Correlation between copy number variations of arm-level result and selected clinical features

Prostate Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C12R3QFX

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 64 arm-level events and 13 clinical features across 271 patients, 34 significant findings detected with Q value < 0.25.

3p gain cnv correlated to 'GLEASON_SCORE'.
8p gain cnv correlated to 'GLEASON_SCORE_COMBINED'.
8q gain cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE_PRIMARY'.
9q gain cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
4p loss cnv correlated to 'NUMBER.OF.LYMPH.NODES', 'GLEASON_SCORE_COMBINED', and 'GLEASON_SCORE'.
5q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
6q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
8q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
10q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
13q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
15q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
17p loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
18p loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
18q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.
21q loss cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
22q loss cnv correlated to 'GLEASON_SCORE_COMBINED', 'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.
xq loss cnv correlated to 'GLEASON_SCORE_COMBINED'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 64 arm-level events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.


		Clinical Features	AGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	HISTOLOGICAL TYPE	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	GLEASON SCORE COMBINED	GLEASON SCORE PRIMARY	GLEASON SCORE SECONDARY	GLEASON SCORE	PSA RESULT PREOP	PSA VALUE	RACE
	nCNV (%)	nWild-Type	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Wilcoxon-test	Wilcoxon-test	Wilcoxon-test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test
9q gain	20 (7%)	251	0.136 (1.00)	0.0146 (1.00)	0.0061 (1.00)	0.32 (1.00)	0.699 (1.00)	0.00139 (1.00)	0.000208 (0.162)	7.08e-05 (0.0562)	0.521 (1.00)	0.000285 (0.221)	0.0586 (1.00)	0.929 (1.00)	0.459 (1.00)
4p loss	8 (3%)	263	0.829 (1.00)	0.384 (1.00)	0.0053 (1.00)	0.14 (1.00)	0.0327 (1.00)	0.000206 (0.161)	2.17e-05 (0.0174)	0.000413 (0.319)	0.0147 (1.00)	5.01e-05 (0.0398)	0.805 (1.00)	0.736 (1.00)	1 (1.00)
5q loss	8 (3%)	263	0.919 (1.00)	0.03 (1.00)	0.0282 (1.00)	1 (1.00)	0.265 (1.00)	0.00646 (1.00)	4.57e-06 (0.00369)	2.92e-05 (0.0233)	0.142 (1.00)	5.76e-06 (0.00465)	0.209 (1.00)	0.945 (1.00)	1 (1.00)
15q loss	15 (6%)	256	0.358 (1.00)	0.00834 (1.00)	0.00942 (1.00)	1 (1.00)	1 (1.00)	0.00152 (1.00)	8.71e-05 (0.0689)	2.46e-05 (0.0197)	0.299 (1.00)	0.000148 (0.117)	0.584 (1.00)	0.262 (1.00)	1 (1.00)
22q loss	20 (7%)	251	0.974 (1.00)	0.0137 (1.00)	0.00827 (1.00)	1 (1.00)	0.277 (1.00)	0.00221 (1.00)	5.58e-06 (0.00451)	1.01e-05 (0.00811)	0.0463 (1.00)	2.24e-05 (0.0179)	0.47 (1.00)	0.143 (1.00)	0.496 (1.00)
8q gain	53 (20%)	218	0.454 (1.00)	0.124 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.807 (1.00)	8.63e-05 (0.0683)	9.63e-05 (0.076)	0.238 (1.00)	0.000944 (0.715)	0.439 (1.00)	0.291 (1.00)	0.731 (1.00)
6q loss	16 (6%)	255	0.776 (1.00)	0.152 (1.00)	0.0754 (1.00)	1 (1.00)	0.718 (1.00)	0.0454 (1.00)	0.000256 (0.199)	0.00366 (1.00)	0.0446 (1.00)	4.95e-05 (0.0393)	0.528 (1.00)	0.222 (1.00)	0.126 (1.00)
10q loss	21 (8%)	250	0.982 (1.00)	0.0661 (1.00)	0.00827 (1.00)	1 (1.00)	0.279 (1.00)	0.00344 (1.00)	1.26e-05 (0.0101)	0.00055 (0.421)	0.0116 (1.00)	3.14e-06 (0.00254)	0.712 (1.00)	0.839 (1.00)	0.586 (1.00)
13q loss	34 (13%)	237	0.099 (1.00)	0.226 (1.00)	0.0299 (1.00)	1 (1.00)	0.581 (1.00)	0.0252 (1.00)	0.000177 (0.139)	0.00605 (1.00)	0.0288 (1.00)	3.41e-05 (0.0272)	0.708 (1.00)	0.495 (1.00)	0.439 (1.00)
17p loss	35 (13%)	236	0.756 (1.00)	0.0453 (1.00)	0.0595 (1.00)	1 (1.00)	0.496 (1.00)	0.0349 (1.00)	0.00014 (0.11)	0.000341 (0.263)	0.269 (1.00)	0.000153 (0.12)	0.508 (1.00)	0.0568 (1.00)	0.704 (1.00)
18p loss	35 (13%)	236	0.302 (1.00)	0.215 (1.00)	0.123 (1.00)	0.502 (1.00)	0.203 (1.00)	0.104 (1.00)	0.00015 (0.118)	0.00668 (1.00)	0.0109 (1.00)	2.81e-05 (0.0224)	0.769 (1.00)	0.843 (1.00)	0.698 (1.00)
18q loss	49 (18%)	222	0.867 (1.00)	0.223 (1.00)	0.00484 (1.00)	1 (1.00)	0.0352 (1.00)	0.0021 (1.00)	2.62e-05 (0.0209)	0.02 (1.00)	0.000561 (0.429)	6.29e-06 (0.00506)	0.372 (1.00)	0.729 (1.00)	0.757 (1.00)
3p gain	17 (6%)	254	0.0162 (1.00)	0.0379 (1.00)	0.682 (1.00)	1 (1.00)	0.869 (1.00)	0.872 (1.00)	0.00177 (1.00)	0.00998 (1.00)	0.107 (1.00)	8.78e-05 (0.0694)	0.32 (1.00)	0.145 (1.00)	0.524 (1.00)
8p gain	33 (12%)	238	0.203 (1.00)	0.235 (1.00)	0.753 (1.00)	1 (1.00)	0.668 (1.00)	0.757 (1.00)	0.000114 (0.0901)	0.00576 (1.00)	0.0323 (1.00)	0.000468 (0.359)	0.16 (1.00)	0.451 (1.00)	0.659 (1.00)
8q loss	12 (4%)	259	0.274 (1.00)	0.00033 (0.256)	0.00433 (1.00)	1 (1.00)	0.104 (1.00)	0.000195 (0.152)	0.013 (1.00)	0.0322 (1.00)	0.15 (1.00)	0.015 (1.00)	0.426 (1.00)	0.0172 (1.00)	1 (1.00)
21q loss	9 (3%)	262	0.705 (1.00)	0.0833 (1.00)	0.0053 (1.00)	1 (1.00)	1 (1.00)	0.000238 (0.185)	0.00306 (1.00)	0.00706 (1.00)	0.289 (1.00)	0.00581 (1.00)	0.0247 (1.00)	0.552 (1.00)	1 (1.00)
xq loss	13 (5%)	258	0.905 (1.00)	0.422 (1.00)	0.0371 (1.00)	0.219 (1.00)	1 (1.00)	0.0124 (1.00)	0.000213 (0.166)	0.000607 (0.463)	0.135 (1.00)	0.000331 (0.256)	0.367 (1.00)	0.12 (1.00)	0.348 (1.00)
1p gain	7 (3%)	264	0.398 (1.00)	0.00916 (1.00)	0.496 (1.00)	1 (1.00)	0.697 (1.00)	0.681 (1.00)	0.0272 (1.00)	0.0209 (1.00)	0.551 (1.00)	0.00436 (1.00)	0.0192 (1.00)	0.215 (1.00)	1 (1.00)
1q gain	13 (5%)	258	0.763 (1.00)	0.0209 (1.00)	0.622 (1.00)	0.219 (1.00)	0.661 (1.00)	0.464 (1.00)	0.00855 (1.00)	0.000607 (0.463)	0.995 (1.00)	0.00279 (1.00)	0.053 (1.00)	0.958 (1.00)	1 (1.00)
2p gain	4 (1%)	267	0.283 (1.00)	0.406 (1.00)	1 (1.00)	1 (1.00)	0.591 (1.00)		0.212 (1.00)	0.575 (1.00)	0.557 (1.00)	0.716 (1.00)	0.923 (1.00)
2q gain	3 (1%)	268	0.0554 (1.00)	0.63 (1.00)	1 (1.00)	1 (1.00)			0.104 (1.00)	0.243 (1.00)	0.652 (1.00)	0.527 (1.00)	0.97 (1.00)
3q gain	24 (9%)	247	0.0129 (1.00)	0.00203 (1.00)	0.72 (1.00)	1 (1.00)	0.913 (1.00)	0.706 (1.00)	0.00277 (1.00)	0.000978 (0.739)	0.448 (1.00)	0.000335 (0.259)	0.0427 (1.00)	0.227 (1.00)	0.636 (1.00)
4p gain	4 (1%)	267	0.289 (1.00)	0.65 (1.00)	1 (1.00)	1 (1.00)	0.632 (1.00)	0.49 (1.00)	0.212 (1.00)	0.915 (1.00)	0.142 (1.00)	0.264 (1.00)	0.595 (1.00)	0.16 (1.00)	1 (1.00)
4q gain	3 (1%)	268	0.495 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.552 (1.00)	0.698 (1.00)	0.651 (1.00)	0.498 (1.00)	0.783 (1.00)	0.692 (1.00)	0.314 (1.00)
5p gain	5 (2%)	266	0.208 (1.00)	0.111 (1.00)	0.365 (1.00)	1 (1.00)	0.436 (1.00)	0.395 (1.00)	0.00379 (1.00)	0.00853 (1.00)	0.482 (1.00)	0.000549 (0.421)	0.168 (1.00)	0.471 (1.00)
7p gain	43 (16%)	228	0.145 (1.00)	0.409 (1.00)	0.549 (1.00)	1 (1.00)	0.176 (1.00)	0.449 (1.00)	0.0886 (1.00)	0.332 (1.00)	0.0733 (1.00)	0.103 (1.00)	0.492 (1.00)	0.827 (1.00)	1 (1.00)
7q gain	41 (15%)	230	0.27 (1.00)	0.536 (1.00)	1 (1.00)	1 (1.00)	0.215 (1.00)	0.685 (1.00)	0.138 (1.00)	0.332 (1.00)	0.143 (1.00)	0.153 (1.00)	0.543 (1.00)	0.51 (1.00)	1 (1.00)
9p gain	9 (3%)	262	0.179 (1.00)	0.305 (1.00)	0.0419 (1.00)	1 (1.00)	1 (1.00)	0.0151 (1.00)	0.159 (1.00)	0.151 (1.00)	0.904 (1.00)	0.0228 (1.00)	0.0139 (1.00)	0.944 (1.00)	0.347 (1.00)
10p gain	6 (2%)	265	0.379 (1.00)	0.721 (1.00)	1 (1.00)	1 (1.00)	0.166 (1.00)	0.438 (1.00)	0.45 (1.00)	0.518 (1.00)	0.127 (1.00)	0.0892 (1.00)	0.59 (1.00)	0.515 (1.00)	1 (1.00)
10q gain	7 (3%)	264	0.311 (1.00)	0.516 (1.00)	0.496 (1.00)	1 (1.00)	0.142 (1.00)	0.555 (1.00)	0.564 (1.00)	0.9 (1.00)	0.706 (1.00)	0.151 (1.00)	0.292 (1.00)	0.123 (1.00)	1 (1.00)
11p gain	7 (3%)	264	0.951 (1.00)	0.0431 (1.00)	0.164 (1.00)	1 (1.00)	0.737 (1.00)	0.152 (1.00)	0.0753 (1.00)	0.00792 (1.00)	0.551 (1.00)	0.0241 (1.00)	0.609 (1.00)	0.845 (1.00)	0.261 (1.00)
11q gain	8 (3%)	263	0.847 (1.00)	0.0294 (1.00)	0.205 (1.00)	1 (1.00)	1 (1.00)	0.223 (1.00)	0.0322 (1.00)	0.00438 (1.00)	0.484 (1.00)	0.0108 (1.00)	0.499 (1.00)	0.51 (1.00)	0.263 (1.00)
12q gain	3 (1%)	268	0.476 (1.00)	0.289 (1.00)	0.202 (1.00)	1 (1.00)	0.22 (1.00)		0.104 (1.00)	0.0232 (1.00)	0.579 (1.00)	0.134 (1.00)	0.0201 (1.00)
14q gain	4 (1%)	267	0.0494 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.328 (1.00)	0.552 (1.00)	0.0203 (1.00)	0.0133 (1.00)	0.696 (1.00)	0.0293 (1.00)	0.954 (1.00)
15q gain	3 (1%)	268	0.739 (1.00)	0.635 (1.00)	1 (1.00)	1 (1.00)	0.591 (1.00)	0.552 (1.00)	0.698 (1.00)	0.52 (1.00)	0.743 (1.00)	0.134 (1.00)	0.258 (1.00)
16p gain	11 (4%)	260	0.0685 (1.00)	0.0077 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.996 (1.00)	0.00352 (1.00)	0.00218 (1.00)	0.168 (1.00)	0.00623 (1.00)	0.783 (1.00)	0.114 (1.00)	1 (1.00)
16q gain	5 (2%)	266	0.0543 (1.00)	0.428 (1.00)	1 (1.00)	1 (1.00)	0.657 (1.00)	0.552 (1.00)	0.234 (1.00)	0.0695 (1.00)	0.937 (1.00)	0.284 (1.00)	0.497 (1.00)		1 (1.00)
17q gain	4 (1%)	267	0.507 (1.00)	0.187 (1.00)	0.0574 (1.00)	1 (1.00)	0.633 (1.00)	0.0109 (1.00)	0.316 (1.00)	0.287 (1.00)	0.93 (1.00)	0.264 (1.00)	0.443 (1.00)	0.637 (1.00)
18p gain	10 (4%)	261	0.221 (1.00)	0.0335 (1.00)	0.0419 (1.00)	1 (1.00)	0.624 (1.00)	0.0151 (1.00)	0.0548 (1.00)	0.281 (1.00)	0.314 (1.00)	0.0171 (1.00)	0.49 (1.00)	0.835 (1.00)	1 (1.00)
18q gain	4 (1%)	267	0.183 (1.00)	0.189 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.49 (1.00)	0.136 (1.00)	0.287 (1.00)	0.204 (1.00)	0.167 (1.00)	0.382 (1.00)	0.629 (1.00)
19q gain	3 (1%)	268	0.854 (1.00)	0.0281 (1.00)	0.288 (1.00)	1 (1.00)	0.589 (1.00)	0.237 (1.00)	0.000986 (0.744)	0.0232 (1.00)	0.00238 (1.00)	0.00141 (1.00)	0.276 (1.00)	0.431 (1.00)	1 (1.00)
20p gain	4 (1%)	267	0.198 (1.00)	0.648 (1.00)	1 (1.00)	1 (1.00)	0.589 (1.00)	0.49 (1.00)	0.0103 (1.00)	0.287 (1.00)	0.0046 (1.00)	0.0907 (1.00)	0.341 (1.00)	0.592 (1.00)
20q gain	7 (3%)	264	0.169 (1.00)	0.044 (1.00)	1 (1.00)	1 (1.00)	0.301 (1.00)	0.355 (1.00)	0.114 (1.00)	0.0496 (1.00)	0.551 (1.00)	0.0946 (1.00)	0.804 (1.00)	1 (1.00)	1 (1.00)
21q gain	5 (2%)	266	0.154 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.438 (1.00)	0.0314 (1.00)	0.0235 (1.00)	0.255 (1.00)	0.0429 (1.00)	0.0422 (1.00)	0.565 (1.00)	1 (1.00)
1p loss	6 (2%)	265	0.907 (1.00)	0.72 (1.00)	1 (1.00)	1 (1.00)	0.695 (1.00)	0.394 (1.00)	0.339 (1.00)	0.0888 (1.00)	0.943 (1.00)	0.408 (1.00)	0.403 (1.00)	0.116 (1.00)	1 (1.00)
2p loss	3 (1%)	268	0.326 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.552 (1.00)	0.503 (1.00)	0.52 (1.00)	0.652 (1.00)	0.562 (1.00)	0.723 (1.00)	0.253 (1.00)
2q loss	4 (1%)	267	0.684 (1.00)	0.653 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.49 (1.00)	0.212 (1.00)	0.287 (1.00)	0.557 (1.00)	0.264 (1.00)	0.478 (1.00)	0.253 (1.00)
4q loss	6 (2%)	265	0.938 (1.00)	0.719 (1.00)	0.496 (1.00)	0.107 (1.00)	0.229 (1.00)	0.681 (1.00)	0.00069 (0.525)	0.00424 (1.00)	0.0543 (1.00)	0.00126 (0.947)	0.754 (1.00)	0.389 (1.00)
5p loss	4 (1%)	267	0.677 (1.00)	0.0189 (1.00)	0.0574 (1.00)	1 (1.00)	0.33 (1.00)	0.0161 (1.00)	0.00702 (1.00)	0.00337 (1.00)	0.204 (1.00)	0.00975 (1.00)	0.336 (1.00)	0.984 (1.00)	1 (1.00)
6p loss	9 (3%)	262	0.317 (1.00)	0.082 (1.00)	0.0585 (1.00)	1 (1.00)	0.541 (1.00)	0.0232 (1.00)	0.00435 (1.00)	0.00075 (0.57)	0.738 (1.00)	0.00042 (0.323)	0.239 (1.00)	0.548 (1.00)	0.304 (1.00)
8p loss	84 (31%)	187	0.641 (1.00)	0.00145 (1.00)	0.167 (1.00)	0.647 (1.00)	0.574 (1.00)	0.112 (1.00)	0.771 (1.00)	0.0136 (1.00)	0.0396 (1.00)	0.875 (1.00)	0.143 (1.00)	0.212 (1.00)	0.161 (1.00)
9p loss	12 (4%)	259	0.868 (1.00)	0.087 (1.00)	0.123 (1.00)	1 (1.00)	0.513 (1.00)	0.112 (1.00)	0.00231 (1.00)	0.0322 (1.00)	0.0185 (1.00)	0.00285 (1.00)	0.582 (1.00)	0.559 (1.00)	1 (1.00)
9q loss	5 (2%)	266	0.209 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.438 (1.00)	0.0314 (1.00)	0.583 (1.00)	0.00661 (1.00)	0.00291 (1.00)	0.338 (1.00)	0.913 (1.00)	1 (1.00)
10p loss	17 (6%)	254	0.281 (1.00)	0.00262 (1.00)	0.061 (1.00)	1 (1.00)	0.455 (1.00)	0.0431 (1.00)	0.00116 (0.877)	0.000417 (0.321)	0.24 (1.00)	0.000424 (0.325)	0.645 (1.00)	0.797 (1.00)	1 (1.00)
12p loss	22 (8%)	249	0.762 (1.00)	0.368 (1.00)	0.0181 (1.00)	1 (1.00)	1 (1.00)	0.0115 (1.00)	0.0277 (1.00)	0.00135 (1.00)	0.774 (1.00)	0.0243 (1.00)	0.354 (1.00)	0.291 (1.00)	1 (1.00)
12q loss	10 (4%)	261	0.942 (1.00)	0.26 (1.00)	0.0777 (1.00)	1 (1.00)	1 (1.00)	0.0615 (1.00)	0.0205 (1.00)	0.0095 (1.00)	0.379 (1.00)	0.00821 (1.00)	0.565 (1.00)	0.973 (1.00)	1 (1.00)
14q loss	10 (4%)	261	0.283 (1.00)	0.217 (1.00)	0.289 (1.00)	1 (1.00)	0.589 (1.00)	0.337 (1.00)	0.00441 (1.00)	0.0095 (1.00)	0.149 (1.00)	0.00821 (1.00)	0.16 (1.00)	0.364 (1.00)	1 (1.00)
16p loss	19 (7%)	252	0.629 (1.00)	1 (1.00)	0.7 (1.00)	1 (1.00)	0.5 (1.00)	0.945 (1.00)	0.158 (1.00)	0.117 (1.00)	0.738 (1.00)	0.0733 (1.00)	0.79 (1.00)	0.579 (1.00)	1 (1.00)
16q loss	50 (18%)	221	0.983 (1.00)	0.245 (1.00)	0.118 (1.00)	1 (1.00)	0.965 (1.00)	0.135 (1.00)	0.00193 (1.00)	0.000782 (0.593)	0.351 (1.00)	0.000896 (0.68)	0.0599 (1.00)	0.618 (1.00)	1 (1.00)
17q loss	7 (3%)	264	0.413 (1.00)	0.521 (1.00)	0.551 (1.00)	1 (1.00)	0.173 (1.00)	0.803 (1.00)	0.0272 (1.00)	0.0496 (1.00)	0.206 (1.00)	0.0411 (1.00)	0.949 (1.00)	0.804 (1.00)	1 (1.00)
19p loss	7 (3%)	264	0.293 (1.00)	0.518 (1.00)	0.551 (1.00)	1 (1.00)	0.376 (1.00)	0.803 (1.00)	0.114 (1.00)	0.0539 (1.00)	0.82 (1.00)	0.151 (1.00)	0.115 (1.00)	0.377 (1.00)	1 (1.00)
19q loss	7 (3%)	264	0.293 (1.00)	0.518 (1.00)	0.551 (1.00)	1 (1.00)	0.378 (1.00)	0.803 (1.00)	0.114 (1.00)	0.0539 (1.00)	0.82 (1.00)	0.151 (1.00)	0.115 (1.00)	0.377 (1.00)	1 (1.00)
20p loss	9 (3%)	262	0.507 (1.00)	0.0226 (1.00)	0.551 (1.00)	1 (1.00)	1 (1.00)	0.723 (1.00)	0.754 (1.00)	0.0374 (1.00)	0.0578 (1.00)	0.875 (1.00)	0.0336 (1.00)	0.995 (1.00)	0.348 (1.00)
20q loss	6 (2%)	265	0.11 (1.00)	0.0684 (1.00)	1 (1.00)	1 (1.00)	0.695 (1.00)	0.438 (1.00)	0.102 (1.00)	0.00424 (1.00)	0.428 (1.00)	0.138 (1.00)	0.232 (1.00)	0.669 (1.00)	1 (1.00)

'3p gain' versus 'GLEASON_SCORE'

P value = 8.78e-05 (Wilcoxon-test), Q value = 0.069

Table S1. Gene #5: '3p gain' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
3P GAIN MUTATED	17	8.2 (1.0)
3P GAIN WILD-TYPE	254	7.3 (0.8)

Figure S1. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #10: 'GLEASON_SCORE'

'8p gain' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000114 (Wilcoxon-test), Q value = 0.09

Table S2. Gene #12: '8p gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
8P GAIN MUTATED	33	7.8 (1.0)
8P GAIN WILD-TYPE	238	7.2 (0.8)

Figure S2. Get High-res Image Gene #12: '8p gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'8q gain' versus 'GLEASON_SCORE_COMBINED'

P value = 8.63e-05 (Wilcoxon-test), Q value = 0.068

Table S3. Gene #13: '8q gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
8Q GAIN MUTATED	53	7.7 (0.9)
8Q GAIN WILD-TYPE	218	7.2 (0.8)

Figure S3. Get High-res Image Gene #13: '8q gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'8q gain' versus 'GLEASON_SCORE_PRIMARY'

P value = 9.63e-05 (Wilcoxon-test), Q value = 0.076

Table S4. Gene #13: '8q gain' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

	nPatients	Mean (Std.Dev)
ALL	271	3.5 (0.6)
8Q GAIN MUTATED	53	3.8 (0.6)
8Q GAIN WILD-TYPE	218	3.4 (0.5)

Figure S4. Get High-res Image Gene #13: '8q gain' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'9q gain' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000208 (Wilcoxon-test), Q value = 0.16

Table S5. Gene #15: '9q gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
9Q GAIN MUTATED	20	7.9 (0.9)
9Q GAIN WILD-TYPE	251	7.2 (0.8)

Figure S5. Get High-res Image Gene #15: '9q gain' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'9q gain' versus 'GLEASON_SCORE_PRIMARY'

P value = 7.08e-05 (Wilcoxon-test), Q value = 0.056

Table S6. Gene #15: '9q gain' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

	nPatients	Mean (Std.Dev)
ALL	271	3.5 (0.6)
9Q GAIN MUTATED	20	4.0 (0.6)
9Q GAIN WILD-TYPE	251	3.4 (0.6)

Figure S6. Get High-res Image Gene #15: '9q gain' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'9q gain' versus 'GLEASON_SCORE'

P value = 0.000285 (Wilcoxon-test), Q value = 0.22

Table S7. Gene #15: '9q gain' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
9Q GAIN MUTATED	20	7.9 (0.9)
9Q GAIN WILD-TYPE	251	7.3 (0.8)

Figure S7. Get High-res Image Gene #15: '9q gain' versus Clinical Feature #10: 'GLEASON_SCORE'

'4p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000206 (Wilcoxon-test), Q value = 0.16

Table S8. Gene #35: '4p loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	223	0.2 (1.2)
4P LOSS MUTATED	8	1.0 (1.3)
4P LOSS WILD-TYPE	215	0.2 (1.2)

Figure S8. Get High-res Image Gene #35: '4p loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

'4p loss' versus 'GLEASON_SCORE_COMBINED'

P value = 2.17e-05 (Wilcoxon-test), Q value = 0.017

Table S9. Gene #35: '4p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
4P LOSS MUTATED	8	8.6 (0.7)
4P LOSS WILD-TYPE	263	7.2 (0.8)

Figure S9. Get High-res Image Gene #35: '4p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'4p loss' versus 'GLEASON_SCORE'

P value = 5.01e-05 (Wilcoxon-test), Q value = 0.04

Table S10. Gene #35: '4p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
4P LOSS MUTATED	8	8.6 (0.7)
4P LOSS WILD-TYPE	263	7.3 (0.8)

Figure S10. Get High-res Image Gene #35: '4p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'5q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 4.57e-06 (Wilcoxon-test), Q value = 0.0037

Table S11. Gene #38: '5q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
5Q LOSS MUTATED	8	8.6 (0.7)
5Q LOSS WILD-TYPE	263	7.2 (0.8)

Figure S11. Get High-res Image Gene #38: '5q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'5q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.92e-05 (Wilcoxon-test), Q value = 0.023

Table S12. Gene #38: '5q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

	nPatients	Mean (Std.Dev)
ALL	271	3.5 (0.6)
5Q LOSS MUTATED	8	4.5 (0.5)
5Q LOSS WILD-TYPE	263	3.5 (0.5)

Figure S12. Get High-res Image Gene #38: '5q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'5q loss' versus 'GLEASON_SCORE'

P value = 5.76e-06 (Wilcoxon-test), Q value = 0.0046

Table S13. Gene #38: '5q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
5Q LOSS MUTATED	8	8.8 (0.7)
5Q LOSS WILD-TYPE	263	7.3 (0.8)

Figure S13. Get High-res Image Gene #38: '5q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'6q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000256 (Wilcoxon-test), Q value = 0.2

Table S14. Gene #40: '6q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
6Q LOSS MUTATED	16	8.0 (0.9)
6Q LOSS WILD-TYPE	255	7.2 (0.8)

Figure S14. Get High-res Image Gene #40: '6q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'6q loss' versus 'GLEASON_SCORE'

P value = 4.95e-05 (Wilcoxon-test), Q value = 0.039

Table S15. Gene #40: '6q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
6Q LOSS MUTATED	16	8.2 (0.9)
6Q LOSS WILD-TYPE	255	7.3 (0.8)

Figure S15. Get High-res Image Gene #40: '6q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'8q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000195 (Wilcoxon-test), Q value = 0.15

Table S16. Gene #42: '8q loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	223	0.2 (1.2)
8Q LOSS MUTATED	12	0.9 (1.2)
8Q LOSS WILD-TYPE	211	0.2 (1.2)

Figure S16. Get High-res Image Gene #42: '8q loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

'10q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 1.26e-05 (Wilcoxon-test), Q value = 0.01

Table S17. Gene #46: '10q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
10Q LOSS MUTATED	21	8.1 (1.0)
10Q LOSS WILD-TYPE	250	7.2 (0.8)

Figure S17. Get High-res Image Gene #46: '10q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'10q loss' versus 'GLEASON_SCORE'

P value = 3.14e-06 (Wilcoxon-test), Q value = 0.0025

Table S18. Gene #46: '10q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
10Q LOSS MUTATED	21	8.2 (1.0)
10Q LOSS WILD-TYPE	250	7.2 (0.8)

Figure S18. Get High-res Image Gene #46: '10q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'13q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000177 (Wilcoxon-test), Q value = 0.14

Table S19. Gene #49: '13q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
13Q LOSS MUTATED	34	7.8 (0.9)
13Q LOSS WILD-TYPE	237	7.2 (0.8)

Figure S19. Get High-res Image Gene #49: '13q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'13q loss' versus 'GLEASON_SCORE'

P value = 3.41e-05 (Wilcoxon-test), Q value = 0.027

Table S20. Gene #49: '13q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
13Q LOSS MUTATED	34	7.9 (1.0)
13Q LOSS WILD-TYPE	237	7.2 (0.8)

Figure S20. Get High-res Image Gene #49: '13q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'15q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 8.71e-05 (Wilcoxon-test), Q value = 0.069

Table S21. Gene #51: '15q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
15Q LOSS MUTATED	15	8.1 (1.0)
15Q LOSS WILD-TYPE	256	7.2 (0.8)

Figure S21. Get High-res Image Gene #51: '15q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'15q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.46e-05 (Wilcoxon-test), Q value = 0.02

Table S22. Gene #51: '15q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

	nPatients	Mean (Std.Dev)
ALL	271	3.5 (0.6)
15Q LOSS MUTATED	15	4.1 (0.5)
15Q LOSS WILD-TYPE	256	3.4 (0.6)

Figure S22. Get High-res Image Gene #51: '15q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'15q loss' versus 'GLEASON_SCORE'

P value = 0.000148 (Wilcoxon-test), Q value = 0.12

Table S23. Gene #51: '15q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
15Q LOSS MUTATED	15	8.2 (1.0)
15Q LOSS WILD-TYPE	256	7.3 (0.8)

Figure S23. Get High-res Image Gene #51: '15q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'17p loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.00014 (Wilcoxon-test), Q value = 0.11

Table S24. Gene #54: '17p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
17P LOSS MUTATED	35	7.7 (0.9)
17P LOSS WILD-TYPE	236	7.2 (0.8)

Figure S24. Get High-res Image Gene #54: '17p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'17p loss' versus 'GLEASON_SCORE'

P value = 0.000153 (Wilcoxon-test), Q value = 0.12

Table S25. Gene #54: '17p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
17P LOSS MUTATED	35	7.8 (0.9)
17P LOSS WILD-TYPE	236	7.3 (0.8)

Figure S25. Get High-res Image Gene #54: '17p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'18p loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.00015 (Wilcoxon-test), Q value = 0.12

Table S26. Gene #56: '18p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
18P LOSS MUTATED	35	7.8 (1.0)
18P LOSS WILD-TYPE	236	7.2 (0.7)

Figure S26. Get High-res Image Gene #56: '18p loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'18p loss' versus 'GLEASON_SCORE'

P value = 2.81e-05 (Wilcoxon-test), Q value = 0.022

Table S27. Gene #56: '18p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
18P LOSS MUTATED	35	7.9 (1.1)
18P LOSS WILD-TYPE	236	7.2 (0.8)

Figure S27. Get High-res Image Gene #56: '18p loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'18q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 2.62e-05 (Wilcoxon-test), Q value = 0.021

Table S28. Gene #57: '18q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
18Q LOSS MUTATED	49	7.8 (1.0)
18Q LOSS WILD-TYPE	222	7.2 (0.7)

Figure S28. Get High-res Image Gene #57: '18q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'18q loss' versus 'GLEASON_SCORE'

P value = 6.29e-06 (Wilcoxon-test), Q value = 0.0051

Table S29. Gene #57: '18q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
18Q LOSS MUTATED	49	7.9 (1.1)
18Q LOSS WILD-TYPE	222	7.2 (0.7)

Figure S29. Get High-res Image Gene #57: '18q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'21q loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000238 (Wilcoxon-test), Q value = 0.19

Table S30. Gene #62: '21q loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	223	0.2 (1.2)
21Q LOSS MUTATED	8	0.9 (1.1)
21Q LOSS WILD-TYPE	215	0.2 (1.2)

Figure S30. Get High-res Image Gene #62: '21q loss' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

'22q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 5.58e-06 (Wilcoxon-test), Q value = 0.0045

Table S31. Gene #63: '22q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
22Q LOSS MUTATED	20	8.2 (1.0)
22Q LOSS WILD-TYPE	251	7.2 (0.8)

Figure S31. Get High-res Image Gene #63: '22q loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'22q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.01e-05 (Wilcoxon-test), Q value = 0.0081

Table S32. Gene #63: '22q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

	nPatients	Mean (Std.Dev)
ALL	271	3.5 (0.6)
22Q LOSS MUTATED	20	4.0 (0.5)
22Q LOSS WILD-TYPE	251	3.4 (0.6)

Figure S32. Get High-res Image Gene #63: '22q loss' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'22q loss' versus 'GLEASON_SCORE'

P value = 2.24e-05 (Wilcoxon-test), Q value = 0.018

Table S33. Gene #63: '22q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
22Q LOSS MUTATED	20	8.2 (1.0)
22Q LOSS WILD-TYPE	251	7.3 (0.8)

Figure S33. Get High-res Image Gene #63: '22q loss' versus Clinical Feature #10: 'GLEASON_SCORE'

'xq loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000213 (Wilcoxon-test), Q value = 0.17

Table S34. Gene #64: 'xq loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

	nPatients	Mean (Std.Dev)
ALL	271	7.3 (0.8)
XQ LOSS MUTATED	13	8.1 (0.9)
XQ LOSS WILD-TYPE	258	7.2 (0.8)

Figure S34. Get High-res Image Gene #64: 'xq loss' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = PRAD-TP.merged_data.txt
Number of patients = 271
Number of significantly arm-level cnvs = 64
Number of selected clinical features = 13
Exclude regions that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

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.

Download Results

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.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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