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

Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

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 76 arm-level results and 10 clinical features across 413 patients, 18 significant findings detected with Q value < 0.25.

3p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
3q gain cnv correlated to 'Time to Death'.
7p gain cnv correlated to 'TUMOR.STAGE'.
13q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
17p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
18p gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
20p gain cnv correlated to 'HISTOLOGICAL.TYPE'.
20q gain cnv correlated to 'HISTOLOGICAL.TYPE'.
Xq gain cnv correlated to 'PATHOLOGICSPREAD(M)'.
2p loss cnv correlated to 'Time to Death'.
2q loss cnv correlated to 'Time to Death'.
3p loss cnv correlated to 'Time to Death'.
6q loss cnv correlated to 'PATHOLOGICSPREAD(M)'.
17p loss cnv correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
18p loss cnv correlated to 'HISTOLOGICAL.TYPE'.
18q loss cnv correlated to 'HISTOLOGICAL.TYPE'.
22q loss cnv correlated to 'HISTOLOGICAL.TYPE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 76 arm-level results and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 18 significant findings detected.


		Clinical Features	Time to Death	AGE	GENDER	HISTOLOGICAL TYPE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION	NEOADJUVANT THERAPY
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
17p loss	164 (40%)	249	0.162 (1.00)	0.339 (1.00)	0.191 (1.00)	5.34e-06 (0.00402)	0.867 (1.00)	0.0039 (1.00)	0.000887 (0.654)	0.000265 (0.197)	0.566 (1.00)	0.885 (1.00)
3p gain	20 (5%)	393	0.00121 (0.892)	0.152 (1.00)	0.496 (1.00)	1 (1.00)	0.686 (1.00)	0.293 (1.00)	0.000107 (0.0799)	0.352 (1.00)	1 (1.00)	0.751 (1.00)
3q gain	30 (7%)	383	4.78e-05 (0.0359)	0.588 (1.00)	0.342 (1.00)	0.783 (1.00)	0.908 (1.00)	0.0835 (1.00)	0.000364 (0.27)	0.0597 (1.00)	1 (1.00)	1 (1.00)
7p gain	200 (48%)	213	0.252 (1.00)	0.362 (1.00)	1 (1.00)	0.00119 (0.875)	0.774 (1.00)	0.00436 (1.00)	0.032 (1.00)	6.45e-05 (0.0483)	0.113 (1.00)	0.321 (1.00)
13q gain	211 (51%)	202	0.76 (1.00)	0.942 (1.00)	0.376 (1.00)	4e-06 (0.00301)	0.946 (1.00)	0.0349 (1.00)	0.127 (1.00)	0.0117 (1.00)	0.249 (1.00)	0.257 (1.00)
17p gain	9 (2%)	404	0.206 (1.00)	0.863 (1.00)	0.739 (1.00)	0.613 (1.00)	0.588 (1.00)	0.801 (1.00)	0.000127 (0.0944)	0.224 (1.00)	1 (1.00)	0.119 (1.00)
18p gain	15 (4%)	398	0.319 (1.00)	0.816 (1.00)	1 (1.00)	0.0351 (1.00)	0.842 (1.00)	0.0119 (1.00)	6.1e-06 (0.00459)	0.635 (1.00)	1 (1.00)	1 (1.00)
20p gain	188 (46%)	225	0.287 (1.00)	0.283 (1.00)	0.0599 (1.00)	6.4e-05 (0.048)	0.58 (1.00)	0.575 (1.00)	0.0382 (1.00)	0.0798 (1.00)	0.594 (1.00)	0.394 (1.00)
20q gain	267 (65%)	146	0.614 (1.00)	0.625 (1.00)	0.257 (1.00)	2.87e-08 (2.17e-05)	0.222 (1.00)	0.242 (1.00)	0.17 (1.00)	0.0248 (1.00)	1 (1.00)	0.462 (1.00)
Xq gain	12 (3%)	401	0.0145 (1.00)	0.315 (1.00)	0.559 (1.00)	0.664 (1.00)	1 (1.00)	0.0919 (1.00)	1.5e-07 (0.000113)	0.616 (1.00)	1 (1.00)	1 (1.00)
2p loss	4 (1%)	409	1.75e-11 (1.33e-08)	0.693 (1.00)	0.626 (1.00)	1 (1.00)	0.77 (1.00)	0.804 (1.00)	0.877 (1.00)	0.906 (1.00)	1 (1.00)	1 (1.00)
2q loss	6 (1%)	407	2.91e-07 (0.000219)	0.81 (1.00)	0.221 (1.00)	1 (1.00)	1 (1.00)	0.847 (1.00)	0.77 (1.00)	0.544 (1.00)	1 (1.00)	1 (1.00)
3p loss	27 (7%)	386	7.69e-05 (0.0574)	0.754 (1.00)	0.325 (1.00)	0.233 (1.00)	0.0627 (1.00)	0.0697 (1.00)	0.026 (1.00)	0.0567 (1.00)	1 (1.00)	0.401 (1.00)
6q loss	21 (5%)	392	0.0115 (1.00)	0.368 (1.00)	1 (1.00)	0.748 (1.00)	0.706 (1.00)	0.0332 (1.00)	0.000182 (0.135)	0.0939 (1.00)	1 (1.00)	1 (1.00)
18p loss	209 (51%)	204	0.365 (1.00)	0.108 (1.00)	1 (1.00)	1.03e-09 (7.8e-07)	0.85 (1.00)	0.00445 (1.00)	0.029 (1.00)	0.000665 (0.492)	1 (1.00)	0.572 (1.00)
18q loss	225 (54%)	188	0.265 (1.00)	0.119 (1.00)	0.429 (1.00)	7.61e-09 (5.77e-06)	0.941 (1.00)	0.00272 (1.00)	0.014 (1.00)	0.000422 (0.313)	0.254 (1.00)	0.888 (1.00)
22q loss	81 (20%)	332	0.527 (1.00)	0.105 (1.00)	0.535 (1.00)	7.26e-05 (0.0543)	0.839 (1.00)	0.0355 (1.00)	0.148 (1.00)	0.0803 (1.00)	0.481 (1.00)	0.153 (1.00)
1p gain	11 (3%)	402	0.44 (1.00)	0.664 (1.00)	1 (1.00)	1 (1.00)	0.616 (1.00)	0.44 (1.00)	0.776 (1.00)	0.483 (1.00)	1 (1.00)	0.376 (1.00)
1q gain	47 (11%)	366	0.889 (1.00)	0.466 (1.00)	0.0868 (1.00)	0.173 (1.00)	0.617 (1.00)	0.313 (1.00)	0.23 (1.00)	0.0686 (1.00)	1 (1.00)	1 (1.00)
2p gain	40 (10%)	373	0.604 (1.00)	0.61 (1.00)	0.869 (1.00)	0.0447 (1.00)	0.239 (1.00)	0.0603 (1.00)	0.895 (1.00)	0.0498 (1.00)	0.264 (1.00)	0.477 (1.00)
2q gain	39 (9%)	374	0.906 (1.00)	0.781 (1.00)	0.738 (1.00)	0.0436 (1.00)	0.286 (1.00)	0.0172 (1.00)	0.786 (1.00)	0.0188 (1.00)	0.258 (1.00)	0.227 (1.00)
4p gain	3 (1%)	410	0.457 (1.00)	0.569 (1.00)	1 (1.00)	0.346 (1.00)	1 (1.00)	0.0652 (1.00)	0.000376 (0.279)	0.19 (1.00)	1 (1.00)	0.366 (1.00)
4q gain	5 (1%)	408	0.445 (1.00)	0.856 (1.00)	0.668 (1.00)	0.508 (1.00)	0.522 (1.00)	0.107 (1.00)	0.291 (1.00)	0.0467 (1.00)	1 (1.00)	0.533 (1.00)
5p gain	39 (9%)	374	0.806 (1.00)	0.0805 (1.00)	0.239 (1.00)	0.453 (1.00)	0.799 (1.00)	0.163 (1.00)	0.347 (1.00)	0.681 (1.00)	1 (1.00)	0.468 (1.00)
5q gain	21 (5%)	392	0.609 (1.00)	0.285 (1.00)	0.374 (1.00)	0.335 (1.00)	0.846 (1.00)	0.113 (1.00)	0.742 (1.00)	0.749 (1.00)	1 (1.00)	0.516 (1.00)
6p gain	50 (12%)	363	0.747 (1.00)	0.574 (1.00)	0.763 (1.00)	0.506 (1.00)	0.369 (1.00)	0.0192 (1.00)	0.995 (1.00)	0.163 (1.00)	1 (1.00)	1 (1.00)
6q gain	45 (11%)	368	0.676 (1.00)	0.9 (1.00)	0.755 (1.00)	1 (1.00)	0.492 (1.00)	0.0176 (1.00)	0.969 (1.00)	0.0792 (1.00)	1 (1.00)	0.494 (1.00)
7q gain	175 (42%)	238	0.313 (1.00)	0.448 (1.00)	0.921 (1.00)	0.0115 (1.00)	0.559 (1.00)	0.204 (1.00)	0.0184 (1.00)	0.0046 (1.00)	0.577 (1.00)	1 (1.00)
8p gain	80 (19%)	333	0.845 (1.00)	0.199 (1.00)	0.618 (1.00)	1 (1.00)	0.237 (1.00)	0.411 (1.00)	0.935 (1.00)	0.61 (1.00)	0.477 (1.00)	1 (1.00)
8q gain	162 (39%)	251	0.61 (1.00)	0.0678 (1.00)	0.267 (1.00)	0.00673 (1.00)	0.0393 (1.00)	0.715 (1.00)	0.3 (1.00)	0.381 (1.00)	0.564 (1.00)	0.772 (1.00)
9p gain	46 (11%)	367	0.0786 (1.00)	0.544 (1.00)	0.347 (1.00)	0.358 (1.00)	0.552 (1.00)	0.607 (1.00)	0.786 (1.00)	0.6 (1.00)	1 (1.00)	0.0115 (1.00)
9q gain	39 (9%)	374	0.0609 (1.00)	0.608 (1.00)	0.179 (1.00)	0.622 (1.00)	0.199 (1.00)	0.262 (1.00)	0.799 (1.00)	0.571 (1.00)	1 (1.00)	0.00301 (1.00)
10p gain	18 (4%)	395	0.00999 (1.00)	0.098 (1.00)	0.813 (1.00)	0.711 (1.00)	0.108 (1.00)	0.0158 (1.00)	0.622 (1.00)	0.125 (1.00)	1 (1.00)	0.154 (1.00)
10q gain	7 (2%)	406	0.788 (1.00)	0.0299 (1.00)	1 (1.00)	0.232 (1.00)	0.481 (1.00)	0.0384 (1.00)	0.86 (1.00)	0.144 (1.00)	1 (1.00)	0.0089 (1.00)
11p gain	18 (4%)	395	0.412 (1.00)	0.198 (1.00)	0.631 (1.00)	0.147 (1.00)	0.215 (1.00)	0.119 (1.00)	0.93 (1.00)	0.106 (1.00)	1 (1.00)	1 (1.00)
11q gain	22 (5%)	391	0.203 (1.00)	0.0508 (1.00)	0.828 (1.00)	0.0957 (1.00)	0.235 (1.00)	0.0445 (1.00)	0.864 (1.00)	0.0183 (1.00)	1 (1.00)	0.215 (1.00)
12p gain	66 (16%)	347	0.659 (1.00)	0.0837 (1.00)	1 (1.00)	0.69 (1.00)	0.537 (1.00)	0.0345 (1.00)	0.446 (1.00)	0.0528 (1.00)	1 (1.00)	0.0514 (1.00)
12q gain	60 (15%)	353	0.845 (1.00)	0.0503 (1.00)	0.889 (1.00)	0.677 (1.00)	0.695 (1.00)	0.0677 (1.00)	0.188 (1.00)	0.0299 (1.00)	1 (1.00)	0.105 (1.00)
14q gain	15 (4%)	398	0.506 (1.00)	0.922 (1.00)	0.43 (1.00)	0.43 (1.00)	0.724 (1.00)	0.81 (1.00)	0.00355 (1.00)	0.706 (1.00)	1 (1.00)	0.244 (1.00)
15q gain	5 (1%)	408	0.493 (1.00)	0.709 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.829 (1.00)	0.825 (1.00)	0.863 (1.00)	1 (1.00)	0.533 (1.00)
16p gain	67 (16%)	346	0.938 (1.00)	0.205 (1.00)	0.79 (1.00)	0.0179 (1.00)	0.696 (1.00)	0.00924 (1.00)	0.662 (1.00)	0.00959 (1.00)	0.413 (1.00)	0.337 (1.00)
16q gain	66 (16%)	347	0.738 (1.00)	0.107 (1.00)	1 (1.00)	0.027 (1.00)	0.699 (1.00)	0.0019 (1.00)	0.633 (1.00)	0.00129 (0.945)	0.408 (1.00)	0.175 (1.00)
17q gain	48 (12%)	365	0.0544 (1.00)	0.335 (1.00)	0.539 (1.00)	0.0648 (1.00)	0.0588 (1.00)	0.329 (1.00)	0.00607 (1.00)	0.433 (1.00)	0.31 (1.00)	0.00325 (1.00)
18q gain	9 (2%)	404	0.699 (1.00)	0.331 (1.00)	0.512 (1.00)	0.102 (1.00)	0.445 (1.00)	0.12 (1.00)	0.909 (1.00)	0.962 (1.00)	1 (1.00)	1 (1.00)
19p gain	34 (8%)	379	0.605 (1.00)	0.445 (1.00)	0.858 (1.00)	0.0669 (1.00)	0.486 (1.00)	0.338 (1.00)	0.168 (1.00)	0.924 (1.00)	1 (1.00)	0.118 (1.00)
19q gain	41 (10%)	372	0.285 (1.00)	0.403 (1.00)	0.869 (1.00)	0.631 (1.00)	0.96 (1.00)	1 (1.00)	0.589 (1.00)	0.876 (1.00)	1 (1.00)	0.634 (1.00)
21q gain	11 (3%)	402	0.152 (1.00)	0.00583 (1.00)	0.762 (1.00)	1 (1.00)	0.0282 (1.00)	0.172 (1.00)	0.799 (1.00)	0.111 (1.00)	1 (1.00)	1 (1.00)
1p loss	51 (12%)	362	0.0103 (1.00)	0.507 (1.00)	1 (1.00)	0.122 (1.00)	0.783 (1.00)	0.0291 (1.00)	0.0303 (1.00)	0.0386 (1.00)	1 (1.00)	0.085 (1.00)
1q loss	18 (4%)	395	0.558 (1.00)	0.256 (1.00)	0.631 (1.00)	1 (1.00)	0.565 (1.00)	0.441 (1.00)	0.424 (1.00)	0.587 (1.00)	1 (1.00)	1 (1.00)
3q loss	12 (3%)	401	0.0351 (1.00)	0.0171 (1.00)	0.0406 (1.00)	0.38 (1.00)	0.744 (1.00)	0.774 (1.00)	0.19 (1.00)	0.103 (1.00)	1 (1.00)	0.388 (1.00)
4p loss	84 (20%)	329	0.00142 (1.00)	0.764 (1.00)	0.807 (1.00)	0.0103 (1.00)	0.719 (1.00)	0.0224 (1.00)	0.00219 (1.00)	0.00624 (1.00)	0.495 (1.00)	0.014 (1.00)
4q loss	68 (16%)	345	0.0221 (1.00)	0.478 (1.00)	0.596 (1.00)	0.0179 (1.00)	0.841 (1.00)	0.103 (1.00)	0.125 (1.00)	0.0769 (1.00)	0.418 (1.00)	0.0352 (1.00)
5p loss	25 (6%)	388	0.761 (1.00)	0.819 (1.00)	1 (1.00)	0.227 (1.00)	0.8 (1.00)	0.145 (1.00)	0.822 (1.00)	0.139 (1.00)	0.171 (1.00)	0.0662 (1.00)
5q loss	38 (9%)	375	0.341 (1.00)	0.867 (1.00)	0.0602 (1.00)	0.0433 (1.00)	0.919 (1.00)	0.00472 (1.00)	0.729 (1.00)	0.271 (1.00)	0.252 (1.00)	0.63 (1.00)
6p loss	12 (3%)	401	0.755 (1.00)	0.625 (1.00)	0.777 (1.00)	1 (1.00)	0.8 (1.00)	0.842 (1.00)	0.366 (1.00)	0.895 (1.00)	1 (1.00)	1 (1.00)
8p loss	93 (23%)	320	0.61 (1.00)	0.641 (1.00)	0.238 (1.00)	0.081 (1.00)	0.836 (1.00)	0.0218 (1.00)	0.118 (1.00)	0.0964 (1.00)	0.536 (1.00)	0.313 (1.00)
8q loss	8 (2%)	405	0.884 (1.00)	0.21 (1.00)	0.293 (1.00)	1 (1.00)	0.601 (1.00)	0.256 (1.00)	0.674 (1.00)	0.132 (1.00)	1 (1.00)	0.607 (1.00)
9p loss	27 (7%)	386	0.21 (1.00)	0.0653 (1.00)	1 (1.00)	0.556 (1.00)	0.158 (1.00)	0.779 (1.00)	0.919 (1.00)	0.752 (1.00)	1 (1.00)	0.401 (1.00)
9q loss	26 (6%)	387	0.736 (1.00)	0.0045 (1.00)	0.311 (1.00)	0.227 (1.00)	0.0141 (1.00)	0.607 (1.00)	0.926 (1.00)	0.23 (1.00)	1 (1.00)	0.773 (1.00)
10p loss	22 (5%)	391	0.811 (1.00)	0.321 (1.00)	0.514 (1.00)	1 (1.00)	0.305 (1.00)	0.559 (1.00)	0.104 (1.00)	0.105 (1.00)	1 (1.00)	1 (1.00)
10q loss	24 (6%)	389	0.28 (1.00)	0.178 (1.00)	0.529 (1.00)	1 (1.00)	0.501 (1.00)	0.52 (1.00)	0.2 (1.00)	0.255 (1.00)	1 (1.00)	1 (1.00)
11p loss	22 (5%)	391	0.235 (1.00)	0.207 (1.00)	1 (1.00)	0.335 (1.00)	0.786 (1.00)	0.532 (1.00)	0.736 (1.00)	0.342 (1.00)	1 (1.00)	0.339 (1.00)
11q loss	27 (7%)	386	0.724 (1.00)	0.285 (1.00)	0.426 (1.00)	0.556 (1.00)	0.354 (1.00)	0.174 (1.00)	0.455 (1.00)	0.36 (1.00)	1 (1.00)	0.401 (1.00)
12p loss	21 (5%)	392	0.278 (1.00)	0.775 (1.00)	0.374 (1.00)	0.0918 (1.00)	0.16 (1.00)	0.0514 (1.00)	0.797 (1.00)	0.245 (1.00)	0.145 (1.00)	1 (1.00)
12q loss	20 (5%)	393	0.389 (1.00)	0.941 (1.00)	0.256 (1.00)	0.0904 (1.00)	0.289 (1.00)	0.0983 (1.00)	0.742 (1.00)	0.164 (1.00)	1 (1.00)	0.751 (1.00)
13q loss	6 (1%)	407	0.237 (1.00)	0.627 (1.00)	1 (1.00)	0.574 (1.00)	0.156 (1.00)	0.0823 (1.00)	0.496 (1.00)	0.196 (1.00)	1 (1.00)	1 (1.00)
14q loss	94 (23%)	319	0.345 (1.00)	0.939 (1.00)	0.64 (1.00)	0.000719 (0.531)	0.893 (1.00)	0.0883 (1.00)	0.266 (1.00)	0.283 (1.00)	1 (1.00)	0.315 (1.00)
15q loss	99 (24%)	314	0.365 (1.00)	0.424 (1.00)	0.908 (1.00)	0.00173 (1.00)	0.687 (1.00)	0.554 (1.00)	0.215 (1.00)	0.208 (1.00)	0.562 (1.00)	0.869 (1.00)
16p loss	9 (2%)	404	0.977 (1.00)	0.999 (1.00)	0.315 (1.00)	0.337 (1.00)	0.897 (1.00)	0.894 (1.00)	0.993 (1.00)	0.477 (1.00)	1 (1.00)	0.368 (1.00)
16q loss	7 (2%)	406	0.478 (1.00)	0.612 (1.00)	0.71 (1.00)	0.232 (1.00)	0.743 (1.00)	1 (1.00)	0.98 (1.00)	0.792 (1.00)	1 (1.00)	1 (1.00)
17q loss	32 (8%)	381	0.702 (1.00)	0.544 (1.00)	0.716 (1.00)	0.101 (1.00)	0.748 (1.00)	0.0518 (1.00)	0.37 (1.00)	0.0488 (1.00)	1 (1.00)	0.0663 (1.00)
19p loss	14 (3%)	399	0.291 (1.00)	0.5 (1.00)	0.275 (1.00)	0.232 (1.00)	0.296 (1.00)	0.928 (1.00)	0.226 (1.00)	0.14 (1.00)	1 (1.00)	0.703 (1.00)
19q loss	13 (3%)	400	0.291 (1.00)	0.73 (1.00)	0.156 (1.00)	0.232 (1.00)	0.222 (1.00)	1 (1.00)	0.166 (1.00)	0.178 (1.00)	1 (1.00)	1 (1.00)
20p loss	33 (8%)	380	0.56 (1.00)	0.806 (1.00)	0.59 (1.00)	0.599 (1.00)	0.735 (1.00)	0.513 (1.00)	0.71 (1.00)	0.508 (1.00)	1 (1.00)	1 (1.00)
21q loss	71 (17%)	342	0.666 (1.00)	0.675 (1.00)	0.896 (1.00)	0.0514 (1.00)	0.152 (1.00)	0.407 (1.00)	0.928 (1.00)	0.857 (1.00)	1 (1.00)	0.348 (1.00)
Xq loss	5 (1%)	408	0.725 (1.00)	0.78 (1.00)	0.668 (1.00)	0.508 (1.00)	0.251 (1.00)	0.107 (1.00)	0.869 (1.00)	0.536 (1.00)	1 (1.00)	0.533 (1.00)

'3p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000107 (Chi-square test), Q value = 0.08

Table S1. Gene #5: '3p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
3P GAIN MUTATED	12	2	1	1	3
3P GAIN WILD-TYPE	300	47	6	0	33

Figure S1. Get High-res Image Gene #5: '3p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'3q gain mutation analysis' versus 'Time to Death'

P value = 4.78e-05 (logrank test), Q value = 0.036

Table S2. Gene #6: '3q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	319	49	0.1 - 135.5 (7.7)
3Q GAIN MUTATED	23	8	0.2 - 46.8 (5.0)
3Q GAIN WILD-TYPE	296	41	0.1 - 135.5 (8.0)

Figure S2. Get High-res Image Gene #6: '3q gain mutation analysis' versus Clinical Feature #1: 'Time to Death'

'7p gain mutation analysis' versus 'TUMOR.STAGE'

P value = 6.45e-05 (Fisher's exact test), Q value = 0.048

Table S3. Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
7P GAIN MUTATED	31	55	68	36
7P GAIN WILD-TYPE	36	102	48	20

Figure S3. Get High-res Image Gene #13: '7p gain mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'13q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4e-06 (Fisher's exact test), Q value = 0.003

Table S4. Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
13Q GAIN MUTATED	198	12
13Q GAIN WILD-TYPE	158	42

Figure S4. Get High-res Image Gene #25: '13q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'17p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000127 (Chi-square test), Q value = 0.094

Table S5. Gene #30: '17p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
17P GAIN MUTATED	5	1	2	0	1
17P GAIN WILD-TYPE	307	48	5	1	35

Figure S5. Get High-res Image Gene #30: '17p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'18p gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 6.1e-06 (Chi-square test), Q value = 0.0046

Table S6. Gene #32: '18p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
18P GAIN MUTATED	11	2	0	1	0
18P GAIN WILD-TYPE	301	47	7	0	36

Figure S6. Get High-res Image Gene #32: '18p gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'20p gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.4e-05 (Fisher's exact test), Q value = 0.048

Table S7. Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
20P GAIN MUTATED	174	11
20P GAIN WILD-TYPE	182	43

Figure S7. Get High-res Image Gene #36: '20p gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'20q gain mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.87e-08 (Fisher's exact test), Q value = 2.2e-05

Table S8. Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
20Q GAIN MUTATED	248	16
20Q GAIN WILD-TYPE	108	38

Figure S8. Get High-res Image Gene #37: '20q gain mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Xq gain mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.5e-07 (Chi-square test), Q value = 0.00011

Table S9. Gene #39: 'Xq gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
XQ GAIN MUTATED	8	2	0	1	0
XQ GAIN WILD-TYPE	304	47	7	0	36

Figure S9. Get High-res Image Gene #39: 'Xq gain mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'2p loss mutation analysis' versus 'Time to Death'

P value = 1.75e-11 (logrank test), Q value = 1.3e-08

Table S10. Gene #42: '2p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	319	49	0.1 - 135.5 (7.7)
2P LOSS MUTATED	3	1	0.3 - 1.0 (1.0)
2P LOSS WILD-TYPE	316	48	0.1 - 135.5 (7.9)

Figure S10. Get High-res Image Gene #42: '2p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'2q loss mutation analysis' versus 'Time to Death'

P value = 2.91e-07 (logrank test), Q value = 0.00022

Table S11. Gene #43: '2q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	319	49	0.1 - 135.5 (7.7)
2Q LOSS MUTATED	4	1	0.3 - 1.0 (1.0)
2Q LOSS WILD-TYPE	315	48	0.1 - 135.5 (8.0)

Figure S11. Get High-res Image Gene #43: '2q loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'3p loss mutation analysis' versus 'Time to Death'

P value = 7.69e-05 (logrank test), Q value = 0.057

Table S12. Gene #44: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	319	49	0.1 - 135.5 (7.7)
3P LOSS MUTATED	16	5	0.3 - 14.5 (5.3)
3P LOSS WILD-TYPE	303	44	0.1 - 135.5 (7.9)

Figure S12. Get High-res Image Gene #44: '3p loss mutation analysis' versus Clinical Feature #1: 'Time to Death'

'6q loss mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000182 (Chi-square test), Q value = 0.14

Table S13. Gene #51: '6q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
6Q LOSS MUTATED	12	4	1	1	3
6Q LOSS WILD-TYPE	300	45	6	0	33

Figure S13. Get High-res Image Gene #51: '6q loss mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'17p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.34e-06 (Fisher's exact test), Q value = 0.004

Table S14. Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
17P LOSS MUTATED	157	7
17P LOSS WILD-TYPE	199	47

Figure S14. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'17p loss mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000265 (Fisher's exact test), Q value = 0.2

Table S15. Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
17P LOSS MUTATED	24	48	52	35
17P LOSS WILD-TYPE	43	109	64	21

Figure S15. Get High-res Image Gene #67: '17p loss mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'18p loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-09 (Fisher's exact test), Q value = 7.8e-07

Table S16. Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
18P LOSS MUTATED	200	7
18P LOSS WILD-TYPE	156	47

Figure S16. Get High-res Image Gene #69: '18p loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'18q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.61e-09 (Fisher's exact test), Q value = 5.8e-06

Table S17. Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
18Q LOSS MUTATED	214	10
18Q LOSS WILD-TYPE	142	44

Figure S17. Get High-res Image Gene #70: '18q loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'22q loss mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.26e-05 (Fisher's exact test), Q value = 0.054

Table S18. Gene #75: '22q loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
22Q LOSS MUTATED	80	1
22Q LOSS WILD-TYPE	276	53

Figure S18. Get High-res Image Gene #75: '22q loss mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Clinical data file = COAD.clin.merged.picked.txt
Number of patients = 413
Number of significantly arm-level cnvs = 76
Number of selected clinical features = 10
Exclude genes 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

Student's t-test analysis

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

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

Chi-square test

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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

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

[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

[4] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[5] 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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