This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 67 focal events and 12 clinical features across 1025 patients, 51 significant findings detected with Q value < 0.25.
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amp_3p25.1 cnv correlated to 'PATHOLOGY.M.STAGE' and 'HISTOLOGICAL.TYPE'.
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amp_3q26.32 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_4q13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_6p23 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_6q21 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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amp_8q24.21 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_10p15.1 cnv correlated to 'HISTOLOGICAL.TYPE' and 'RACE'.
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amp_11p13 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_12p13.33 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_15q26.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_17q23.1 cnv correlated to 'PATHOLOGY.T.STAGE', 'GENDER', and 'HISTOLOGICAL.TYPE'.
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amp_19q12 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_20q13.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_1p36.13 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_1p22.1 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_2q37.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_3p21.31 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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del_4p16.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_4q35.1 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_5q11.2 cnv correlated to 'AGE', 'HISTOLOGICAL.TYPE', and 'RACE'.
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del_5q21.3 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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del_6q27 cnv correlated to 'AGE'.
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del_7p22.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_8p23.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_9p23 cnv correlated to 'Time to Death', 'PATHOLOGY.T.STAGE', and 'HISTOLOGICAL.TYPE'.
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del_9p21.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_9q21.11 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_9q34.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_10q26.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_11p15.5 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_13q14.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_14q24.1 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
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del_15q13.1 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_16q24.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_17q21.31 cnv correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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del_19p13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_19q13.32 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_20p13 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 | |
amp 17q23 1 | 407 (40%) | 618 |
0.0827 (1.00) |
0.523 (1.00) |
0.0174 (1.00) |
0.00026 (0.197) |
0.374 (1.00) |
0.00041 (0.307) |
3.56e-05 (0.0273) |
2e-05 (0.0154) |
0.775 (1.00) |
0.331 (1.00) |
0.178 (1.00) |
0.728 (1.00) |
del 5q11 2 | 267 (26%) | 758 |
0.255 (1.00) |
6.28e-05 (0.048) |
0.273 (1.00) |
0.0008 (0.591) |
0.328 (1.00) |
0.0894 (1.00) |
0.0762 (1.00) |
1e-05 (0.00804) |
0.474 (1.00) |
0.0881 (1.00) |
0.00015 (0.114) |
0.701 (1.00) |
del 9p23 | 311 (30%) | 714 |
0.000221 (0.167) |
0.278 (1.00) |
0.00261 (1.00) |
0.00033 (0.249) |
0.00182 (1.00) |
0.0118 (1.00) |
0.0993 (1.00) |
1e-05 (0.00804) |
0.495 (1.00) |
0.0415 (1.00) |
0.495 (1.00) |
0.855 (1.00) |
amp 3p25 1 | 193 (19%) | 832 |
0.0175 (1.00) |
0.174 (1.00) |
0.0141 (1.00) |
0.00036 (0.271) |
0.0317 (1.00) |
0.00018 (0.137) |
0.7 (1.00) |
9e-05 (0.0687) |
0.476 (1.00) |
0.374 (1.00) |
0.414 (1.00) |
1 (1.00) |
amp 6q21 | 192 (19%) | 833 |
0.0994 (1.00) |
0.411 (1.00) |
0.0902 (1.00) |
0.00012 (0.0914) |
0.192 (1.00) |
0.615 (1.00) |
0.7 (1.00) |
1e-05 (0.00804) |
0.37 (1.00) |
0.0625 (1.00) |
0.178 (1.00) |
0.828 (1.00) |
amp 10p15 1 | 297 (29%) | 728 |
0.205 (1.00) |
0.589 (1.00) |
0.296 (1.00) |
0.152 (1.00) |
0.5 (1.00) |
0.492 (1.00) |
0.526 (1.00) |
1e-05 (0.00804) |
0.217 (1.00) |
0.16 (1.00) |
3e-05 (0.023) |
0.57 (1.00) |
del 3p21 31 | 334 (33%) | 691 |
0.00558 (1.00) |
0.00518 (1.00) |
0.148 (1.00) |
2e-05 (0.0154) |
0.723 (1.00) |
0.752 (1.00) |
0.755 (1.00) |
1e-05 (0.00804) |
0.233 (1.00) |
0.481 (1.00) |
0.0181 (1.00) |
0.589 (1.00) |
del 5q21 3 | 259 (25%) | 766 |
0.354 (1.00) |
0.00175 (1.00) |
0.157 (1.00) |
0.00012 (0.0914) |
0.0681 (1.00) |
0.25 (1.00) |
0.0751 (1.00) |
1e-05 (0.00804) |
0.171 (1.00) |
0.00171 (1.00) |
0.00046 (0.343) |
0.701 (1.00) |
del 14q24 1 | 334 (33%) | 691 |
0.0345 (1.00) |
0.271 (1.00) |
0.268 (1.00) |
0.00026 (0.197) |
0.269 (1.00) |
0.981 (1.00) |
0.755 (1.00) |
1e-05 (0.00804) |
0.0527 (1.00) |
0.256 (1.00) |
0.00379 (1.00) |
0.858 (1.00) |
del 17q21 31 | 349 (34%) | 676 |
0.515 (1.00) |
0.000312 (0.235) |
0.312 (1.00) |
0.0767 (1.00) |
0.114 (1.00) |
0.148 (1.00) |
0.35 (1.00) |
1e-05 (0.00804) |
0.462 (1.00) |
0.552 (1.00) |
0.00067 (0.498) |
1 (1.00) |
amp 3q26 32 | 325 (32%) | 700 |
0.953 (1.00) |
0.465 (1.00) |
0.15 (1.00) |
0.00045 (0.337) |
0.3 (1.00) |
0.00643 (1.00) |
0.75 (1.00) |
1e-05 (0.00804) |
0.0428 (1.00) |
0.107 (1.00) |
0.00481 (1.00) |
0.143 (1.00) |
amp 4q13 3 | 158 (15%) | 867 |
0.0331 (1.00) |
0.302 (1.00) |
0.855 (1.00) |
0.196 (1.00) |
0.605 (1.00) |
0.169 (1.00) |
0.39 (1.00) |
1e-05 (0.00804) |
0.288 (1.00) |
0.908 (1.00) |
0.175 (1.00) |
0.23 (1.00) |
amp 6p23 | 285 (28%) | 740 |
0.912 (1.00) |
0.341 (1.00) |
0.56 (1.00) |
0.0022 (1.00) |
0.259 (1.00) |
0.678 (1.00) |
0.307 (1.00) |
1e-05 (0.00804) |
0.185 (1.00) |
0.938 (1.00) |
0.00284 (1.00) |
0.703 (1.00) |
amp 8q24 21 | 651 (64%) | 374 |
0.145 (1.00) |
0.0596 (1.00) |
0.404 (1.00) |
0.0261 (1.00) |
0.423 (1.00) |
0.00637 (1.00) |
0.345 (1.00) |
1e-05 (0.00804) |
0.0947 (1.00) |
0.608 (1.00) |
0.00415 (1.00) |
0.292 (1.00) |
amp 11p13 | 215 (21%) | 810 |
0.664 (1.00) |
0.38 (1.00) |
0.675 (1.00) |
0.384 (1.00) |
0.98 (1.00) |
0.434 (1.00) |
0.256 (1.00) |
1e-05 (0.00804) |
0.264 (1.00) |
0.466 (1.00) |
0.29 (1.00) |
0.676 (1.00) |
amp 12p13 33 | 271 (26%) | 754 |
0.926 (1.00) |
0.423 (1.00) |
0.382 (1.00) |
0.00082 (0.605) |
0.762 (1.00) |
0.419 (1.00) |
0.305 (1.00) |
1e-05 (0.00804) |
0.267 (1.00) |
0.466 (1.00) |
0.0403 (1.00) |
0.0848 (1.00) |
amp 15q26 3 | 187 (18%) | 838 |
0.213 (1.00) |
0.00459 (1.00) |
0.592 (1.00) |
0.297 (1.00) |
0.986 (1.00) |
0.0272 (1.00) |
0.123 (1.00) |
1e-05 (0.00804) |
0.416 (1.00) |
0.532 (1.00) |
0.0321 (1.00) |
0.375 (1.00) |
amp 19q12 | 271 (26%) | 754 |
0.47 (1.00) |
0.432 (1.00) |
0.076 (1.00) |
0.651 (1.00) |
0.0626 (1.00) |
0.211 (1.00) |
0.494 (1.00) |
1e-05 (0.00804) |
0.477 (1.00) |
0.00756 (1.00) |
0.0528 (1.00) |
0.848 (1.00) |
amp 20q13 2 | 523 (51%) | 502 |
0.45 (1.00) |
0.656 (1.00) |
0.166 (1.00) |
0.0042 (1.00) |
0.00484 (1.00) |
0.053 (1.00) |
0.0646 (1.00) |
1e-05 (0.00804) |
0.000782 (0.579) |
0.161 (1.00) |
0.327 (1.00) |
0.498 (1.00) |
del 1p36 13 | 427 (42%) | 598 |
0.074 (1.00) |
0.0433 (1.00) |
0.00435 (1.00) |
1e-05 (0.00804) |
0.00073 (0.542) |
0.187 (1.00) |
0.0601 (1.00) |
0.0052 (1.00) |
0.137 (1.00) |
0.000912 (0.671) |
0.972 (1.00) |
0.729 (1.00) |
del 1p22 1 | 345 (34%) | 680 |
0.00325 (1.00) |
0.119 (1.00) |
0.00956 (1.00) |
1e-05 (0.00804) |
0.00456 (1.00) |
0.407 (1.00) |
0.522 (1.00) |
0.334 (1.00) |
0.824 (1.00) |
0.000943 (0.693) |
0.497 (1.00) |
0.206 (1.00) |
del 2q37 3 | 304 (30%) | 721 |
0.713 (1.00) |
0.563 (1.00) |
0.248 (1.00) |
0.00261 (1.00) |
0.348 (1.00) |
0.441 (1.00) |
1 (1.00) |
1e-05 (0.00804) |
0.092 (1.00) |
0.261 (1.00) |
0.0166 (1.00) |
0.344 (1.00) |
del 4p16 3 | 323 (32%) | 702 |
0.76 (1.00) |
0.0657 (1.00) |
0.102 (1.00) |
0.00039 (0.293) |
0.699 (1.00) |
0.27 (1.00) |
1 (1.00) |
1e-05 (0.00804) |
0.292 (1.00) |
0.752 (1.00) |
0.0317 (1.00) |
0.716 (1.00) |
del 4q35 1 | 326 (32%) | 699 |
0.0859 (1.00) |
0.403 (1.00) |
0.243 (1.00) |
0.00342 (1.00) |
0.768 (1.00) |
0.00312 (1.00) |
0.518 (1.00) |
1e-05 (0.00804) |
0.548 (1.00) |
0.828 (1.00) |
0.0142 (1.00) |
0.142 (1.00) |
del 6q27 | 358 (35%) | 667 |
0.0976 (1.00) |
1.52e-05 (0.0117) |
0.438 (1.00) |
0.655 (1.00) |
0.0317 (1.00) |
0.454 (1.00) |
0.346 (1.00) |
0.245 (1.00) |
0.0563 (1.00) |
0.367 (1.00) |
0.718 (1.00) |
0.283 (1.00) |
del 7p22 3 | 133 (13%) | 892 |
0.907 (1.00) |
0.273 (1.00) |
0.332 (1.00) |
0.223 (1.00) |
0.0612 (1.00) |
0.129 (1.00) |
0.377 (1.00) |
1e-05 (0.00804) |
0.604 (1.00) |
0.0291 (1.00) |
0.581 (1.00) |
0.609 (1.00) |
del 8p23 2 | 532 (52%) | 493 |
0.15 (1.00) |
0.554 (1.00) |
0.996 (1.00) |
0.0158 (1.00) |
0.177 (1.00) |
0.229 (1.00) |
0.55 (1.00) |
1e-05 (0.00804) |
0.889 (1.00) |
0.924 (1.00) |
0.0041 (1.00) |
0.866 (1.00) |
del 9p21 3 | 346 (34%) | 679 |
0.0357 (1.00) |
0.389 (1.00) |
0.0179 (1.00) |
0.00161 (1.00) |
0.00493 (1.00) |
0.0497 (1.00) |
0.051 (1.00) |
1e-05 (0.00804) |
0.416 (1.00) |
0.088 (1.00) |
0.246 (1.00) |
0.858 (1.00) |
del 9q21 11 | 287 (28%) | 738 |
0.267 (1.00) |
0.884 (1.00) |
0.256 (1.00) |
0.0603 (1.00) |
0.254 (1.00) |
0.544 (1.00) |
0.0831 (1.00) |
1e-05 (0.00804) |
0.0621 (1.00) |
0.562 (1.00) |
0.065 (1.00) |
0.25 (1.00) |
del 9q34 2 | 285 (28%) | 740 |
0.836 (1.00) |
0.975 (1.00) |
0.0771 (1.00) |
0.00844 (1.00) |
0.0938 (1.00) |
0.482 (1.00) |
0.0136 (1.00) |
1e-05 (0.00804) |
0.073 (1.00) |
0.202 (1.00) |
0.0364 (1.00) |
0.254 (1.00) |
del 10q26 3 | 307 (30%) | 718 |
0.0668 (1.00) |
0.667 (1.00) |
0.248 (1.00) |
0.0511 (1.00) |
0.174 (1.00) |
0.296 (1.00) |
0.521 (1.00) |
2e-05 (0.0154) |
0.402 (1.00) |
0.367 (1.00) |
0.148 (1.00) |
0.00904 (1.00) |
del 11p15 5 | 296 (29%) | 729 |
0.0446 (1.00) |
0.753 (1.00) |
0.133 (1.00) |
0.00281 (1.00) |
0.482 (1.00) |
0.127 (1.00) |
0.525 (1.00) |
5e-05 (0.0382) |
0.488 (1.00) |
0.867 (1.00) |
0.00951 (1.00) |
0.342 (1.00) |
del 13q14 2 | 474 (46%) | 551 |
0.111 (1.00) |
0.651 (1.00) |
0.669 (1.00) |
0.0168 (1.00) |
0.542 (1.00) |
0.735 (1.00) |
0.763 (1.00) |
1e-05 (0.00804) |
0.183 (1.00) |
0.713 (1.00) |
0.0947 (1.00) |
0.175 (1.00) |
del 15q13 1 | 357 (35%) | 668 |
0.395 (1.00) |
0.299 (1.00) |
0.0985 (1.00) |
0.00139 (1.00) |
0.0223 (1.00) |
0.534 (1.00) |
1 (1.00) |
1e-05 (0.00804) |
0.0665 (1.00) |
0.0781 (1.00) |
0.0912 (1.00) |
0.86 (1.00) |
del 16q24 3 | 653 (64%) | 372 |
0.461 (1.00) |
0.00055 (0.41) |
0.0568 (1.00) |
0.151 (1.00) |
0.489 (1.00) |
0.204 (1.00) |
1 (1.00) |
1e-05 (0.00804) |
0.424 (1.00) |
0.473 (1.00) |
0.0162 (1.00) |
0.159 (1.00) |
del 19p13 3 | 343 (33%) | 682 |
0.0847 (1.00) |
0.00637 (1.00) |
0.808 (1.00) |
0.0473 (1.00) |
0.796 (1.00) |
0.437 (1.00) |
0.353 (1.00) |
1e-05 (0.00804) |
0.824 (1.00) |
0.0645 (1.00) |
0.00644 (1.00) |
1 (1.00) |
del 19q13 32 | 200 (20%) | 825 |
0.386 (1.00) |
0.479 (1.00) |
0.538 (1.00) |
0.441 (1.00) |
0.0994 (1.00) |
0.42 (1.00) |
1 (1.00) |
1e-05 (0.00804) |
0.0104 (1.00) |
0.892 (1.00) |
0.366 (1.00) |
0.522 (1.00) |
del 20p13 | 155 (15%) | 870 |
0.187 (1.00) |
0.0725 (1.00) |
0.249 (1.00) |
0.434 (1.00) |
0.936 (1.00) |
0.177 (1.00) |
0.224 (1.00) |
1e-05 (0.00804) |
0.118 (1.00) |
0.95 (1.00) |
0.13 (1.00) |
0.809 (1.00) |
amp 1p22 3 | 235 (23%) | 790 |
0.786 (1.00) |
0.313 (1.00) |
0.271 (1.00) |
0.0134 (1.00) |
0.00805 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.205 (1.00) |
0.561 (1.00) |
0.00782 (1.00) |
0.025 (1.00) |
1 (1.00) |
amp 1q21 3 | 746 (73%) | 279 |
0.751 (1.00) |
0.916 (1.00) |
0.256 (1.00) |
0.0153 (1.00) |
0.607 (1.00) |
0.423 (1.00) |
0.182 (1.00) |
0.0396 (1.00) |
0.583 (1.00) |
0.846 (1.00) |
0.23 (1.00) |
0.0588 (1.00) |
amp 1q44 | 744 (73%) | 281 |
0.0215 (1.00) |
0.396 (1.00) |
0.155 (1.00) |
0.00704 (1.00) |
0.338 (1.00) |
0.154 (1.00) |
1 (1.00) |
0.00152 (1.00) |
0.876 (1.00) |
0.535 (1.00) |
0.0173 (1.00) |
0.0855 (1.00) |
amp 5p15 33 | 372 (36%) | 653 |
0.274 (1.00) |
0.171 (1.00) |
0.458 (1.00) |
0.272 (1.00) |
0.0132 (1.00) |
0.0374 (1.00) |
0.54 (1.00) |
0.129 (1.00) |
0.0947 (1.00) |
0.909 (1.00) |
0.375 (1.00) |
0.596 (1.00) |
amp 8p11 23 | 390 (38%) | 635 |
0.0552 (1.00) |
0.0928 (1.00) |
0.0295 (1.00) |
0.618 (1.00) |
0.13 (1.00) |
0.12 (1.00) |
0.547 (1.00) |
0.468 (1.00) |
0.719 (1.00) |
0.0111 (1.00) |
0.824 (1.00) |
0.602 (1.00) |
amp 8p11 21 | 402 (39%) | 623 |
0.813 (1.00) |
0.0921 (1.00) |
0.693 (1.00) |
0.858 (1.00) |
0.805 (1.00) |
0.453 (1.00) |
0.542 (1.00) |
0.00553 (1.00) |
0.316 (1.00) |
0.588 (1.00) |
0.172 (1.00) |
0.601 (1.00) |
amp 10q22 3 | 149 (15%) | 876 |
0.0953 (1.00) |
0.924 (1.00) |
0.285 (1.00) |
0.162 (1.00) |
0.243 (1.00) |
0.0794 (1.00) |
0.667 (1.00) |
0.00075 (0.556) |
0.114 (1.00) |
0.158 (1.00) |
0.148 (1.00) |
1 (1.00) |
amp 11q13 3 | 381 (37%) | 644 |
0.258 (1.00) |
0.286 (1.00) |
0.462 (1.00) |
0.0608 (1.00) |
0.557 (1.00) |
0.269 (1.00) |
0.112 (1.00) |
0.237 (1.00) |
0.885 (1.00) |
0.801 (1.00) |
0.352 (1.00) |
0.596 (1.00) |
amp 11q14 1 | 252 (25%) | 773 |
0.309 (1.00) |
0.319 (1.00) |
0.364 (1.00) |
0.0774 (1.00) |
0.103 (1.00) |
0.102 (1.00) |
0.151 (1.00) |
0.00491 (1.00) |
0.746 (1.00) |
0.687 (1.00) |
0.195 (1.00) |
0.424 (1.00) |
amp 12q15 | 265 (26%) | 760 |
0.142 (1.00) |
0.276 (1.00) |
0.0988 (1.00) |
0.00846 (1.00) |
0.00367 (1.00) |
0.163 (1.00) |
0.00887 (1.00) |
0.015 (1.00) |
0.936 (1.00) |
0.00836 (1.00) |
0.512 (1.00) |
0.326 (1.00) |
amp 13q34 | 172 (17%) | 853 |
0.677 (1.00) |
0.0808 (1.00) |
0.248 (1.00) |
0.00929 (1.00) |
0.244 (1.00) |
0.0218 (1.00) |
0.228 (1.00) |
0.00419 (1.00) |
1 (1.00) |
0.0558 (1.00) |
0.69 (1.00) |
0.822 (1.00) |
amp 14q21 1 | 207 (20%) | 818 |
0.417 (1.00) |
0.142 (1.00) |
0.102 (1.00) |
0.0152 (1.00) |
0.0141 (1.00) |
0.097 (1.00) |
1 (1.00) |
0.04 (1.00) |
0.487 (1.00) |
0.00786 (1.00) |
0.716 (1.00) |
0.281 (1.00) |
amp 17p11 2 | 143 (14%) | 882 |
0.203 (1.00) |
0.356 (1.00) |
0.406 (1.00) |
0.104 (1.00) |
0.678 (1.00) |
0.552 (1.00) |
0.189 (1.00) |
0.539 (1.00) |
0.0554 (1.00) |
0.265 (1.00) |
0.626 (1.00) |
1 (1.00) |
amp 17q12 | 319 (31%) | 706 |
0.109 (1.00) |
0.783 (1.00) |
0.475 (1.00) |
0.111 (1.00) |
0.142 (1.00) |
0.0442 (1.00) |
0.0053 (1.00) |
0.00044 (0.33) |
0.29 (1.00) |
0.474 (1.00) |
0.00091 (0.671) |
1 (1.00) |
amp 19p13 12 | 218 (21%) | 807 |
0.547 (1.00) |
0.809 (1.00) |
0.466 (1.00) |
0.348 (1.00) |
0.187 (1.00) |
0.0578 (1.00) |
0.0627 (1.00) |
0.0645 (1.00) |
0.0324 (1.00) |
0.00122 (0.893) |
0.289 (1.00) |
0.838 (1.00) |
amp 19q13 42 | 264 (26%) | 761 |
0.482 (1.00) |
0.386 (1.00) |
0.916 (1.00) |
0.393 (1.00) |
0.753 (1.00) |
0.00442 (1.00) |
0.163 (1.00) |
0.00964 (1.00) |
0.201 (1.00) |
0.109 (1.00) |
0.748 (1.00) |
0.439 (1.00) |
del 6p25 3 | 194 (19%) | 831 |
0.441 (1.00) |
0.0585 (1.00) |
0.349 (1.00) |
0.00784 (1.00) |
0.139 (1.00) |
0.398 (1.00) |
0.137 (1.00) |
0.0685 (1.00) |
0.0611 (1.00) |
0.567 (1.00) |
0.646 (1.00) |
0.52 (1.00) |
del 6q15 | 341 (33%) | 684 |
0.529 (1.00) |
0.0647 (1.00) |
0.325 (1.00) |
0.439 (1.00) |
0.0589 (1.00) |
0.476 (1.00) |
1 (1.00) |
0.319 (1.00) |
0.182 (1.00) |
0.0236 (1.00) |
0.101 (1.00) |
0.589 (1.00) |
del 7q36 1 | 195 (19%) | 830 |
0.167 (1.00) |
0.994 (1.00) |
0.418 (1.00) |
0.143 (1.00) |
0.29 (1.00) |
0.173 (1.00) |
1 (1.00) |
0.00034 (0.256) |
1 (1.00) |
0.95 (1.00) |
0.581 (1.00) |
0.282 (1.00) |
del 8p11 21 | 188 (18%) | 837 |
0.0397 (1.00) |
0.128 (1.00) |
0.834 (1.00) |
0.294 (1.00) |
0.23 (1.00) |
0.192 (1.00) |
0.232 (1.00) |
0.00068 (0.505) |
0.366 (1.00) |
0.238 (1.00) |
0.183 (1.00) |
1 (1.00) |
del 10q23 31 | 308 (30%) | 717 |
0.529 (1.00) |
0.156 (1.00) |
0.236 (1.00) |
0.0148 (1.00) |
0.161 (1.00) |
0.43 (1.00) |
0.189 (1.00) |
0.00045 (0.337) |
0.222 (1.00) |
0.343 (1.00) |
0.16 (1.00) |
0.0264 (1.00) |
del 11q23 3 | 520 (51%) | 505 |
0.758 (1.00) |
0.211 (1.00) |
0.0781 (1.00) |
0.0204 (1.00) |
0.0997 (1.00) |
0.156 (1.00) |
0.0643 (1.00) |
0.126 (1.00) |
1 (1.00) |
0.229 (1.00) |
0.0223 (1.00) |
0.736 (1.00) |
del 12p13 1 | 179 (17%) | 846 |
0.539 (1.00) |
0.548 (1.00) |
0.118 (1.00) |
0.292 (1.00) |
0.873 (1.00) |
0.212 (1.00) |
0.418 (1.00) |
0.00553 (1.00) |
0.311 (1.00) |
0.434 (1.00) |
0.577 (1.00) |
1 (1.00) |
del 12q23 1 | 194 (19%) | 831 |
0.944 (1.00) |
0.168 (1.00) |
0.456 (1.00) |
0.0246 (1.00) |
0.701 (1.00) |
0.701 (1.00) |
0.7 (1.00) |
0.0057 (1.00) |
0.929 (1.00) |
0.271 (1.00) |
0.00621 (1.00) |
0.831 (1.00) |
del 12q24 31 | 198 (19%) | 827 |
0.222 (1.00) |
0.152 (1.00) |
0.661 (1.00) |
0.0361 (1.00) |
0.576 (1.00) |
0.484 (1.00) |
0.136 (1.00) |
0.0746 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.149 (1.00) |
0.52 (1.00) |
del 17p12 | 614 (60%) | 411 |
0.503 (1.00) |
0.00188 (1.00) |
0.479 (1.00) |
0.0702 (1.00) |
0.751 (1.00) |
0.46 (1.00) |
0.54 (1.00) |
0.00171 (1.00) |
0.319 (1.00) |
0.669 (1.00) |
0.0823 (1.00) |
0.862 (1.00) |
del 18q23 | 337 (33%) | 688 |
0.0244 (1.00) |
0.359 (1.00) |
0.0475 (1.00) |
0.022 (1.00) |
0.0829 (1.00) |
0.885 (1.00) |
0.355 (1.00) |
0.00139 (1.00) |
0.101 (1.00) |
0.355 (1.00) |
0.0492 (1.00) |
0.857 (1.00) |
del 21q11 2 | 203 (20%) | 822 |
0.356 (1.00) |
0.514 (1.00) |
0.0131 (1.00) |
0.0096 (1.00) |
0.0295 (1.00) |
0.179 (1.00) |
0.703 (1.00) |
0.00101 (0.741) |
0.381 (1.00) |
0.274 (1.00) |
0.58 (1.00) |
0.207 (1.00) |
del 22q13 32 | 464 (45%) | 561 |
0.504 (1.00) |
0.509 (1.00) |
0.682 (1.00) |
0.288 (1.00) |
0.663 (1.00) |
0.623 (1.00) |
0.558 (1.00) |
0.00349 (1.00) |
0.00491 (1.00) |
0.971 (1.00) |
0.498 (1.00) |
0.735 (1.00) |
P value = 0.00018 (Fisher's exact test), Q value = 0.14
nPatients | CM0 (I+) | M0 | M1 | MX |
---|---|---|---|---|
ALL | 5 | 854 | 19 | 147 |
AMP PEAK 4(3P25.1) MUTATED | 0 | 176 | 6 | 11 |
AMP PEAK 4(3P25.1) WILD-TYPE | 5 | 678 | 13 | 136 |
P value = 9e-05 (Fisher's exact test), Q value = 0.069
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 4(3P25.1) MUTATED | 1 | 165 | 13 | 1 | 5 | 1 | 7 |
AMP PEAK 4(3P25.1) WILD-TYPE | 0 | 589 | 162 | 5 | 24 | 14 | 37 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 5(3Q26.32) MUTATED | 1 | 286 | 12 | 5 | 6 | 1 | 13 |
AMP PEAK 5(3Q26.32) WILD-TYPE | 0 | 468 | 163 | 1 | 23 | 14 | 31 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 6(4Q13.3) MUTATED | 0 | 140 | 6 | 2 | 1 | 1 | 8 |
AMP PEAK 6(4Q13.3) WILD-TYPE | 1 | 614 | 169 | 4 | 28 | 14 | 36 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 8(6P23) MUTATED | 0 | 239 | 22 | 4 | 5 | 2 | 12 |
AMP PEAK 8(6P23) WILD-TYPE | 1 | 515 | 153 | 2 | 24 | 13 | 32 |
P value = 0.00012 (Fisher's exact test), Q value = 0.091
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
AMP PEAK 9(6Q21) MUTATED | 30 | 138 | 20 | 4 |
AMP PEAK 9(6Q21) WILD-TYPE | 235 | 456 | 104 | 35 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 9(6Q21) MUTATED | 1 | 164 | 14 | 3 | 1 | 0 | 9 |
AMP PEAK 9(6Q21) WILD-TYPE | 0 | 590 | 161 | 3 | 28 | 15 | 35 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 12(8Q24.21) MUTATED | 1 | 532 | 63 | 6 | 16 | 5 | 27 |
AMP PEAK 12(8Q24.21) WILD-TYPE | 0 | 222 | 112 | 0 | 13 | 10 | 17 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 13(10P15.1) MUTATED | 1 | 257 | 19 | 5 | 5 | 0 | 9 |
AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 497 | 156 | 1 | 24 | 15 | 35 |
P value = 3e-05 (Fisher's exact test), Q value = 0.023
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 56 | 158 | 717 |
AMP PEAK 13(10P15.1) MUTATED | 1 | 14 | 69 | 184 |
AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 42 | 89 | 533 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 15(11P13) MUTATED | 1 | 184 | 14 | 3 | 2 | 2 | 9 |
AMP PEAK 15(11P13) WILD-TYPE | 0 | 570 | 161 | 3 | 27 | 13 | 35 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 18(12P13.33) MUTATED | 1 | 223 | 25 | 4 | 9 | 1 | 8 |
AMP PEAK 18(12P13.33) WILD-TYPE | 0 | 531 | 150 | 2 | 20 | 14 | 36 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 22(15Q26.3) MUTATED | 0 | 163 | 8 | 3 | 4 | 3 | 5 |
AMP PEAK 22(15Q26.3) WILD-TYPE | 1 | 591 | 167 | 3 | 25 | 12 | 39 |
P value = 0.00026 (Fisher's exact test), Q value = 0.2
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
AMP PEAK 25(17Q23.1) MUTATED | 77 | 263 | 47 | 18 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 188 | 331 | 77 | 21 |
P value = 3.56e-05 (Fisher's exact test), Q value = 0.027
nPatients | FEMALE | MALE |
---|---|---|
ALL | 1014 | 11 |
AMP PEAK 25(17Q23.1) MUTATED | 396 | 11 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 618 | 0 |
P value = 2e-05 (Fisher's exact test), Q value = 0.015
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 25(17Q23.1) MUTATED | 1 | 332 | 40 | 3 | 9 | 5 | 16 |
AMP PEAK 25(17Q23.1) WILD-TYPE | 0 | 422 | 135 | 3 | 20 | 10 | 28 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 27(19Q12) MUTATED | 0 | 221 | 27 | 6 | 5 | 2 | 10 |
AMP PEAK 27(19Q12) WILD-TYPE | 1 | 533 | 148 | 0 | 24 | 13 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
AMP PEAK 29(20Q13.2) MUTATED | 1 | 442 | 48 | 1 | 11 | 1 | 19 |
AMP PEAK 29(20Q13.2) WILD-TYPE | 0 | 312 | 127 | 5 | 18 | 14 | 25 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 1(1P36.13) MUTATED | 78 | 275 | 48 | 25 |
DEL PEAK 1(1P36.13) WILD-TYPE | 187 | 319 | 76 | 14 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 2(1P22.1) MUTATED | 64 | 216 | 41 | 24 |
DEL PEAK 2(1P22.1) WILD-TYPE | 201 | 378 | 83 | 15 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 3(2Q37.3) MUTATED | 0 | 254 | 22 | 3 | 10 | 3 | 11 |
DEL PEAK 3(2Q37.3) WILD-TYPE | 1 | 500 | 153 | 3 | 19 | 12 | 33 |
P value = 2e-05 (Fisher's exact test), Q value = 0.015
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 4(3P21.31) MUTATED | 55 | 229 | 39 | 10 |
DEL PEAK 4(3P21.31) WILD-TYPE | 210 | 365 | 85 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 4(3P21.31) MUTATED | 1 | 279 | 37 | 1 | 5 | 0 | 11 |
DEL PEAK 4(3P21.31) WILD-TYPE | 0 | 475 | 138 | 5 | 24 | 15 | 33 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 5(4P16.3) MUTATED | 1 | 272 | 25 | 4 | 7 | 0 | 14 |
DEL PEAK 5(4P16.3) WILD-TYPE | 0 | 482 | 150 | 2 | 22 | 15 | 30 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 6(4Q35.1) MUTATED | 1 | 279 | 28 | 4 | 3 | 0 | 10 |
DEL PEAK 6(4Q35.1) WILD-TYPE | 0 | 475 | 147 | 2 | 26 | 15 | 34 |
P value = 6.28e-05 (Wilcoxon-test), Q value = 0.048
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1012 | 58.6 (13.2) |
DEL PEAK 7(5Q11.2) MUTATED | 265 | 56.0 (13.3) |
DEL PEAK 7(5Q11.2) WILD-TYPE | 747 | 59.6 (13.1) |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 7(5Q11.2) MUTATED | 1 | 237 | 8 | 5 | 4 | 1 | 10 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 517 | 167 | 1 | 25 | 14 | 34 |
P value = 0.00015 (Fisher's exact test), Q value = 0.11
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 56 | 158 | 717 |
DEL PEAK 7(5Q11.2) MUTATED | 1 | 19 | 60 | 167 |
DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 37 | 98 | 550 |
P value = 0.00012 (Fisher's exact test), Q value = 0.091
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 8(5Q21.3) MUTATED | 52 | 176 | 17 | 12 |
DEL PEAK 8(5Q21.3) WILD-TYPE | 213 | 418 | 107 | 27 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 8(5Q21.3) MUTATED | 1 | 234 | 4 | 6 | 4 | 0 | 9 |
DEL PEAK 8(5Q21.3) WILD-TYPE | 0 | 520 | 171 | 0 | 25 | 15 | 35 |
P value = 1.52e-05 (Wilcoxon-test), Q value = 0.012
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1012 | 58.6 (13.2) |
DEL PEAK 11(6Q27) MUTATED | 354 | 56.0 (12.7) |
DEL PEAK 11(6Q27) WILD-TYPE | 658 | 60.0 (13.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 12(7P22.3) MUTATED | 0 | 120 | 3 | 1 | 3 | 0 | 6 |
DEL PEAK 12(7P22.3) WILD-TYPE | 1 | 634 | 172 | 5 | 26 | 15 | 38 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 14(8P23.2) MUTATED | 1 | 435 | 53 | 3 | 11 | 3 | 25 |
DEL PEAK 14(8P23.2) WILD-TYPE | 0 | 319 | 122 | 3 | 18 | 12 | 19 |
P value = 0.000221 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 1005 | 119 | 0.0 - 234.3 (22.4) |
DEL PEAK 16(9P23) MUTATED | 306 | 45 | 0.1 - 162.1 (20.8) |
DEL PEAK 16(9P23) WILD-TYPE | 699 | 74 | 0.0 - 234.3 (23.6) |
P value = 0.00033 (Fisher's exact test), Q value = 0.25
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 16(9P23) MUTATED | 58 | 200 | 34 | 19 |
DEL PEAK 16(9P23) WILD-TYPE | 207 | 394 | 90 | 20 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 16(9P23) MUTATED | 0 | 263 | 20 | 3 | 9 | 5 | 11 |
DEL PEAK 16(9P23) WILD-TYPE | 1 | 491 | 155 | 3 | 20 | 10 | 33 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 17(9P21.3) MUTATED | 1 | 295 | 19 | 4 | 11 | 5 | 11 |
DEL PEAK 17(9P21.3) WILD-TYPE | 0 | 459 | 156 | 2 | 18 | 10 | 33 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 18(9Q21.11) MUTATED | 0 | 242 | 20 | 2 | 10 | 3 | 10 |
DEL PEAK 18(9Q21.11) WILD-TYPE | 1 | 512 | 155 | 4 | 19 | 12 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 19(9Q34.2) MUTATED | 0 | 245 | 18 | 4 | 6 | 3 | 8 |
DEL PEAK 19(9Q34.2) WILD-TYPE | 1 | 509 | 157 | 2 | 23 | 12 | 36 |
P value = 2e-05 (Fisher's exact test), Q value = 0.015
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 21(10Q26.3) MUTATED | 0 | 251 | 29 | 5 | 7 | 1 | 13 |
DEL PEAK 21(10Q26.3) WILD-TYPE | 1 | 503 | 146 | 1 | 22 | 14 | 31 |
P value = 5e-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 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 22(11P15.5) MUTATED | 0 | 242 | 28 | 4 | 10 | 2 | 10 |
DEL PEAK 22(11P15.5) WILD-TYPE | 1 | 512 | 147 | 2 | 19 | 13 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 27(13Q14.2) MUTATED | 0 | 380 | 59 | 5 | 11 | 2 | 16 |
DEL PEAK 27(13Q14.2) WILD-TYPE | 1 | 374 | 116 | 1 | 18 | 13 | 28 |
P value = 0.00026 (Fisher's exact test), Q value = 0.2
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 265 | 594 | 124 | 39 |
DEL PEAK 28(14Q24.1) MUTATED | 64 | 226 | 33 | 10 |
DEL PEAK 28(14Q24.1) WILD-TYPE | 201 | 368 | 91 | 29 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 28(14Q24.1) MUTATED | 1 | 285 | 29 | 4 | 3 | 1 | 10 |
DEL PEAK 28(14Q24.1) WILD-TYPE | 0 | 469 | 146 | 2 | 26 | 14 | 34 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 29(15Q13.1) MUTATED | 1 | 295 | 35 | 4 | 8 | 1 | 12 |
DEL PEAK 29(15Q13.1) WILD-TYPE | 0 | 459 | 140 | 2 | 21 | 14 | 32 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 30(16Q24.3) MUTATED | 0 | 456 | 157 | 3 | 20 | 1 | 16 |
DEL PEAK 30(16Q24.3) WILD-TYPE | 1 | 298 | 18 | 3 | 9 | 14 | 28 |
P value = 0.000312 (Wilcoxon-test), Q value = 0.24
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 1012 | 58.6 (13.2) |
DEL PEAK 32(17Q21.31) MUTATED | 342 | 56.8 (13.4) |
DEL PEAK 32(17Q21.31) WILD-TYPE | 670 | 59.6 (13.0) |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 32(17Q21.31) MUTATED | 0 | 283 | 33 | 4 | 11 | 1 | 16 |
DEL PEAK 32(17Q21.31) WILD-TYPE | 1 | 471 | 142 | 2 | 18 | 14 | 28 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 34(19P13.3) MUTATED | 1 | 292 | 19 | 5 | 8 | 4 | 13 |
DEL PEAK 34(19P13.3) WILD-TYPE | 0 | 462 | 156 | 1 | 21 | 11 | 31 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 35(19Q13.32) MUTATED | 0 | 177 | 6 | 3 | 5 | 3 | 5 |
DEL PEAK 35(19Q13.32) WILD-TYPE | 1 | 577 | 169 | 3 | 24 | 12 | 39 |
P value = 1e-05 (Fisher's exact test), Q value = 0.008
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 754 | 175 | 6 | 29 | 15 | 44 |
DEL PEAK 36(20P13) MUTATED | 1 | 136 | 9 | 2 | 2 | 0 | 5 |
DEL PEAK 36(20P13) WILD-TYPE | 0 | 618 | 166 | 4 | 27 | 15 | 39 |
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = BRCA-TP.merged_data.txt
-
Number of patients = 1025
-
Number of significantly focal cnvs = 67
-
Number of selected clinical features = 12
-
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.