1.00) |
0.871 (1.00) |
0.599 (1.00) |
0.536 (1.00) |
0.582 (1.00) |
0.595 (1.00) |
0.307 (1.00) |
0.223 (1.00) |
0.935 (1.00) |
0.393 (1.00) |
0.245 (1.00) |
0.689 (1.00) |
8p gain | 270 (27%) | 725 |
0.787 (1.00) |
0.878 (1.00) |
0.569 (1.00) |
0.814 (1.00) |
0.726 (1.00) |
0.252 (1.00) |
0.502 (1.00) |
0.384 (1.00) |
0.937 (1.00) |
0.79 (1.00) |
0.168 (1.00) |
1 (1.00) |
9p gain | 128 (13%) | 867 |
0.767 (1.00) |
0.95 (1.00) |
0.167 (1.00) |
0.479 (1.00) |
0.146 (1.00) |
0.794 (1.00) |
0.377 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.714 (1.00) |
0.622 (1.00) |
0.803 (1.00) |
9q gain | 108 (11%) | 887 |
0.18 (1.00) |
0.73 (1.00) |
0.513 (1.00) |
0.46 (1.00) |
0.206 (1.00) |
0.972 (1.00) |
0.62 (1.00) |
0.319 (1.00) |
0.574 (1.00) |
0.874 (1.00) |
0.366 (1.00) |
1 (1.00) |
10q gain | 117 (12%) | 878 |
0.638 (1.00) |
0.414 (1.00) |
0.623 (1.00) |
0.325 (1.00) |
0.819 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.0217 (1.00) |
0.063 (1.00) |
0.319 (1.00) |
0.102 (1.00) |
0.592 (1.00) |
11p gain | 129 (13%) | 866 |
0.465 (1.00) |
0.991 (1.00) |
0.938 (1.00) |
0.729 (1.00) |
0.231 (1.00) |
0.706 (1.00) |
0.643 (1.00) |
0.00523 (1.00) |
0.917 (1.00) |
0.0482 (1.00) |
0.709 (1.00) |
0.455 (1.00) |
11q gain | 89 (9%) | 906 |
0.103 (1.00) |
0.972 (1.00) |
0.654 (1.00) |
0.71 (1.00) |
0.393 (1.00) |
0.753 (1.00) |
1 (1.00) |
0.00123 (1.00) |
0.624 (1.00) |
0.192 (1.00) |
0.201 (1.00) |
0.562 (1.00) |
12p gain | 214 (22%) | 781 |
0.252 (1.00) |
0.805 (1.00) |
0.648 (1.00) |
0.12 (1.00) |
0.114 (1.00) |
0.736 (1.00) |
0.0653 (1.00) |
0.0172 (1.00) |
0.231 (1.00) |
0.452 (1.00) |
0.62 (1.00) |
0.403 (1.00) |
12q gain | 181 (18%) | 814 |
0.155 (1.00) |
0.303 (1.00) |
0.137 (1.00) |
0.0428 (1.00) |
0.00631 (1.00) |
0.523 (1.00) |
0.034 (1.00) |
0.0618 (1.00) |
0.172 (1.00) |
0.0068 (1.00) |
0.71 (1.00) |
0.375 (1.00) |
13q gain | 86 (9%) | 909 |
0.777 (1.00) |
0.423 (1.00) |
0.674 (1.00) |
0.422 (1.00) |
0.469 (1.00) |
0.297 (1.00) |
0.613 (1.00) |
0.004 (1.00) |
0.382 (1.00) |
0.789 (1.00) |
0.417 (1.00) |
0.121 (1.00) |
14q gain | 134 (13%) | 861 |
0.43 (1.00) |
0.0845 (1.00) |
0.196 (1.00) |
0.164 (1.00) |
0.057 (1.00) |
0.676 (1.00) |
0.377 (1.00) |
0.142 (1.00) |
0.537 (1.00) |
0.0339 (1.00) |
0.719 (1.00) |
0.212 (1.00) |
15q gain | 83 (8%) | 912 |
0.37 (1.00) |
0.812 (1.00) |
0.696 (1.00) |
0.835 (1.00) |
0.931 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.00135 (1.00) |
0.164 (1.00) |
0.997 (1.00) |
0.204 (1.00) |
1 (1.00) |
16p gain | 443 (45%) | 552 |
0.897 (1.00) |
0.0163 (1.00) |
0.616 (1.00) |
0.8 (1.00) |
0.402 (1.00) |
0.909 (1.00) |
0.553 (1.00) |
0.0419 (1.00) |
0.437 (1.00) |
0.716 (1.00) |
0.164 (1.00) |
0.126 (1.00) |
16q gain | 129 (13%) | 866 |
0.0707 (1.00) |
0.783 (1.00) |
0.21 (1.00) |
0.301 (1.00) |
0.188 (1.00) |
0.158 (1.00) |
0.0429 (1.00) |
0.143 (1.00) |
1 (1.00) |
0.273 (1.00) |
0.51 (1.00) |
0.213 (1.00) |
17p gain | 101 (10%) | 894 |
0.157 (1.00) |
0.913 (1.00) |
0.155 (1.00) |
0.0243 (1.00) |
0.0814 (1.00) |
0.477 (1.00) |
0.00275 (1.00) |
0.123 (1.00) |
0.0618 (1.00) |
0.879 (1.00) |
0.656 (1.00) |
0.777 (1.00) |
17q gain | 208 (21%) | 787 |
0.0498 (1.00) |
0.663 (1.00) |
0.806 (1.00) |
0.272 (1.00) |
0.675 (1.00) |
0.18 (1.00) |
0.00243 (1.00) |
0.0653 (1.00) |
0.0464 (1.00) |
0.293 (1.00) |
0.856 (1.00) |
0.676 (1.00) |
18p gain | 163 (16%) | 832 |
0.287 (1.00) |
0.298 (1.00) |
0.0636 (1.00) |
0.391 (1.00) |
0.0249 (1.00) |
0.607 (1.00) |
0.699 (1.00) |
0.00394 (1.00) |
0.506 (1.00) |
0.0163 (1.00) |
0.00043 (0.401) |
0.102 (1.00) |
18q gain | 138 (14%) | 857 |
0.813 (1.00) |
0.692 (1.00) |
0.139 (1.00) |
0.247 (1.00) |
0.249 (1.00) |
0.0686 (1.00) |
0.656 (1.00) |
0.0449 (1.00) |
0.418 (1.00) |
0.281 (1.00) |
0.207 (1.00) |
0.213 (1.00) |
19p gain | 170 (17%) | 825 |
0.971 (1.00) |
0.721 (1.00) |
0.311 (1.00) |
0.199 (1.00) |
0.205 (1.00) |
0.16 (1.00) |
0.102 (1.00) |
0.196 (1.00) |
0.224 (1.00) |
0.0175 (1.00) |
0.865 (1.00) |
1 (1.00) |
19q gain | 201 (20%) | 794 |
0.543 (1.00) |
0.105 (1.00) |
0.273 (1.00) |
0.68 (1.00) |
0.107 (1.00) |
0.0435 (1.00) |
0.247 (1.00) |
0.442 (1.00) |
0.382 (1.00) |
0.014 (1.00) |
0.935 (1.00) |
0.833 (1.00) |
22q gain | 94 (9%) | 901 |
0.127 (1.00) |
0.714 (1.00) |
0.304 (1.00) |
0.101 (1.00) |
0.384 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.00196 (1.00) |
0.188 (1.00) |
0.144 (1.00) |
0.027 (1.00) |
1 (1.00) |
1q loss | 50 (5%) | 945 |
0.378 (1.00) |
0.275 (1.00) |
0.795 (1.00) |
0.314 (1.00) |
0.0424 (1.00) |
0.333 (1.00) |
1 (1.00) |
0.199 (1.00) |
1 (1.00) |
0.14 (1.00) |
0.456 (1.00) |
1 (1.00) |
2p loss | 168 (17%) | 827 |
0.703 (1.00) |
0.324 (1.00) |
0.318 (1.00) |
0.475 (1.00) |
0.0604 (1.00) |
0.094 (1.00) |
1 (1.00) |
0.309 (1.00) |
0.024 (1.00) |
0.419 (1.00) |
0.435 (1.00) |
0.0531 (1.00) |
2q loss | 190 (19%) | 805 |
0.265 (1.00) |
0.413 (1.00) |
0.143 (1.00) |
0.373 (1.00) |
0.0693 (1.00) |
0.0696 (1.00) |
1 (1.00) |
0.134 (1.00) |
0.108 (1.00) |
0.166 (1.00) |
0.564 (1.00) |
0.044 (1.00) |
3p loss | 170 (17%) | 825 |
0.362 (1.00) |
0.0735 (1.00) |
0.843 (1.00) |
0.00089 (0.821) |
0.862 (1.00) |
0.756 (1.00) |
0.228 (1.00) |
0.00536 (1.00) |
0.0116 (1.00) |
0.827 (1.00) |
0.0967 (1.00) |
0.0461 (1.00) |
3q loss | 93 (9%) | 902 |
0.137 (1.00) |
0.326 (1.00) |
0.326 (1.00) |
0.00045 (0.419) |
0.707 (1.00) |
0.61 (1.00) |
0.613 (1.00) |
0.0698 (1.00) |
0.022 (1.00) |
0.836 (1.00) |
0.2 (1.00) |
0.0414 (1.00) |
6p loss | 170 (17%) | 825 |
0.843 (1.00) |
0.0591 (1.00) |
0.888 (1.00) |
0.434 (1.00) |
0.697 (1.00) |
0.0446 (1.00) |
0.701 (1.00) |
0.576 (1.00) |
0.161 (1.00) |
0.99 (1.00) |
0.689 (1.00) |
0.494 (1.00) |
6q loss | 250 (25%) | 745 |
0.604 (1.00) |
0.00129 (1.00) |
0.667 (1.00) |
0.309 (1.00) |
0.403 (1.00) |
0.404 (1.00) |
0.308 (1.00) |
0.682 (1.00) |
0.0151 (1.00) |
0.307 (1.00) |
0.959 (1.00) |
0.556 (1.00) |
7p loss | 104 (10%) | 891 |
0.581 (1.00) |
0.576 (1.00) |
0.448 (1.00) |
0.458 (1.00) |
0.0634 (1.00) |
0.143 (1.00) |
0.617 (1.00) |
0.00369 (1.00) |
0.422 (1.00) |
0.264 (1.00) |
0.396 (1.00) |
0.165 (1.00) |
7q loss | 113 (11%) | 882 |
0.0884 (1.00) |
0.161 (1.00) |
0.524 (1.00) |
0.447 (1.00) |
0.306 (1.00) |
0.139 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.377 (1.00) |
0.887 (1.00) |
0.875 (1.00) |
0.0256 (1.00) |
8q loss | 81 (8%) | 914 |
0.044 (1.00) |
0.23 (1.00) |
0.934 (1.00) |
0.496 (1.00) |
0.36 (1.00) |
0.497 (1.00) |
1 (1.00) |
0.823 (1.00) |
0.156 (1.00) |
0.664 (1.00) |
0.0145 (1.00) |
0.543 (1.00) |
10p loss | 159 (16%) | 836 |
0.0214 (1.00) |
0.661 (1.00) |
0.0387 (1.00) |
0.0111 (1.00) |
0.124 (1.00) |
0.00863 (1.00) |
0.229 (1.00) |
0.0942 (1.00) |
0.924 (1.00) |
0.182 (1.00) |
0.395 (1.00) |
0.345 (1.00) |
10q loss | 213 (21%) | 782 |
0.0265 (1.00) |
0.972 (1.00) |
0.151 (1.00) |
0.0113 (1.00) |
0.168 (1.00) |
0.0148 (1.00) |
0.473 (1.00) |
0.0141 (1.00) |
1 (1.00) |
0.42 (1.00) |
0.0615 (1.00) |
0.0597 (1.00) |
11p loss | 253 (25%) | 742 |
0.259 (1.00) |
0.689 (1.00) |
0.147 (1.00) |
0.0781 (1.00) |
0.0392 (1.00) |
0.872 (1.00) |
0.739 (1.00) |
0.125 (1.00) |
0.518 (1.00) |
0.159 (1.00) |
0.00242 (1.00) |
0.0724 (1.00) |
11q loss | 338 (34%) | 657 |
0.893 (1.00) |
0.811 (1.00) |
0.265 (1.00) |
0.235 (1.00) |
0.0228 (1.00) |
0.483 (1.00) |
0.199 (1.00) |
0.411 (1.00) |
0.553 (1.00) |
0.265 (1.00) |
0.00313 (1.00) |
0.857 (1.00) |
12p loss | 139 (14%) | 856 |
0.462 (1.00) |
0.331 (1.00) |
0.326 (1.00) |
0.0282 (1.00) |
0.553 (1.00) |
0.147 (1.00) |
1 (1.00) |
0.00201 (1.00) |
0.362 (1.00) |
0.304 (1.00) |
0.319 (1.00) |
0.463 (1.00) |
12q loss | 117 (12%) | 878 |
0.693 (1.00) |
0.0139 (1.00) |
0.263 (1.00) |
0.0187 (1.00) |
0.577 (1.00) |
0.21 (1.00) |
0.628 (1.00) |
0.00088 (0.813) |
0.445 (1.00) |
0.0706 (1.00) |
0.0401 (1.00) |
0.608 (1.00) |
16p loss | 154 (15%) | 841 |
0.689 (1.00) |
0.557 (1.00) |
0.249 (1.00) |
0.982 (1.00) |
0.0986 (1.00) |
0.592 (1.00) |
0.683 (1.00) |
0.132 (1.00) |
0.383 (1.00) |
0.066 (1.00) |
0.00646 (1.00) |
0.818 (1.00) |
17p loss | 532 (53%) | 463 |
0.343 (1.00) |
0.0139 (1.00) |
0.102 (1.00) |
0.00609 (1.00) |
0.844 (1.00) |
0.801 (1.00) |
0.364 (1.00) |
0.00856 (1.00) |
0.888 (1.00) |
0.986 (1.00) |
0.121 (1.00) |
0.866 (1.00) |
17q loss | 250 (25%) | 745 |
0.952 (1.00) |
0.0881 (1.00) |
0.891 (1.00) |
0.461 (1.00) |
0.292 (1.00) |
0.22 (1.00) |
0.075 (1.00) |
0.00085 (0.786) |
1 (1.00) |
0.594 (1.00) |
0.00347 (1.00) |
1 (1.00) |
18q loss | 294 (30%) | 701 |
0.00126 (1.00) |
0.0178 (1.00) |
0.0607 (1.00) |
0.0584 (1.00) |
0.134 (1.00) |
0.767 (1.00) |
1 (1.00) |
0.0101 (1.00) |
0.397 (1.00) |
0.331 (1.00) |
0.156 (1.00) |
0.458 (1.00) |
20p loss | 85 (9%) | 910 |
0.24 (1.00) |
0.189 (1.00) |
0.494 (1.00) |
0.0679 (1.00) |
0.691 (1.00) |
0.414 (1.00) |
1 (1.00) |
0.0556 (1.00) |
0.317 (1.00) |
0.932 (1.00) |
0.2 (1.00) |
0.207 (1.00) |
20q loss | 47 (5%) | 948 |
0.195 (1.00) |
0.0751 (1.00) |
0.0716 (1.00) |
0.012 (1.00) |
0.917 (1.00) |
0.307 (1.00) |
1 (1.00) |
0.122 (1.00) |
0.619 (1.00) |
0.152 (1.00) |
0.0951 (1.00) |
0.0822 (1.00) |
21q loss | 164 (16%) | 831 |
0.731 (1.00) |
0.431 (1.00) |
0.0527 (1.00) |
0.437 (1.00) |
0.0267 (1.00) |
0.423 (1.00) |
0.228 (1.00) |
0.028 (1.00) |
0.395 (1.00) |
0.167 (1.00) |
0.112 (1.00) |
0.25 (1.00) |
22q loss | 440 (44%) | 555 |
0.152 (1.00) |
0.618 (1.00) |
0.699 (1.00) |
0.552 (1.00) |
0.312 (1.00) |
0.475 (1.00) |
0.551 (1.00) |
0.00204 (1.00) |
0.00111 (1.00) |
0.258 (1.00) |
0.382 (1.00) |
0.865 (1.00) |
xq loss | 164 (16%) | 831 |
0.65 (1.00) |
0.127 (1.00) |
0.469 (1.00) |
0.0257 (1.00) |
0.623 (1.00) |
0.106 (1.00) |
0.403 (1.00) |
0.0366 (1.00) |
0.777 (1.00) |
0.433 (1.00) |
0.365 (1.00) |
1 (1.00) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
2P GAIN MUTATED | 1 | 102 | 4 | 1 | 0 | 0 | 5 |
2P GAIN WILD-TYPE | 0 | 633 | 162 | 4 | 29 | 14 | 39 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
3Q GAIN MUTATED | 0 | 170 | 8 | 3 | 6 | 1 | 9 |
3Q GAIN WILD-TYPE | 1 | 565 | 158 | 2 | 23 | 13 | 35 |
P value = 0.00021 (Fisher's exact test), Q value = 0.2
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
6P GAIN MUTATED | 0 | 155 | 16 | 4 | 3 | 1 | 10 |
6P GAIN WILD-TYPE | 1 | 580 | 150 | 1 | 26 | 13 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
8Q GAIN MUTATED | 1 | 400 | 47 | 4 | 12 | 4 | 25 |
8Q GAIN WILD-TYPE | 0 | 335 | 119 | 1 | 17 | 10 | 19 |
P value = 6e-05 (Fisher's exact test), Q value = 0.056
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
10P GAIN MUTATED | 0 | 171 | 16 | 3 | 4 | 0 | 6 |
10P GAIN WILD-TYPE | 1 | 564 | 150 | 2 | 25 | 14 | 38 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
20P GAIN MUTATED | 0 | 321 | 37 | 1 | 9 | 1 | 13 |
20P GAIN WILD-TYPE | 1 | 414 | 129 | 4 | 20 | 13 | 31 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
20Q GAIN MUTATED | 0 | 350 | 41 | 1 | 9 | 1 | 15 |
20Q GAIN WILD-TYPE | 1 | 385 | 125 | 4 | 20 | 13 | 29 |
P value = 3e-05 (Fisher's exact test), Q value = 0.028
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
21Q GAIN MUTATED | 0 | 160 | 15 | 2 | 0 | 1 | 9 |
21Q GAIN WILD-TYPE | 1 | 575 | 151 | 3 | 29 | 13 | 35 |
P value = 0.00018 (Fisher's exact test), Q value = 0.17
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
XQ GAIN MUTATED | 1 | 110 | 8 | 2 | 1 | 3 | 4 |
XQ GAIN WILD-TYPE | 0 | 625 | 158 | 3 | 28 | 11 | 40 |
P value = 6e-05 (Fisher's exact test), Q value = 0.056
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 80 | 77 | 9 | 9 | 335 | 224 | 2 | 138 | 27 | 59 | 17 | 1 | 16 |
1P LOSS MUTATED | 12 | 11 | 1 | 3 | 73 | 39 | 1 | 42 | 16 | 18 | 6 | 0 | 4 |
1P LOSS WILD-TYPE | 68 | 66 | 8 | 6 | 262 | 185 | 1 | 96 | 11 | 41 | 11 | 1 | 12 |
P value = 3e-05 (Fisher's exact test), Q value = 0.028
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 581 | 117 | 36 |
1P LOSS MUTATED | 46 | 133 | 27 | 20 |
1P LOSS WILD-TYPE | 212 | 448 | 90 | 16 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
4P LOSS MUTATED | 1 | 271 | 27 | 2 | 7 | 0 | 15 |
4P LOSS WILD-TYPE | 0 | 464 | 139 | 3 | 22 | 14 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
4Q LOSS MUTATED | 0 | 240 | 24 | 1 | 7 | 0 | 15 |
4Q LOSS WILD-TYPE | 1 | 495 | 142 | 4 | 22 | 14 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
5P LOSS MUTATED | 0 | 114 | 2 | 3 | 4 | 0 | 6 |
5P LOSS WILD-TYPE | 1 | 621 | 164 | 2 | 25 | 14 | 38 |
P value = 0.000261 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 982 | 58.7 (13.1) |
5Q LOSS MUTATED | 210 | 55.9 (13.4) |
5Q LOSS WILD-TYPE | 772 | 59.4 (12.9) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
5Q LOSS MUTATED | 1 | 192 | 3 | 3 | 4 | 0 | 8 |
5Q LOSS WILD-TYPE | 0 | 543 | 163 | 2 | 25 | 14 | 36 |
P value = 9e-05 (Fisher's exact test), Q value = 0.085
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 56 | 137 | 708 |
5Q LOSS MUTATED | 0 | 17 | 48 | 131 |
5Q LOSS WILD-TYPE | 1 | 39 | 89 | 577 |
P value = 2e-05 (Fisher's exact test), Q value = 0.019
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
8P LOSS MUTATED | 1 | 297 | 35 | 2 | 8 | 1 | 17 |
8P LOSS WILD-TYPE | 0 | 438 | 131 | 3 | 21 | 13 | 27 |
P value = 0.00014 (Fisher's exact test), Q value = 0.13
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 581 | 117 | 36 |
9P LOSS MUTATED | 55 | 194 | 29 | 18 |
9P LOSS WILD-TYPE | 203 | 387 | 88 | 18 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
9P LOSS MUTATED | 0 | 252 | 20 | 3 | 9 | 3 | 9 |
9P LOSS WILD-TYPE | 1 | 483 | 146 | 2 | 20 | 11 | 35 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
9Q LOSS MUTATED | 0 | 225 | 18 | 2 | 9 | 3 | 11 |
9Q LOSS WILD-TYPE | 1 | 510 | 148 | 3 | 20 | 11 | 33 |
P value = 0.00025 (Fisher's exact test), Q value = 0.23
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
13Q LOSS MUTATED | 0 | 329 | 48 | 4 | 10 | 2 | 14 |
13Q LOSS WILD-TYPE | 1 | 406 | 118 | 1 | 19 | 12 | 30 |
P value = 4e-05 (Fisher's exact test), Q value = 0.038
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
14Q LOSS MUTATED | 0 | 200 | 22 | 4 | 3 | 1 | 9 |
14Q LOSS WILD-TYPE | 1 | 535 | 144 | 1 | 26 | 13 | 35 |
P value = 0.00018 (Fisher's exact test), Q value = 0.17
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
15Q LOSS MUTATED | 0 | 242 | 26 | 3 | 9 | 2 | 14 |
15Q LOSS WILD-TYPE | 1 | 493 | 140 | 2 | 20 | 12 | 30 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
16Q LOSS MUTATED | 0 | 379 | 130 | 2 | 19 | 1 | 14 |
16Q LOSS WILD-TYPE | 1 | 356 | 36 | 3 | 10 | 13 | 30 |
P value = 9.48e-07 (logrank test), Q value = 0.00091
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 974 | 114 | 0.0 - 234.3 (21.4) |
18P LOSS MUTATED | 285 | 51 | 0.0 - 189.0 (20.3) |
18P LOSS WILD-TYPE | 689 | 63 | 0.0 - 234.3 (22.4) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
19P LOSS MUTATED | 0 | 157 | 6 | 1 | 3 | 3 | 5 |
19P LOSS WILD-TYPE | 1 | 578 | 160 | 4 | 26 | 11 | 39 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0096
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 735 | 166 | 5 | 29 | 14 | 44 |
19Q LOSS MUTATED | 0 | 133 | 4 | 1 | 3 | 3 | 4 |
19Q LOSS WILD-TYPE | 1 | 602 | 162 | 4 | 26 | 11 | 40 |
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Copy number data file = transformed.cor.cli.txt
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Clinical data file = BRCA-TP.merged_data.txt
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Number of patients = 995
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Number of significantly arm-level cnvs = 80
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Number of selected clinical features = 12
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Exclude regions 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.