This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 68 focal events and 10 clinical features across 957 patients, 39 significant findings detected with Q value < 0.25.
-
amp_3p25.1 cnv correlated to 'PATHOLOGY.M.STAGE'.
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amp_3q26.32 cnv correlated to 'HISTOLOGICAL.TYPE'.
-
amp_4q13.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
-
amp_6p23 cnv correlated to 'HISTOLOGICAL.TYPE'.
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amp_6q21 cnv correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
-
amp_8q24.21 cnv correlated to 'HISTOLOGICAL.TYPE'.
-
amp_10p15.1 cnv correlated to 'HISTOLOGICAL.TYPE'.
-
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' and 'GENDER'.
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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_1p21.2 cnv correlated to 'PATHOLOGY.T.STAGE'.
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del_2q37.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_3p14.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_4p16.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_4q34.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_5q11.2 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_5q21.3 cnv correlated to '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 'HISTOLOGICAL.TYPE'.
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del_9p21.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_9q34.3 cnv correlated to 'HISTOLOGICAL.TYPE'.
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del_10q26.3 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 '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'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 68 focal events and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 39 significant findings detected.
|
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 |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | |
| amp 6q21 | 179 (19%) | 778 |
0.0132 (1.00) |
0.373 (1.00) |
0.0734 (1.00) |
7.77e-05 (0.0506) |
0.159 (1.00) |
0.817 (1.00) |
0.698 (1.00) |
2e-05 (0.0131) |
0.414 (1.00) |
0.143 (1.00) |
| amp 17q23 1 | 388 (41%) | 569 |
0.104 (1.00) |
0.693 (1.00) |
0.00986 (1.00) |
0.000156 (0.101) |
0.473 (1.00) |
0.00122 (0.763) |
0.000112 (0.0724) |
0.000539 (0.343) |
1 (1.00) |
0.144 (1.00) |
| del 17q21 31 | 332 (35%) | 625 |
0.556 (1.00) |
0.000185 (0.119) |
0.163 (1.00) |
0.104 (1.00) |
0.118 (1.00) |
0.164 (1.00) |
0.508 (1.00) |
1.32e-05 (0.00874) |
0.603 (1.00) |
0.411 (1.00) |
| amp 3p25 1 | 186 (19%) | 771 |
0.0144 (1.00) |
0.184 (1.00) |
0.0177 (1.00) |
0.0004 (0.256) |
0.0269 (1.00) |
0.000155 (0.0999) |
0.697 (1.00) |
0.00113 (0.711) |
0.591 (1.00) |
0.718 (1.00) |
| amp 3q26 32 | 305 (32%) | 652 |
0.787 (1.00) |
0.401 (1.00) |
0.298 (1.00) |
0.00301 (1.00) |
0.359 (1.00) |
0.00357 (1.00) |
0.734 (1.00) |
2.09e-12 (1.41e-09) |
0.0674 (1.00) |
0.223 (1.00) |
| amp 4q13 3 | 149 (16%) | 808 |
0.0574 (1.00) |
0.391 (1.00) |
0.896 (1.00) |
0.127 (1.00) |
0.673 (1.00) |
0.507 (1.00) |
0.66 (1.00) |
1.73e-05 (0.0114) |
0.328 (1.00) |
0.709 (1.00) |
| amp 6p23 | 258 (27%) | 699 |
0.592 (1.00) |
0.179 (1.00) |
0.43 (1.00) |
0.00989 (1.00) |
0.232 (1.00) |
0.545 (1.00) |
0.303 (1.00) |
1.71e-05 (0.0113) |
0.11 (1.00) |
0.275 (1.00) |
| amp 8q24 21 | 608 (64%) | 349 |
0.0538 (1.00) |
0.0515 (1.00) |
0.147 (1.00) |
0.0136 (1.00) |
0.399 (1.00) |
0.00973 (1.00) |
0.342 (1.00) |
1.73e-13 (1.17e-10) |
0.0767 (1.00) |
0.344 (1.00) |
| amp 10p15 1 | 271 (28%) | 686 |
0.137 (1.00) |
0.764 (1.00) |
0.216 (1.00) |
0.382 (1.00) |
0.617 (1.00) |
0.638 (1.00) |
0.298 (1.00) |
1.33e-08 (8.91e-06) |
0.115 (1.00) |
0.88 (1.00) |
| amp 11p13 | 199 (21%) | 758 |
0.453 (1.00) |
0.499 (1.00) |
0.804 (1.00) |
0.505 (1.00) |
0.982 (1.00) |
0.421 (1.00) |
0.442 (1.00) |
1.37e-05 (0.00903) |
0.19 (1.00) |
0.401 (1.00) |
| amp 12p13 33 | 251 (26%) | 706 |
0.944 (1.00) |
0.238 (1.00) |
0.469 (1.00) |
0.00358 (1.00) |
0.761 (1.00) |
0.396 (1.00) |
0.469 (1.00) |
6.23e-05 (0.0407) |
0.146 (1.00) |
0.922 (1.00) |
| amp 15q26 3 | 175 (18%) | 782 |
0.207 (1.00) |
0.00659 (1.00) |
0.454 (1.00) |
0.548 (1.00) |
0.956 (1.00) |
0.0222 (1.00) |
0.0916 (1.00) |
3.08e-05 (0.0202) |
0.409 (1.00) |
0.872 (1.00) |
| amp 19q12 | 247 (26%) | 710 |
0.194 (1.00) |
0.29 (1.00) |
0.148 (1.00) |
0.755 (1.00) |
0.0726 (1.00) |
0.0352 (1.00) |
0.292 (1.00) |
6.32e-05 (0.0412) |
0.225 (1.00) |
0.135 (1.00) |
| amp 20q13 2 | 487 (51%) | 470 |
0.498 (1.00) |
0.244 (1.00) |
0.145 (1.00) |
0.018 (1.00) |
0.00971 (1.00) |
0.0468 (1.00) |
0.108 (1.00) |
1.82e-13 (1.23e-10) |
0.000661 (0.419) |
1 (1.00) |
| del 1p36 13 | 400 (42%) | 557 |
0.115 (1.00) |
0.197 (1.00) |
0.00206 (1.00) |
2.16e-06 (0.00144) |
0.000511 (0.325) |
0.229 (1.00) |
0.104 (1.00) |
0.0125 (1.00) |
0.222 (1.00) |
0.0112 (1.00) |
| del 1p21 2 | 319 (33%) | 638 |
0.0475 (1.00) |
0.095 (1.00) |
0.0113 (1.00) |
3.13e-05 (0.0205) |
0.00659 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.652 (1.00) |
0.0342 (1.00) |
| del 2q37 3 | 287 (30%) | 670 |
0.692 (1.00) |
0.652 (1.00) |
0.461 (1.00) |
0.00655 (1.00) |
0.323 (1.00) |
0.576 (1.00) |
0.732 (1.00) |
8.37e-05 (0.0543) |
0.0749 (1.00) |
0.601 (1.00) |
| del 3p14 3 | 300 (31%) | 657 |
0.0178 (1.00) |
0.000614 (0.39) |
0.647 (1.00) |
0.000894 (0.564) |
0.453 (1.00) |
0.45 (1.00) |
1 (1.00) |
7.6e-06 (0.00504) |
0.146 (1.00) |
0.897 (1.00) |
| del 4p16 3 | 300 (31%) | 657 |
0.733 (1.00) |
0.197 (1.00) |
0.164 (1.00) |
0.000393 (0.252) |
0.575 (1.00) |
0.566 (1.00) |
0.733 (1.00) |
3.93e-06 (0.00262) |
0.193 (1.00) |
0.882 (1.00) |
| del 4q34 3 | 310 (32%) | 647 |
0.0489 (1.00) |
0.917 (1.00) |
0.328 (1.00) |
0.0045 (1.00) |
0.752 (1.00) |
0.0164 (1.00) |
0.514 (1.00) |
6.48e-07 (0.000434) |
0.65 (1.00) |
0.781 (1.00) |
| del 5q11 2 | 250 (26%) | 707 |
0.228 (1.00) |
0.00107 (0.672) |
0.312 (1.00) |
0.00643 (1.00) |
0.631 (1.00) |
0.226 (1.00) |
0.0715 (1.00) |
5.61e-11 (3.79e-08) |
0.375 (1.00) |
0.581 (1.00) |
| del 5q21 3 | 240 (25%) | 717 |
0.308 (1.00) |
0.0105 (1.00) |
0.197 (1.00) |
0.002 (1.00) |
0.163 (1.00) |
0.367 (1.00) |
0.0743 (1.00) |
1.34e-14 (9.09e-12) |
0.0863 (1.00) |
0.0285 (1.00) |
| del 6q27 | 329 (34%) | 628 |
0.087 (1.00) |
7.67e-06 (0.00508) |
0.358 (1.00) |
0.747 (1.00) |
0.0255 (1.00) |
0.106 (1.00) |
0.508 (1.00) |
0.376 (1.00) |
0.0167 (1.00) |
0.443 (1.00) |
| del 7p22 3 | 124 (13%) | 833 |
0.942 (1.00) |
0.163 (1.00) |
0.529 (1.00) |
0.261 (1.00) |
0.0552 (1.00) |
0.308 (1.00) |
0.377 (1.00) |
0.000235 (0.151) |
0.46 (1.00) |
0.0589 (1.00) |
| del 8p23 2 | 499 (52%) | 458 |
0.0786 (1.00) |
0.698 (1.00) |
0.96 (1.00) |
0.0112 (1.00) |
0.13 (1.00) |
0.181 (1.00) |
0.346 (1.00) |
2.29e-09 (1.54e-06) |
0.723 (1.00) |
0.72 (1.00) |
| del 9p23 | 299 (31%) | 658 |
0.00109 (0.688) |
0.538 (1.00) |
0.00477 (1.00) |
0.000489 (0.312) |
0.00337 (1.00) |
0.0328 (1.00) |
0.301 (1.00) |
1.71e-05 (0.0112) |
0.878 (1.00) |
0.32 (1.00) |
| del 9p21 3 | 333 (35%) | 624 |
0.0347 (1.00) |
0.782 (1.00) |
0.0111 (1.00) |
0.000693 (0.439) |
0.00548 (1.00) |
0.113 (1.00) |
0.105 (1.00) |
3.76e-09 (2.52e-06) |
0.655 (1.00) |
0.592 (1.00) |
| del 9q34 3 | 262 (27%) | 695 |
0.893 (1.00) |
0.78 (1.00) |
0.0435 (1.00) |
0.00324 (1.00) |
0.0502 (1.00) |
0.979 (1.00) |
0.03 (1.00) |
2.2e-06 (0.00147) |
0.204 (1.00) |
0.319 (1.00) |
| del 10q26 3 | 286 (30%) | 671 |
0.0424 (1.00) |
0.882 (1.00) |
0.18 (1.00) |
0.0906 (1.00) |
0.151 (1.00) |
0.3 (1.00) |
0.732 (1.00) |
0.000303 (0.195) |
0.439 (1.00) |
0.176 (1.00) |
| del 13q14 2 | 444 (46%) | 513 |
0.0945 (1.00) |
0.399 (1.00) |
0.592 (1.00) |
0.0348 (1.00) |
0.422 (1.00) |
0.899 (1.00) |
0.527 (1.00) |
8.52e-05 (0.0552) |
0.177 (1.00) |
0.0988 (1.00) |
| del 14q24 1 | 312 (33%) | 645 |
0.0601 (1.00) |
0.177 (1.00) |
0.449 (1.00) |
0.00238 (1.00) |
0.329 (1.00) |
0.976 (1.00) |
0.736 (1.00) |
2.6e-08 (1.74e-05) |
0.0339 (1.00) |
0.484 (1.00) |
| del 15q13 1 | 333 (35%) | 624 |
0.173 (1.00) |
0.132 (1.00) |
0.183 (1.00) |
0.00385 (1.00) |
0.0826 (1.00) |
0.147 (1.00) |
0.746 (1.00) |
7.28e-06 (0.00483) |
0.037 (1.00) |
0.805 (1.00) |
| del 16q24 3 | 609 (64%) | 348 |
0.132 (1.00) |
0.00152 (0.95) |
0.196 (1.00) |
0.214 (1.00) |
0.485 (1.00) |
0.178 (1.00) |
1 (1.00) |
1.92e-15 (1.31e-12) |
0.417 (1.00) |
0.778 (1.00) |
| del 19p13 3 | 318 (33%) | 639 |
0.181 (1.00) |
0.00772 (1.00) |
0.743 (1.00) |
0.171 (1.00) |
0.904 (1.00) |
0.432 (1.00) |
0.178 (1.00) |
1.2e-10 (8.08e-08) |
0.598 (1.00) |
0.0427 (1.00) |
| del 19q13 32 | 188 (20%) | 769 |
0.778 (1.00) |
0.569 (1.00) |
0.405 (1.00) |
0.408 (1.00) |
0.0728 (1.00) |
0.435 (1.00) |
0.697 (1.00) |
9.2e-07 (0.000614) |
0.00561 (1.00) |
0.369 (1.00) |
| del 20p13 | 145 (15%) | 812 |
0.0917 (1.00) |
0.0667 (1.00) |
0.517 (1.00) |
0.612 (1.00) |
0.795 (1.00) |
0.314 (1.00) |
0.654 (1.00) |
7.99e-05 (0.0519) |
0.0744 (1.00) |
0.269 (1.00) |
| amp 1p22 3 | 210 (22%) | 747 |
0.911 (1.00) |
0.379 (1.00) |
0.401 (1.00) |
0.027 (1.00) |
0.0251 (1.00) |
0.447 (1.00) |
1 (1.00) |
0.157 (1.00) |
0.932 (1.00) |
0.0488 (1.00) |
| amp 1q21 3 | 690 (72%) | 267 |
0.772 (1.00) |
0.907 (1.00) |
0.313 (1.00) |
0.0157 (1.00) |
0.794 (1.00) |
0.476 (1.00) |
0.478 (1.00) |
0.163 (1.00) |
0.429 (1.00) |
0.877 (1.00) |
| amp 1q44 | 688 (72%) | 269 |
0.0552 (1.00) |
0.563 (1.00) |
0.224 (1.00) |
0.0121 (1.00) |
0.533 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.0178 (1.00) |
0.693 (1.00) |
0.972 (1.00) |
| amp 5p15 33 | 350 (37%) | 607 |
0.126 (1.00) |
0.183 (1.00) |
0.65 (1.00) |
0.349 (1.00) |
0.00771 (1.00) |
0.0429 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.0771 (1.00) |
0.981 (1.00) |
| amp 8p11 23 | 365 (38%) | 592 |
0.0436 (1.00) |
0.184 (1.00) |
0.0748 (1.00) |
0.661 (1.00) |
0.195 (1.00) |
0.0248 (1.00) |
0.333 (1.00) |
0.637 (1.00) |
0.715 (1.00) |
0.0267 (1.00) |
| amp 8p11 21 | 371 (39%) | 586 |
0.741 (1.00) |
0.108 (1.00) |
0.721 (1.00) |
0.916 (1.00) |
0.835 (1.00) |
0.276 (1.00) |
0.332 (1.00) |
0.0366 (1.00) |
0.191 (1.00) |
0.798 (1.00) |
| amp 10q22 3 | 137 (14%) | 820 |
0.0876 (1.00) |
0.487 (1.00) |
0.119 (1.00) |
0.057 (1.00) |
0.404 (1.00) |
0.025 (1.00) |
1 (1.00) |
0.0164 (1.00) |
0.0848 (1.00) |
0.269 (1.00) |
| amp 11q13 3 | 356 (37%) | 601 |
0.337 (1.00) |
0.281 (1.00) |
0.741 (1.00) |
0.139 (1.00) |
0.722 (1.00) |
0.404 (1.00) |
0.187 (1.00) |
0.114 (1.00) |
1 (1.00) |
0.987 (1.00) |
| amp 11q14 1 | 236 (25%) | 721 |
0.348 (1.00) |
0.286 (1.00) |
0.524 (1.00) |
0.145 (1.00) |
0.212 (1.00) |
0.0381 (1.00) |
0.273 (1.00) |
0.00298 (1.00) |
0.622 (1.00) |
0.581 (1.00) |
| amp 12q15 | 249 (26%) | 708 |
0.132 (1.00) |
0.523 (1.00) |
0.139 (1.00) |
0.0124 (1.00) |
0.00868 (1.00) |
0.154 (1.00) |
0.00428 (1.00) |
0.0293 (1.00) |
1 (1.00) |
0.225 (1.00) |
| amp 13q34 | 163 (17%) | 794 |
0.588 (1.00) |
0.0406 (1.00) |
0.188 (1.00) |
0.00991 (1.00) |
0.336 (1.00) |
0.0207 (1.00) |
0.227 (1.00) |
0.023 (1.00) |
1 (1.00) |
0.122 (1.00) |
| amp 14q21 1 | 195 (20%) | 762 |
0.493 (1.00) |
0.075 (1.00) |
0.0898 (1.00) |
0.0126 (1.00) |
0.0126 (1.00) |
0.285 (1.00) |
0.697 (1.00) |
0.19 (1.00) |
0.66 (1.00) |
0.0734 (1.00) |
| amp 17q12 | 304 (32%) | 653 |
0.134 (1.00) |
0.865 (1.00) |
0.416 (1.00) |
0.0602 (1.00) |
0.152 (1.00) |
0.146 (1.00) |
0.00229 (1.00) |
0.00536 (1.00) |
0.493 (1.00) |
0.944 (1.00) |
| amp 19p13 12 | 198 (21%) | 759 |
0.746 (1.00) |
0.898 (1.00) |
0.676 (1.00) |
0.289 (1.00) |
0.277 (1.00) |
0.168 (1.00) |
0.0368 (1.00) |
0.00877 (1.00) |
0.00656 (1.00) |
0.0898 (1.00) |
| amp 19q13 42 | 247 (26%) | 710 |
0.509 (1.00) |
0.139 (1.00) |
0.965 (1.00) |
0.434 (1.00) |
0.76 (1.00) |
0.00247 (1.00) |
0.137 (1.00) |
0.0359 (1.00) |
0.225 (1.00) |
0.618 (1.00) |
| del 6p25 3 | 184 (19%) | 773 |
0.824 (1.00) |
0.01 (1.00) |
0.461 (1.00) |
0.0359 (1.00) |
0.283 (1.00) |
0.276 (1.00) |
0.415 (1.00) |
0.123 (1.00) |
0.0583 (1.00) |
0.291 (1.00) |
| del 6q15 | 316 (33%) | 641 |
0.711 (1.00) |
0.0224 (1.00) |
0.108 (1.00) |
0.365 (1.00) |
0.0345 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.463 (1.00) |
0.175 (1.00) |
0.253 (1.00) |
| del 7q36 1 | 184 (19%) | 773 |
0.0792 (1.00) |
0.937 (1.00) |
0.647 (1.00) |
0.25 (1.00) |
0.231 (1.00) |
0.364 (1.00) |
1 (1.00) |
0.00986 (1.00) |
0.928 (1.00) |
0.924 (1.00) |
| del 8p11 21 | 183 (19%) | 774 |
0.0429 (1.00) |
0.17 (1.00) |
0.647 (1.00) |
0.157 (1.00) |
0.244 (1.00) |
0.332 (1.00) |
0.223 (1.00) |
0.0109 (1.00) |
0.857 (1.00) |
0.37 (1.00) |
| del 9q21 11 | 271 (28%) | 686 |
0.402 (1.00) |
0.861 (1.00) |
0.178 (1.00) |
0.0492 (1.00) |
0.174 (1.00) |
0.374 (1.00) |
0.157 (1.00) |
0.000436 (0.279) |
0.115 (1.00) |
0.375 (1.00) |
| del 10q23 31 | 284 (30%) | 673 |
0.597 (1.00) |
0.344 (1.00) |
0.247 (1.00) |
0.0266 (1.00) |
0.235 (1.00) |
0.324 (1.00) |
0.297 (1.00) |
0.00154 (0.964) |
0.14 (1.00) |
0.291 (1.00) |
| del 11p15 5 | 276 (29%) | 681 |
0.137 (1.00) |
0.622 (1.00) |
0.254 (1.00) |
0.0159 (1.00) |
0.441 (1.00) |
0.39 (1.00) |
0.486 (1.00) |
0.0042 (1.00) |
0.435 (1.00) |
0.192 (1.00) |
| del 11q13 1 | 210 (22%) | 747 |
0.42 (1.00) |
0.952 (1.00) |
0.257 (1.00) |
0.128 (1.00) |
0.21 (1.00) |
0.657 (1.00) |
0.464 (1.00) |
0.737 (1.00) |
0.798 (1.00) |
0.954 (1.00) |
| del 11q23 2 | 485 (51%) | 472 |
0.621 (1.00) |
0.171 (1.00) |
0.152 (1.00) |
0.019 (1.00) |
0.0604 (1.00) |
0.378 (1.00) |
0.108 (1.00) |
0.222 (1.00) |
0.944 (1.00) |
0.891 (1.00) |
| del 11q25 | 449 (47%) | 508 |
0.362 (1.00) |
0.016 (1.00) |
0.1 (1.00) |
0.00473 (1.00) |
0.0985 (1.00) |
0.635 (1.00) |
0.0524 (1.00) |
0.0412 (1.00) |
0.67 (1.00) |
0.825 (1.00) |
| del 12p13 2 | 164 (17%) | 793 |
0.746 (1.00) |
0.536 (1.00) |
0.138 (1.00) |
0.188 (1.00) |
0.903 (1.00) |
0.0175 (1.00) |
0.388 (1.00) |
0.0182 (1.00) |
0.778 (1.00) |
0.64 (1.00) |
| del 12q24 31 | 180 (19%) | 777 |
0.198 (1.00) |
0.283 (1.00) |
0.689 (1.00) |
0.0402 (1.00) |
0.698 (1.00) |
0.636 (1.00) |
0.223 (1.00) |
0.0804 (1.00) |
0.856 (1.00) |
0.249 (1.00) |
| del 17p12 | 580 (61%) | 377 |
0.578 (1.00) |
0.000804 (0.508) |
0.483 (1.00) |
0.0509 (1.00) |
0.675 (1.00) |
0.55 (1.00) |
0.331 (1.00) |
0.00299 (1.00) |
0.425 (1.00) |
0.989 (1.00) |
| del 18q23 | 311 (32%) | 646 |
0.0328 (1.00) |
0.389 (1.00) |
0.116 (1.00) |
0.0648 (1.00) |
0.0902 (1.00) |
0.669 (1.00) |
0.736 (1.00) |
0.00941 (1.00) |
0.0816 (1.00) |
0.373 (1.00) |
| del 21q11 2 | 189 (20%) | 768 |
0.478 (1.00) |
0.441 (1.00) |
0.0185 (1.00) |
0.0688 (1.00) |
0.0285 (1.00) |
0.454 (1.00) |
0.696 (1.00) |
0.0136 (1.00) |
0.328 (1.00) |
0.226 (1.00) |
| del 22q11 1 | 407 (43%) | 550 |
0.525 (1.00) |
0.861 (1.00) |
0.591 (1.00) |
0.553 (1.00) |
0.377 (1.00) |
0.306 (1.00) |
0.53 (1.00) |
0.0294 (1.00) |
0.00156 (0.974) |
0.494 (1.00) |
| del 22q13 31 | 438 (46%) | 519 |
0.425 (1.00) |
0.465 (1.00) |
0.799 (1.00) |
0.359 (1.00) |
0.573 (1.00) |
0.49 (1.00) |
0.526 (1.00) |
0.0327 (1.00) |
0.0017 (1.00) |
0.682 (1.00) |
P value = 0.000155 (Fisher's exact test), Q value = 0.1
Table S1. Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
| nPatients | CM0 (I+) | M0 | M1 | MX |
|---|---|---|---|---|
| ALL | 2 | 825 | 15 | 115 |
| AMP PEAK 4(3P25.1) MUTATED | 0 | 172 | 6 | 8 |
| AMP PEAK 4(3P25.1) WILD-TYPE | 2 | 653 | 9 | 107 |
Figure S1. Get High-res Image Gene #4: 'amp_3p25.1' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'
P value = 2.09e-12 (Chi-square test), Q value = 1.4e-09
Table S2. Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 5(3Q26.32) MUTATED | 1 | 268 | 12 | 4 | 5 | 1 | 13 |
| AMP PEAK 5(3Q26.32) WILD-TYPE | 0 | 442 | 142 | 1 | 23 | 13 | 31 |
Figure S2. Get High-res Image Gene #5: 'amp_3q26.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.73e-05 (Chi-square test), Q value = 0.011
Table S3. Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 6(4Q13.3) MUTATED | 0 | 134 | 4 | 2 | 1 | 1 | 7 |
| AMP PEAK 6(4Q13.3) WILD-TYPE | 1 | 576 | 150 | 3 | 27 | 13 | 37 |
Figure S3. Get High-res Image Gene #6: 'amp_4q13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.71e-05 (Chi-square test), Q value = 0.011
Table S4. Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 8(6P23) MUTATED | 0 | 219 | 17 | 3 | 4 | 2 | 12 |
| AMP PEAK 8(6P23) WILD-TYPE | 1 | 491 | 137 | 2 | 24 | 12 | 32 |
Figure S4. Get High-res Image Gene #8: 'amp_6p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.77e-05 (Fisher's exact test), Q value = 0.051
Table S5. Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 248 | 556 | 114 | 36 |
| AMP PEAK 9(6Q21) MUTATED | 27 | 130 | 19 | 3 |
| AMP PEAK 9(6Q21) WILD-TYPE | 221 | 426 | 95 | 33 |
Figure S5. Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 2e-05 (Chi-square test), Q value = 0.013
Table S6. Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 9(6Q21) MUTATED | 1 | 152 | 13 | 3 | 1 | 0 | 9 |
| AMP PEAK 9(6Q21) WILD-TYPE | 0 | 558 | 141 | 2 | 27 | 14 | 35 |
Figure S6. Get High-res Image Gene #9: 'amp_6q21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.73e-13 (Chi-square test), Q value = 1.2e-10
Table S7. Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 12(8Q24.21) MUTATED | 1 | 498 | 56 | 5 | 15 | 5 | 27 |
| AMP PEAK 12(8Q24.21) WILD-TYPE | 0 | 212 | 98 | 0 | 13 | 9 | 17 |
Figure S7. Get High-res Image Gene #12: 'amp_8q24.21' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.33e-08 (Chi-square test), Q value = 8.9e-06
Table S8. Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 13(10P15.1) MUTATED | 1 | 234 | 17 | 4 | 5 | 0 | 9 |
| AMP PEAK 13(10P15.1) WILD-TYPE | 0 | 476 | 137 | 1 | 23 | 14 | 35 |
Figure S8. Get High-res Image Gene #13: 'amp_10p15.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.37e-05 (Chi-square test), Q value = 0.009
Table S9. Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 15(11P13) MUTATED | 1 | 170 | 13 | 3 | 1 | 2 | 9 |
| AMP PEAK 15(11P13) WILD-TYPE | 0 | 540 | 141 | 2 | 27 | 12 | 35 |
Figure S9. Get High-res Image Gene #15: 'amp_11p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 6.23e-05 (Chi-square test), Q value = 0.041
Table S10. Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 18(12P13.33) MUTATED | 1 | 207 | 22 | 4 | 8 | 1 | 8 |
| AMP PEAK 18(12P13.33) WILD-TYPE | 0 | 503 | 132 | 1 | 20 | 13 | 36 |
Figure S10. Get High-res Image Gene #18: 'amp_12p13.33' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.08e-05 (Chi-square test), Q value = 0.02
Table S11. Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 22(15Q26.3) MUTATED | 0 | 154 | 6 | 2 | 4 | 3 | 5 |
| AMP PEAK 22(15Q26.3) WILD-TYPE | 1 | 556 | 148 | 3 | 24 | 11 | 39 |
Figure S11. Get High-res Image Gene #22: 'amp_15q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000156 (Fisher's exact test), Q value = 0.1
Table S12. Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 248 | 556 | 114 | 36 |
| AMP PEAK 24(17Q23.1) MUTATED | 72 | 252 | 45 | 17 |
| AMP PEAK 24(17Q23.1) WILD-TYPE | 176 | 304 | 69 | 19 |
Figure S12. Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 0.000112 (Fisher's exact test), Q value = 0.072
Table S13. Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'
| nPatients | FEMALE | MALE |
|---|---|---|
| ALL | 947 | 10 |
| AMP PEAK 24(17Q23.1) MUTATED | 378 | 10 |
| AMP PEAK 24(17Q23.1) WILD-TYPE | 569 | 0 |
Figure S13. Get High-res Image Gene #24: 'amp_17q23.1' versus Clinical Feature #7: 'GENDER'
P value = 6.32e-05 (Chi-square test), Q value = 0.041
Table S14. Gene #26: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 26(19Q12) MUTATED | 0 | 202 | 23 | 5 | 5 | 2 | 10 |
| AMP PEAK 26(19Q12) WILD-TYPE | 1 | 508 | 131 | 0 | 23 | 12 | 34 |
Figure S14. Get High-res Image Gene #26: 'amp_19q12' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.82e-13 (Chi-square test), Q value = 1.2e-10
Table S15. Gene #28: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| AMP PEAK 28(20Q13.2) MUTATED | 1 | 415 | 40 | 1 | 10 | 1 | 19 |
| AMP PEAK 28(20Q13.2) WILD-TYPE | 0 | 295 | 114 | 4 | 18 | 13 | 25 |
Figure S15. Get High-res Image Gene #28: 'amp_20q13.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.16e-06 (Fisher's exact test), Q value = 0.0014
Table S16. Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 248 | 556 | 114 | 36 |
| DEL PEAK 1(1P36.13) MUTATED | 74 | 257 | 44 | 24 |
| DEL PEAK 1(1P36.13) WILD-TYPE | 174 | 299 | 70 | 12 |
Figure S16. Get High-res Image Gene #29: 'del_1p36.13' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 3.13e-05 (Fisher's exact test), Q value = 0.021
Table S17. Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 248 | 556 | 114 | 36 |
| DEL PEAK 2(1P21.2) MUTATED | 57 | 205 | 36 | 20 |
| DEL PEAK 2(1P21.2) WILD-TYPE | 191 | 351 | 78 | 16 |
Figure S17. Get High-res Image Gene #30: 'del_1p21.2' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 8.37e-05 (Chi-square test), Q value = 0.054
Table S18. Gene #31: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 3(2Q37.3) MUTATED | 0 | 241 | 20 | 2 | 9 | 3 | 11 |
| DEL PEAK 3(2Q37.3) WILD-TYPE | 1 | 469 | 134 | 3 | 19 | 11 | 33 |
Figure S18. Get High-res Image Gene #31: 'del_2q37.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.6e-06 (Chi-square test), Q value = 0.005
Table S19. Gene #32: 'del_3p14.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 4(3P14.3) MUTATED | 0 | 257 | 27 | 2 | 4 | 0 | 10 |
| DEL PEAK 4(3P14.3) WILD-TYPE | 1 | 453 | 127 | 3 | 24 | 14 | 34 |
Figure S19. Get High-res Image Gene #32: 'del_3p14.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.93e-06 (Chi-square test), Q value = 0.0026
Table S20. Gene #33: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 5(4P16.3) MUTATED | 1 | 252 | 24 | 3 | 6 | 0 | 14 |
| DEL PEAK 5(4P16.3) WILD-TYPE | 0 | 458 | 130 | 2 | 22 | 14 | 30 |
Figure S20. Get High-res Image Gene #33: 'del_4p16.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 6.48e-07 (Chi-square test), Q value = 0.00043
Table S21. Gene #34: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 6(4Q34.3) MUTATED | 1 | 263 | 26 | 3 | 4 | 0 | 12 |
| DEL PEAK 6(4Q34.3) WILD-TYPE | 0 | 447 | 128 | 2 | 24 | 14 | 32 |
Figure S21. Get High-res Image Gene #34: 'del_4q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 5.61e-11 (Chi-square test), Q value = 3.8e-08
Table S22. Gene #35: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 7(5Q11.2) MUTATED | 1 | 221 | 8 | 4 | 4 | 1 | 10 |
| DEL PEAK 7(5Q11.2) WILD-TYPE | 0 | 489 | 146 | 1 | 24 | 13 | 34 |
Figure S22. Get High-res Image Gene #35: 'del_5q11.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.34e-14 (Chi-square test), Q value = 9.1e-12
Table S23. Gene #36: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 8(5Q21.3) MUTATED | 1 | 216 | 4 | 5 | 4 | 0 | 9 |
| DEL PEAK 8(5Q21.3) WILD-TYPE | 0 | 494 | 150 | 0 | 24 | 14 | 35 |
Figure S23. Get High-res Image Gene #36: 'del_5q21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.67e-06 (t-test), Q value = 0.0051
Table S24. Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 954 | 58.6 (13.2) |
| DEL PEAK 11(6Q27) MUTATED | 328 | 56.0 (12.7) |
| DEL PEAK 11(6Q27) WILD-TYPE | 626 | 60.0 (13.3) |
Figure S24. Get High-res Image Gene #39: 'del_6q27' versus Clinical Feature #2: 'AGE'
P value = 0.000235 (Chi-square test), Q value = 0.15
Table S25. Gene #40: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 12(7P22.3) MUTATED | 0 | 113 | 3 | 0 | 2 | 0 | 6 |
| DEL PEAK 12(7P22.3) WILD-TYPE | 1 | 597 | 151 | 5 | 26 | 14 | 38 |
Figure S25. Get High-res Image Gene #40: 'del_7p22.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.29e-09 (Chi-square test), Q value = 1.5e-06
Table S26. Gene #42: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 14(8P23.2) MUTATED | 1 | 411 | 45 | 3 | 10 | 3 | 25 |
| DEL PEAK 14(8P23.2) WILD-TYPE | 0 | 299 | 109 | 2 | 18 | 11 | 19 |
Figure S26. Get High-res Image Gene #42: 'del_8p23.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.71e-05 (Chi-square test), Q value = 0.011
Table S27. Gene #44: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 16(9P23) MUTATED | 0 | 253 | 20 | 2 | 8 | 5 | 11 |
| DEL PEAK 16(9P23) WILD-TYPE | 1 | 457 | 134 | 3 | 20 | 9 | 33 |
Figure S27. Get High-res Image Gene #44: 'del_9p23' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.76e-09 (Chi-square test), Q value = 2.5e-06
Table S28. Gene #45: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 17(9P21.3) MUTATED | 1 | 283 | 19 | 4 | 10 | 5 | 11 |
| DEL PEAK 17(9P21.3) WILD-TYPE | 0 | 427 | 135 | 1 | 18 | 9 | 33 |
Figure S28. Get High-res Image Gene #45: 'del_9p21.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.2e-06 (Chi-square test), Q value = 0.0015
Table S29. Gene #47: 'del_9q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 19(9Q34.3) MUTATED | 0 | 223 | 17 | 4 | 6 | 3 | 8 |
| DEL PEAK 19(9Q34.3) WILD-TYPE | 1 | 487 | 137 | 1 | 22 | 11 | 36 |
Figure S29. Get High-res Image Gene #47: 'del_9q34.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000303 (Chi-square test), Q value = 0.19
Table S30. Gene #49: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 21(10Q26.3) MUTATED | 0 | 234 | 27 | 4 | 6 | 1 | 13 |
| DEL PEAK 21(10Q26.3) WILD-TYPE | 1 | 476 | 127 | 1 | 22 | 13 | 31 |
Figure S30. Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 8.52e-05 (Chi-square test), Q value = 0.055
Table S31. Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 28(13Q14.2) MUTATED | 0 | 360 | 51 | 4 | 10 | 2 | 16 |
| DEL PEAK 28(13Q14.2) WILD-TYPE | 1 | 350 | 103 | 1 | 18 | 12 | 28 |
Figure S31. Get High-res Image Gene #56: 'del_13q14.2' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 2.6e-08 (Chi-square test), Q value = 1.7e-05
Table S32. Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 29(14Q24.1) MUTATED | 1 | 267 | 25 | 4 | 3 | 1 | 10 |
| DEL PEAK 29(14Q24.1) WILD-TYPE | 0 | 443 | 129 | 1 | 25 | 13 | 34 |
Figure S32. Get High-res Image Gene #57: 'del_14q24.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.28e-06 (Chi-square test), Q value = 0.0048
Table S33. Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 30(15Q13.1) MUTATED | 1 | 276 | 30 | 4 | 8 | 1 | 12 |
| DEL PEAK 30(15Q13.1) WILD-TYPE | 0 | 434 | 124 | 1 | 20 | 13 | 32 |
Figure S33. Get High-res Image Gene #58: 'del_15q13.1' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.92e-15 (Chi-square test), Q value = 1.3e-12
Table S34. Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 31(16Q24.3) MUTATED | 0 | 434 | 137 | 2 | 19 | 1 | 16 |
| DEL PEAK 31(16Q24.3) WILD-TYPE | 1 | 276 | 17 | 3 | 9 | 13 | 28 |
Figure S34. Get High-res Image Gene #59: 'del_16q24.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 0.000185 (t-test), Q value = 0.12
Table S35. Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 954 | 58.6 (13.2) |
| DEL PEAK 33(17Q21.31) MUTATED | 331 | 56.4 (13.4) |
| DEL PEAK 33(17Q21.31) WILD-TYPE | 623 | 59.8 (12.9) |
Figure S35. Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #2: 'AGE'
P value = 1.32e-05 (Chi-square test), Q value = 0.0087
Table S36. Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 33(17Q21.31) MUTATED | 0 | 272 | 28 | 4 | 10 | 1 | 16 |
| DEL PEAK 33(17Q21.31) WILD-TYPE | 1 | 438 | 126 | 1 | 18 | 13 | 28 |
Figure S36. Get High-res Image Gene #61: 'del_17q21.31' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.2e-10 (Chi-square test), Q value = 8.1e-08
Table S37. Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 35(19P13.3) MUTATED | 1 | 274 | 14 | 4 | 7 | 4 | 13 |
| DEL PEAK 35(19P13.3) WILD-TYPE | 0 | 436 | 140 | 1 | 21 | 10 | 31 |
Figure S37. Get High-res Image Gene #63: 'del_19p13.3' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 9.2e-07 (Chi-square test), Q value = 0.00061
Table S38. Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 36(19Q13.32) MUTATED | 0 | 166 | 6 | 3 | 4 | 3 | 5 |
| DEL PEAK 36(19Q13.32) WILD-TYPE | 1 | 544 | 148 | 2 | 24 | 11 | 39 |
Figure S38. Get High-res Image Gene #64: 'del_19q13.32' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 7.99e-05 (Chi-square test), Q value = 0.052
Table S39. Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 710 | 154 | 5 | 28 | 14 | 44 |
| DEL PEAK 37(20P13) MUTATED | 1 | 127 | 8 | 2 | 2 | 0 | 5 |
| DEL PEAK 37(20P13) WILD-TYPE | 0 | 583 | 146 | 3 | 26 | 14 | 39 |
Figure S39. Get High-res Image Gene #65: 'del_20p13' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
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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 = 957
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Number of significantly focal cnvs = 68
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Number of selected clinical features = 10
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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 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 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.