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

Adrenocortical Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18051ZD

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 82 arm-level events and 12 clinical features across 90 patients, 14 significant findings detected with Q value < 0.25.

2p gain cnv correlated to 'Time to Death'.
10q gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', and 'RESIDUAL_TUMOR'.
11p gain cnv correlated to 'Time to Death'.
11q gain cnv correlated to 'Time to Death'.
4p loss cnv correlated to 'Time to Death'.
4q loss cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.
16p loss cnv correlated to 'Time to Death' and 'RESIDUAL_TUMOR'.
17p loss cnv correlated to 'Time to Death'.
19p loss cnv correlated to 'Time to Death'.
20p loss cnv correlated to 'RESIDUAL_TUMOR'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 14 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGIC STAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	GENDER	RADIATION THERAPY	HISTOLOGICAL TYPE	RESIDUAL TUMOR	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
10q gain	26 (29%)	64	0.00137 (0.168)	0.266 (1.00)	0.00182 (0.179)	0.00552 (0.322)	1 (1.00)	1 (1.00)	0.771 (1.00)	0.511 (1.00)	0.0012 (0.168)	0.763 (1.00)	1 (1.00)	0.421 (1.00)
4q loss	10 (11%)	80	0.000266 (0.0655)	0.691 (1.00)	0.00522 (0.322)	0.00156 (0.171)	1 (1.00)	0.484 (1.00)	0.0835 (0.858)	1 (1.00)	0.0126 (0.427)	0.818 (1.00)	1 (1.00)	0.548 (1.00)
16p loss	4 (4%)	86	0.000834 (0.137)	0.732 (1.00)	0.0441 (0.678)	0.0361 (0.647)	0.388 (1.00)	0.606 (1.00)	0.506 (1.00)	1 (1.00)	0.00286 (0.217)		1 (1.00)	0.321 (1.00)
2p gain	13 (14%)	77	0.000374 (0.0735)	0.818 (1.00)	0.381 (1.00)	0.144 (0.944)	0.347 (1.00)	0.205 (1.00)	0.727 (1.00)	1 (1.00)	0.227 (1.00)	0.235 (1.00)	0.17 (0.982)	0.587 (1.00)
11p gain	5 (6%)	85	0.0001 (0.0328)	0.364 (1.00)	0.158 (0.963)	0.0425 (0.663)	1 (1.00)	0.656 (1.00)	0.579 (1.00)	1 (1.00)	0.0108 (0.427)		1 (1.00)	0.569 (1.00)
11q gain	6 (7%)	84	5.25e-05 (0.0258)	0.698 (1.00)	0.118 (0.89)	0.0617 (0.731)	1 (1.00)	0.66 (1.00)	1 (1.00)	1 (1.00)	0.0641 (0.743)	0.318 (1.00)	1 (1.00)	1 (1.00)
4p loss	9 (10%)	81	3.72e-06 (0.00366)	0.408 (1.00)	0.0529 (0.731)	0.0124 (0.427)	1 (1.00)	1 (1.00)	0.0537 (0.731)	1 (1.00)	0.0208 (0.502)	1 (1.00)	1 (1.00)	1 (1.00)
17p loss	33 (37%)	57	0.00316 (0.222)	0.492 (1.00)	0.0812 (0.858)	0.18 (0.982)	0.737 (1.00)	0.255 (1.00)	0.405 (1.00)	1 (1.00)	0.15 (0.949)	0.747 (1.00)	0.702 (1.00)	0.403 (1.00)
19p loss	5 (6%)	85	0.00287 (0.217)	0.603 (1.00)	0.195 (1.00)	0.285 (1.00)	1 (1.00)	1 (1.00)	0.576 (1.00)	1 (1.00)	0.159 (0.963)		1 (1.00)	1 (1.00)
20p loss	9 (10%)	81	0.828 (1.00)	0.595 (1.00)	0.555 (1.00)	0.745 (1.00)	1 (1.00)	0.156 (0.963)	0.385 (1.00)	1 (1.00)	0.00218 (0.195)	0.969 (1.00)	0.276 (1.00)	0.548 (1.00)
1p gain	4 (4%)	86	0.0866 (0.858)	0.487 (1.00)	1 (1.00)	0.746 (1.00)	1 (1.00)	0.294 (1.00)	0.576 (1.00)	1 (1.00)	0.305 (1.00)	0.318 (1.00)	0.148 (0.945)	1 (1.00)
1q gain	8 (9%)	82	0.0407 (0.663)	0.798 (1.00)	0.734 (1.00)	0.455 (1.00)	0.589 (1.00)	0.047 (0.7)	1 (1.00)	1 (1.00)	0.511 (1.00)	0.173 (0.982)	0.245 (1.00)	0.548 (1.00)
2q gain	13 (14%)	77	0.0146 (0.478)	0.667 (1.00)	0.291 (1.00)	0.377 (1.00)	1 (1.00)	0.205 (1.00)	1 (1.00)	1 (1.00)	0.538 (1.00)	0.235 (1.00)	0.184 (0.982)	0.645 (1.00)
3p gain	14 (16%)	76	0.182 (0.982)	0.49 (1.00)	0.547 (1.00)	0.831 (1.00)	1 (1.00)	1 (1.00)	0.036 (0.647)	0.0252 (0.541)	0.745 (1.00)	0.581 (1.00)	1 (1.00)	1 (1.00)
3q gain	16 (18%)	74	0.266 (1.00)	0.598 (1.00)	0.328 (1.00)	0.671 (1.00)	1 (1.00)	1 (1.00)	0.035 (0.647)	0.0367 (0.647)	0.477 (1.00)	0.581 (1.00)	1 (1.00)	1 (1.00)
4p gain	38 (42%)	52	0.177 (0.982)	0.974 (1.00)	0.881 (1.00)	0.896 (1.00)	1 (1.00)	0.823 (1.00)	0.432 (1.00)	0.204 (1.00)	0.183 (0.982)	0.718 (1.00)	1 (1.00)	0.443 (1.00)
4q gain	35 (39%)	55	0.272 (1.00)	0.83 (1.00)	0.826 (1.00)	0.763 (1.00)	1 (1.00)	0.495 (1.00)	0.787 (1.00)	0.429 (1.00)	0.878 (1.00)	0.567 (1.00)	1 (1.00)	1 (1.00)
5p gain	57 (63%)	33	0.451 (1.00)	0.854 (1.00)	0.694 (1.00)	0.893 (1.00)	1 (1.00)	1 (1.00)	0.272 (1.00)	1 (1.00)	0.559 (1.00)	0.621 (1.00)	1 (1.00)	0.226 (1.00)
5q gain	55 (61%)	35	0.577 (1.00)	0.593 (1.00)	0.884 (1.00)	0.838 (1.00)	1 (1.00)	0.657 (1.00)	0.295 (1.00)	1 (1.00)	0.793 (1.00)	0.621 (1.00)	0.161 (0.971)	0.115 (0.89)
6p gain	18 (20%)	72	0.66 (1.00)	0.0275 (0.552)	0.497 (1.00)	0.253 (1.00)	0.679 (1.00)	0.588 (1.00)	0.506 (1.00)	1 (1.00)	0.0254 (0.541)	0.407 (1.00)	0.0911 (0.858)	0.0548 (0.731)
6q gain	16 (18%)	74	0.765 (1.00)	0.2 (1.00)	0.114 (0.89)	0.172 (0.982)	0.2 (1.00)	0.399 (1.00)	0.179 (0.982)	0.635 (1.00)	0.117 (0.89)	0.127 (0.896)	0.0591 (0.731)	0.613 (1.00)
7p gain	48 (53%)	42	0.815 (1.00)	0.51 (1.00)	0.168 (0.982)	0.232 (1.00)	0.336 (1.00)	1 (1.00)	0.793 (1.00)	0.621 (1.00)	0.771 (1.00)	0.361 (1.00)	0.215 (1.00)	0.435 (1.00)
7q gain	48 (53%)	42	0.512 (1.00)	0.859 (1.00)	0.107 (0.89)	0.224 (1.00)	0.336 (1.00)	1 (1.00)	0.431 (1.00)	0.621 (1.00)	0.769 (1.00)	0.268 (1.00)	0.217 (1.00)	0.115 (0.89)
8p gain	32 (36%)	58	0.222 (1.00)	0.508 (1.00)	0.442 (1.00)	0.635 (1.00)	0.484 (1.00)	1 (1.00)	0.786 (1.00)	0.546 (1.00)	1 (1.00)	1 (1.00)	0.29 (1.00)	0.421 (1.00)
8q gain	38 (42%)	52	0.649 (1.00)	0.49 (1.00)	0.348 (1.00)	0.534 (1.00)	0.51 (1.00)	1 (1.00)	0.594 (1.00)	0.449 (1.00)	0.799 (1.00)	0.83 (1.00)	0.342 (1.00)	0.7 (1.00)
9p gain	21 (23%)	69	0.123 (0.896)	0.643 (1.00)	0.0583 (0.731)	0.338 (1.00)	0.0106 (0.427)	1 (1.00)	0.0606 (0.731)	0.264 (1.00)	0.126 (0.896)	0.0118 (0.427)	1 (1.00)	0.412 (1.00)
9q gain	27 (30%)	63	0.00579 (0.322)	0.669 (1.00)	0.0174 (0.502)	0.0594 (0.731)	0.00805 (0.377)	0.631 (1.00)	0.567 (1.00)	0.356 (1.00)	0.0221 (0.506)	0.0177 (0.502)	0.665 (1.00)	1 (1.00)
10p gain	25 (28%)	65	0.011 (0.427)	0.397 (1.00)	0.00622 (0.322)	0.0162 (0.502)	1 (1.00)	1 (1.00)	1 (1.00)	0.691 (1.00)	0.00989 (0.427)	0.763 (1.00)	1 (1.00)	0.421 (1.00)
12p gain	64 (71%)	26	0.894 (1.00)	0.287 (1.00)	0.701 (1.00)	0.61 (1.00)	1 (1.00)	0.464 (1.00)	0.38 (1.00)	1 (1.00)	0.639 (1.00)	0.703 (1.00)	0.648 (1.00)	0.0898 (0.858)
12q gain	64 (71%)	26	0.917 (1.00)	0.415 (1.00)	0.703 (1.00)	0.65 (1.00)	0.718 (1.00)	0.464 (1.00)	0.38 (1.00)	1 (1.00)	0.655 (1.00)	0.703 (1.00)	0.0821 (0.858)	0.0898 (0.858)
13q gain	6 (7%)	84	0.839 (1.00)	0.651 (1.00)	0.735 (1.00)	0.722 (1.00)	0.526 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.501 (1.00)	0.633 (1.00)	1 (1.00)	0.548 (1.00)
14q gain	21 (23%)	69	0.13 (0.896)	0.426 (1.00)	0.182 (0.982)	0.311 (1.00)	0.241 (1.00)	0.606 (1.00)	0.0606 (0.731)	0.671 (1.00)	0.73 (1.00)	0.149 (0.946)	1 (1.00)	0.374 (1.00)
15q gain	11 (12%)	79	0.779 (1.00)	0.46 (1.00)	0.795 (1.00)	0.71 (1.00)	1 (1.00)	1 (1.00)	0.425 (1.00)	1 (1.00)	1 (1.00)	0.917 (1.00)	1 (1.00)	1 (1.00)
16p gain	50 (56%)	40	0.522 (1.00)	0.606 (1.00)	0.471 (1.00)	0.145 (0.944)	0.745 (1.00)	0.267 (1.00)	0.791 (1.00)	1 (1.00)	0.87 (1.00)	0.515 (1.00)	0.72 (1.00)	0.267 (1.00)
16q gain	47 (52%)	43	0.35 (1.00)	0.929 (1.00)	0.832 (1.00)	0.611 (1.00)	1 (1.00)	0.269 (1.00)	0.112 (0.89)	1 (1.00)	0.932 (1.00)	0.394 (1.00)	0.115 (0.89)	0.699 (1.00)
17p gain	5 (6%)	85	0.291 (1.00)	0.622 (1.00)	0.158 (0.963)	0.107 (0.89)	1 (1.00)	1 (1.00)	1 (1.00)	0.0701 (0.802)	0.503 (1.00)	0.318 (1.00)	0.146 (0.944)	0.444 (1.00)
17q gain	7 (8%)	83	0.124 (0.896)	0.488 (1.00)	0.69 (1.00)	0.469 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.0211 (0.502)	0.585 (1.00)		1 (1.00)	0.548 (1.00)
18p gain	6 (7%)	84	0.129 (0.896)	0.452 (1.00)	0.342 (1.00)	0.33 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.207 (1.00)		0.212 (1.00)	1 (1.00)
18q gain	5 (6%)	85	0.309 (1.00)	0.833 (1.00)	0.832 (1.00)	0.29 (1.00)	1 (1.00)	0.656 (1.00)	0.579 (1.00)	1 (1.00)	0.111 (0.89)		0.181 (0.982)	0.569 (1.00)
19p gain	56 (62%)	34	0.289 (1.00)	0.119 (0.89)	0.181 (0.982)	0.207 (1.00)	0.737 (1.00)	0.821 (1.00)	0.105 (0.89)	1 (1.00)	0.774 (1.00)	0.552 (1.00)	1 (1.00)	0.124 (0.896)
19q gain	52 (58%)	38	0.318 (1.00)	0.0203 (0.502)	0.198 (1.00)	0.326 (1.00)	0.182 (0.982)	0.378 (1.00)	0.108 (0.89)	0.787 (1.00)	0.253 (1.00)	0.321 (1.00)	1 (1.00)	0.124 (0.896)
20p gain	46 (51%)	44	0.141 (0.937)	0.495 (1.00)	0.339 (1.00)	0.796 (1.00)	1 (1.00)	0.188 (0.986)	0.3 (1.00)	0.616 (1.00)	0.463 (1.00)	0.917 (1.00)	0.492 (1.00)	1 (1.00)
20q gain	49 (54%)	41	0.542 (1.00)	0.964 (1.00)	0.32 (1.00)	0.857 (1.00)	0.336 (1.00)	0.187 (0.986)	0.431 (1.00)	0.62 (1.00)	0.245 (1.00)	0.396 (1.00)	0.217 (1.00)	0.71 (1.00)
21q gain	31 (34%)	59	0.68 (1.00)	0.154 (0.957)	0.936 (1.00)	0.941 (1.00)	0.0836 (0.858)	0.818 (1.00)	0.4 (1.00)	0.396 (1.00)	0.972 (1.00)	0.0907 (0.858)	0.272 (1.00)	0.443 (1.00)
22q gain	3 (3%)	87	0.131 (0.896)	0.208 (1.00)	1 (1.00)	1 (1.00)	0.307 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.625 (1.00)		1 (1.00)	1 (1.00)
xp gain	43 (48%)	47	0.822 (1.00)	0.856 (1.00)	0.977 (1.00)	0.96 (1.00)	0.517 (1.00)	1 (1.00)	0.792 (1.00)	0.617 (1.00)	0.147 (0.944)	0.316 (1.00)	0.36 (1.00)	0.115 (0.89)
xq gain	41 (46%)	49	0.54 (1.00)	0.82 (1.00)	0.838 (1.00)	1 (1.00)	0.745 (1.00)	0.824 (1.00)	0.597 (1.00)	0.624 (1.00)	0.182 (0.982)	0.699 (1.00)	0.345 (1.00)	0.26 (1.00)
1p loss	29 (32%)	61	0.902 (1.00)	0.866 (1.00)	0.958 (1.00)	0.952 (1.00)	1 (1.00)	1 (1.00)	0.26 (1.00)	0.257 (1.00)	1 (1.00)	0.292 (1.00)	1 (1.00)	1 (1.00)
1q loss	21 (23%)	69	0.928 (1.00)	0.309 (1.00)	0.512 (1.00)	0.716 (1.00)	0.689 (1.00)	0.433 (1.00)	0.344 (1.00)	0.0815 (0.858)	0.607 (1.00)	0.814 (1.00)	1 (1.00)	1 (1.00)
2p loss	16 (18%)	74	0.0502 (0.731)	0.569 (1.00)	1 (1.00)	0.756 (1.00)	0.677 (1.00)	0.399 (1.00)	0.502 (1.00)	0.0376 (0.647)	0.89 (1.00)	0.581 (1.00)	1 (1.00)	1 (1.00)
2q loss	14 (16%)	76	0.0897 (0.858)	0.854 (1.00)	0.7 (1.00)	0.841 (1.00)	1 (1.00)	0.545 (1.00)	0.456 (1.00)	0.0253 (0.541)	0.938 (1.00)	0.753 (1.00)	1 (1.00)	1 (1.00)
3p loss	19 (21%)	71	0.0584 (0.731)	0.452 (1.00)	0.0867 (0.858)	0.302 (1.00)	1 (1.00)	0.276 (1.00)	0.734 (1.00)	0.666 (1.00)	0.02 (0.502)	0.77 (1.00)	1 (1.00)	1 (1.00)
3q loss	19 (21%)	71	0.109 (0.89)	0.722 (1.00)	0.175 (0.982)	0.561 (1.00)	1 (1.00)	0.43 (1.00)	0.745 (1.00)	0.662 (1.00)	0.13 (0.896)	0.77 (1.00)	0.234 (1.00)	0.277 (1.00)
5p loss	7 (8%)	83	0.285 (1.00)	0.958 (1.00)	0.349 (1.00)	0.113 (0.89)	0.584 (1.00)	0.688 (1.00)	1 (1.00)	1 (1.00)	0.241 (1.00)	0.235 (1.00)	1 (1.00)	0.548 (1.00)
5q loss	5 (6%)	85	0.786 (1.00)	0.591 (1.00)	0.245 (1.00)	0.638 (1.00)	0.461 (1.00)	0.335 (1.00)	1 (1.00)	1 (1.00)	0.0908 (0.858)		1 (1.00)	1 (1.00)
6p loss	19 (21%)	71	0.11 (0.89)	0.35 (1.00)	0.0845 (0.858)	0.145 (0.944)	0.445 (1.00)	1 (1.00)	1 (1.00)	0.0629 (0.737)	0.246 (1.00)	0.5 (1.00)	1 (1.00)	0.571 (1.00)
6q loss	22 (24%)	68	0.0259 (0.541)	0.254 (1.00)	0.00727 (0.358)	0.0184 (0.502)	0.706 (1.00)	0.453 (1.00)	1 (1.00)	0.0924 (0.858)	0.0424 (0.663)	0.671 (1.00)	1 (1.00)	1 (1.00)
7p loss	5 (6%)	85	0.109 (0.89)	0.718 (1.00)	0.332 (1.00)	0.285 (1.00)	1 (1.00)	0.0461 (0.698)	0.576 (1.00)	1 (1.00)	0.173 (0.982)		1 (1.00)	1 (1.00)
7q loss	6 (7%)	84	0.0173 (0.502)	0.61 (1.00)	0.0389 (0.648)	0.0195 (0.502)	1 (1.00)	0.411 (1.00)	1 (1.00)	1 (1.00)	0.261 (1.00)		1 (1.00)	1 (1.00)
8p loss	16 (18%)	74	0.821 (1.00)	0.768 (1.00)	0.671 (1.00)	0.97 (1.00)	0.365 (1.00)	1 (1.00)	0.725 (1.00)	1 (1.00)	0.0269 (0.552)	0.854 (1.00)	1 (1.00)	1 (1.00)
8q loss	12 (13%)	78	0.892 (1.00)	0.639 (1.00)	0.578 (1.00)	1 (1.00)	0.107 (0.89)	0.534 (1.00)	1 (1.00)	1 (1.00)	0.0794 (0.858)	0.25 (1.00)	1 (1.00)	1 (1.00)
9p loss	20 (22%)	70	0.174 (0.982)	0.506 (1.00)	0.846 (1.00)	0.622 (1.00)	0.683 (1.00)	0.599 (1.00)	0.061 (0.731)	0.665 (1.00)	0.821 (1.00)	0.193 (1.00)	1 (1.00)	0.645 (1.00)
9q loss	12 (13%)	78	0.985 (1.00)	0.771 (1.00)	0.194 (1.00)	0.519 (1.00)	0.35 (1.00)	1 (1.00)	0.69 (1.00)	1 (1.00)	0.487 (1.00)	0.235 (1.00)	1 (1.00)	1 (1.00)
10p loss	12 (13%)	78	0.311 (1.00)	0.934 (1.00)	0.185 (0.986)	1 (1.00)	0.134 (0.91)	1 (1.00)	1 (1.00)	0.0615 (0.731)	0.526 (1.00)	0.116 (0.89)	1 (1.00)	0.444 (1.00)
10q loss	10 (11%)	80	0.383 (1.00)	0.298 (1.00)	0.306 (1.00)	0.713 (1.00)	0.317 (1.00)	1 (1.00)	1 (1.00)	0.0424 (0.663)	0.479 (1.00)	0.152 (0.951)	1 (1.00)	1 (1.00)
11p loss	23 (26%)	67	0.602 (1.00)	0.582 (1.00)	0.176 (0.982)	0.716 (1.00)	0.697 (1.00)	0.317 (1.00)	1 (1.00)	0.103 (0.89)	0.421 (1.00)	0.671 (1.00)	1 (1.00)	1 (1.00)
11q loss	22 (24%)	68	0.219 (1.00)	0.436 (1.00)	0.0338 (0.647)	0.207 (1.00)	1 (1.00)	0.302 (1.00)	1 (1.00)	0.0922 (0.858)	0.746 (1.00)	0.854 (1.00)	1 (1.00)	0.569 (1.00)
12p loss	5 (6%)	85	0.181 (0.982)	0.241 (1.00)	0.334 (1.00)	0.287 (1.00)	1 (1.00)	0.335 (1.00)	1 (1.00)	1 (1.00)	0.058 (0.731)	0.318 (1.00)	1 (1.00)	1 (1.00)
12q loss	4 (4%)	86	0.0594 (0.731)	0.463 (1.00)	0.331 (1.00)	0.284 (1.00)	1 (1.00)	0.606 (1.00)	1 (1.00)	1 (1.00)	0.0574 (0.731)	0.318 (1.00)	1 (1.00)	1 (1.00)
13q loss	39 (43%)	51	0.114 (0.89)	0.536 (1.00)	0.481 (1.00)	0.921 (1.00)	0.51 (1.00)	0.51 (1.00)	1 (1.00)	0.204 (1.00)	0.869 (1.00)	0.606 (1.00)	0.507 (1.00)	1 (1.00)
14q loss	18 (20%)	72	0.72 (1.00)	0.793 (1.00)	0.834 (1.00)	0.781 (1.00)	0.68 (1.00)	0.782 (1.00)	1 (1.00)	0.0523 (0.731)	0.529 (1.00)	0.265 (1.00)	0.219 (1.00)	0.129 (0.896)
15q loss	21 (23%)	69	0.679 (1.00)	0.519 (1.00)	0.65 (1.00)	0.7 (1.00)	1 (1.00)	0.606 (1.00)	0.218 (1.00)	0.0828 (0.858)	0.961 (1.00)	0.333 (1.00)	1 (1.00)	0.664 (1.00)
16q loss	5 (6%)	85	0.0193 (0.502)	0.214 (1.00)	0.246 (1.00)	0.139 (0.931)	0.461 (1.00)	1 (1.00)	0.275 (1.00)	1 (1.00)	0.114 (0.89)		1 (1.00)	0.444 (1.00)
17q loss	25 (28%)	65	0.0381 (0.647)	0.982 (1.00)	0.278 (1.00)	0.467 (1.00)	0.717 (1.00)	0.0125 (0.427)	0.55 (1.00)	0.691 (1.00)	0.314 (1.00)	0.583 (1.00)	1 (1.00)	0.658 (1.00)
18p loss	37 (41%)	53	0.599 (1.00)	0.892 (1.00)	0.205 (1.00)	0.494 (1.00)	1 (1.00)	0.37 (1.00)	0.295 (1.00)	0.589 (1.00)	0.182 (0.982)	0.816 (1.00)	0.294 (1.00)	1 (1.00)
18q loss	35 (39%)	55	0.934 (1.00)	0.747 (1.00)	0.272 (1.00)	0.52 (1.00)	1 (1.00)	0.11 (0.89)	0.584 (1.00)	0.429 (1.00)	0.649 (1.00)	0.816 (1.00)	0.273 (1.00)	1 (1.00)
19q loss	4 (4%)	86	0.0746 (0.843)	0.124 (0.896)	0.874 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.576 (1.00)	1 (1.00)	0.732 (1.00)	0.318 (1.00)	1 (1.00)	1 (1.00)
20q loss	3 (3%)	87	0.408 (1.00)	0.582 (1.00)	0.704 (1.00)	0.524 (1.00)	1 (1.00)	0.549 (1.00)	1 (1.00)	1 (1.00)	0.0381 (0.647)		1 (1.00)	0.321 (1.00)
21q loss	15 (17%)	75	0.0214 (0.502)	0.468 (1.00)	0.672 (1.00)	0.416 (1.00)	1 (1.00)	0.565 (1.00)	0.502 (1.00)	0.0308 (0.606)	0.519 (1.00)	0.475 (1.00)	1 (1.00)	1 (1.00)
22q loss	48 (53%)	42	0.0059 (0.322)	0.236 (1.00)	0.188 (0.986)	0.082 (0.858)	1 (1.00)	0.374 (1.00)	1 (1.00)	1 (1.00)	0.755 (1.00)	0.51 (1.00)	1 (1.00)	0.117 (0.89)
xp loss	16 (18%)	74	0.859 (1.00)	0.138 (0.93)	0.861 (1.00)	0.866 (1.00)	1 (1.00)	0.778 (1.00)	0.502 (1.00)	0.634 (1.00)	0.652 (1.00)	0.475 (1.00)	0.42 (1.00)	0.325 (1.00)
xq loss	16 (18%)	74	0.936 (1.00)	0.131 (0.896)	0.455 (1.00)	0.422 (1.00)	0.677 (1.00)	1 (1.00)	0.29 (1.00)	0.633 (1.00)	0.651 (1.00)	0.485 (1.00)	0.445 (1.00)	0.317 (1.00)

'2p gain' versus 'Time to Death'

P value = 0.000374 (logrank test), Q value = 0.074

Table S1. Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
2P GAIN MUTATED	13	10	0.0 - 91.3 (16.4)
2P GAIN WILD-TYPE	77	23	4.1 - 153.6 (39.5)

Figure S1. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'Time to Death'

P value = 0.00137 (logrank test), Q value = 0.17

Table S2. Gene #20: '10q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
10Q GAIN MUTATED	26	15	0.0 - 91.3 (32.0)
10Q GAIN WILD-TYPE	64	18	4.1 - 153.6 (43.9)

Figure S2. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #1: 'Time to Death'

'10q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00182 (Fisher's exact test), Q value = 0.18

Table S3. Gene #20: '10q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	9	43	18	18
10Q GAIN MUTATED	0	8	6	11
10Q GAIN WILD-TYPE	9	35	12	7

Figure S3. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0012 (Fisher's exact test), Q value = 0.17

Table S4. Gene #20: '10q gain' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	63	7	12	5
10Q GAIN MUTATED	12	2	9	1
10Q GAIN WILD-TYPE	51	5	3	4

Figure S4. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

'11p gain' versus 'Time to Death'

P value = 1e-04 (logrank test), Q value = 0.033

Table S5. Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
11P GAIN MUTATED	5	5	0.0 - 60.9 (14.3)
11P GAIN WILD-TYPE	85	28	4.1 - 153.6 (39.2)

Figure S5. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #1: 'Time to Death'

'11q gain' versus 'Time to Death'

P value = 5.25e-05 (logrank test), Q value = 0.026

Table S6. Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
11Q GAIN MUTATED	6	6	12.6 - 60.9 (16.2)
11Q GAIN WILD-TYPE	84	27	0.0 - 153.6 (39.4)

Figure S6. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'Time to Death'

P value = 3.72e-06 (logrank test), Q value = 0.0037

Table S7. Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
4P LOSS MUTATED	9	7	4.1 - 39.5 (18.1)
4P LOSS WILD-TYPE	81	26	0.0 - 153.6 (42.5)

Figure S7. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'Time to Death'

P value = 0.000266 (logrank test), Q value = 0.066

Table S8. Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
4Q LOSS MUTATED	10	7	5.2 - 46.5 (18.1)
4Q LOSS WILD-TYPE	80	26	0.0 - 153.6 (41.0)

Figure S8. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00156 (Fisher's exact test), Q value = 0.17

Table S9. Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	9	48	11	20
4Q LOSS MUTATED	1	1	1	7
4Q LOSS WILD-TYPE	8	47	10	13

Figure S9. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p loss' versus 'Time to Death'

P value = 0.000834 (logrank test), Q value = 0.14

Table S10. Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
16P LOSS MUTATED	4	4	16.1 - 39.4 (18.1)
16P LOSS WILD-TYPE	86	29	0.0 - 153.6 (39.4)

Figure S10. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00286 (Fisher's exact test), Q value = 0.22

Table S11. Gene #69: '16p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	63	7	12	5
16P LOSS MUTATED	0	2	1	1
16P LOSS WILD-TYPE	63	5	11	4

Figure S11. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

'17p loss' versus 'Time to Death'

P value = 0.00316 (logrank test), Q value = 0.22

Table S12. Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
17P LOSS MUTATED	33	18	4.1 - 95.2 (32.7)
17P LOSS WILD-TYPE	57	15	0.0 - 153.6 (43.3)

Figure S12. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'Time to Death'

P value = 0.00287 (logrank test), Q value = 0.22

Table S13. Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	90	33	0.0 - 153.6 (38.9)
19P LOSS MUTATED	5	4	12.6 - 44.5 (18.1)
19P LOSS WILD-TYPE	85	29	0.0 - 153.6 (39.4)

Figure S13. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

'20p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00218 (Fisher's exact test), Q value = 0.2

Table S14. Gene #77: '20p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	63	7	12	5
20P LOSS MUTATED	3	4	0	0
20P LOSS WILD-TYPE	60	3	12	5

Figure S14. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #9: 'RESIDUAL_TUMOR'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/22522856/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/22489368/ACC-TP.merged_data.txt
Number of patients = 90
Number of significantly arm-level cnvs = 82
Number of selected clinical features = 12
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

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

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] 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)

[3] 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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