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

Colon Adenocarcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_23

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 (2013): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1DJ5CXV

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 79 arm-level events and 11 clinical features across 421 patients, 12 significant findings detected with Q value < 0.25.

3P GAIN MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.
12Q GAIN MUTATION ANALYSIS cnv correlated to 'NUMBER.OF.LYMPH.NODES'.
13Q GAIN MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
14Q GAIN MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.
20Q GAIN MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
4P LOSS MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.M.STAGE'.
5Q LOSS MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.
14Q LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
17P LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
18P LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
18Q LOSS MUTATION ANALYSIS cnv correlated to 'HISTOLOGICAL.TYPE'.
22Q LOSS MUTATION ANALYSIS cnv correlated to 'PATHOLOGY.N.STAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 79 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 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	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES
	nCNV (%)	nWild-Type	logrank test	t-test	Chi-square test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test
3P GAIN MUTATION ANALYSIS	39 (9%)	382	0.242 (1.00)	0.0867 (1.00)	0.00131 (1.00)	0.906 (1.00)	0.196 (1.00)	5.57e-05 (0.048)	0.867 (1.00)	0.451 (1.00)	1 (1.00)	0.832 (1.00)	0.171 (1.00)
12Q GAIN MUTATION ANALYSIS	80 (19%)	341	0.879 (1.00)	0.0353 (1.00)	0.0208 (1.00)	0.437 (1.00)	0.0127 (1.00)	0.0131 (1.00)	1 (1.00)	0.36 (1.00)	1 (1.00)	0.371 (1.00)	6.71e-05 (0.0578)
13Q GAIN MUTATION ANALYSIS	243 (58%)	178	0.469 (1.00)	0.288 (1.00)	0.0171 (1.00)	0.988 (1.00)	0.016 (1.00)	0.0192 (1.00)	0.43 (1.00)	1.46e-06 (0.00127)	0.266 (1.00)	0.0415 (1.00)	0.75 (1.00)
14Q GAIN MUTATION ANALYSIS	34 (8%)	387	0.954 (1.00)	0.945 (1.00)	0.652 (1.00)	0.937 (1.00)	0.618 (1.00)	6.56e-05 (0.0565)	0.371 (1.00)	0.186 (1.00)	1 (1.00)	0.727 (1.00)	0.404 (1.00)
20Q GAIN MUTATION ANALYSIS	298 (71%)	123	0.753 (1.00)	0.257 (1.00)	0.00211 (1.00)	0.206 (1.00)	0.0585 (1.00)	0.00764 (1.00)	0.334 (1.00)	9.79e-06 (0.00847)	0.559 (1.00)	0.134 (1.00)	0.0892 (1.00)
4P LOSS MUTATION ANALYSIS	124 (29%)	297	0.052 (1.00)	0.699 (1.00)	0.00454 (1.00)	0.63 (1.00)	0.00169 (1.00)	0.000157 (0.135)	0.915 (1.00)	0.0104 (1.00)	0.0251 (1.00)	0.0301 (1.00)	0.0102 (1.00)
5Q LOSS MUTATION ANALYSIS	70 (17%)	351	0.198 (1.00)	0.203 (1.00)	0.0504 (1.00)	0.82 (1.00)	0.000197 (0.169)	0.0866 (1.00)	0.515 (1.00)	0.25 (1.00)	0.0731 (1.00)	0.602 (1.00)	0.00351 (1.00)
14Q LOSS MUTATION ANALYSIS	124 (29%)	297	0.194 (1.00)	0.836 (1.00)	0.161 (1.00)	0.658 (1.00)	0.111 (1.00)	0.0352 (1.00)	1 (1.00)	4.7e-05 (0.0406)	0.559 (1.00)	0.565 (1.00)	0.796 (1.00)
17P LOSS MUTATION ANALYSIS	216 (51%)	205	0.156 (1.00)	0.0669 (1.00)	0.000939 (0.792)	0.847 (1.00)	0.000566 (0.482)	0.00818 (1.00)	0.0977 (1.00)	1.08e-05 (0.00937)	0.249 (1.00)	0.0508 (1.00)	0.000929 (0.785)
18P LOSS MUTATION ANALYSIS	233 (55%)	188	0.619 (1.00)	0.0992 (1.00)	0.00136 (1.00)	0.949 (1.00)	0.00632 (1.00)	0.00304 (1.00)	0.556 (1.00)	3.8e-10 (3.3e-07)	0.257 (1.00)	0.0312 (1.00)	0.0253 (1.00)
18Q LOSS MUTATION ANALYSIS	250 (59%)	171	0.682 (1.00)	0.0782 (1.00)	0.000318 (0.272)	0.722 (1.00)	0.000687 (0.585)	0.0038 (1.00)	0.426 (1.00)	1.74e-09 (1.51e-06)	0.275 (1.00)	0.145 (1.00)	0.0787 (1.00)
22Q LOSS MUTATION ANALYSIS	131 (31%)	290	0.328 (1.00)	0.84 (1.00)	0.00411 (1.00)	0.575 (1.00)	0.000273 (0.235)	0.0182 (1.00)	0.675 (1.00)	0.00453 (1.00)	1 (1.00)	0.494 (1.00)	0.0104 (1.00)
1P GAIN MUTATION ANALYSIS	27 (6%)	394	0.431 (1.00)	0.242 (1.00)	0.909 (1.00)	0.953 (1.00)	0.722 (1.00)	0.357 (1.00)	0.557 (1.00)	0.556 (1.00)	0.181 (1.00)	0.0719 (1.00)	0.266 (1.00)
1Q GAIN MUTATION ANALYSIS	72 (17%)	349	0.608 (1.00)	0.709 (1.00)	0.0488 (1.00)	0.645 (1.00)	0.124 (1.00)	0.00305 (1.00)	0.156 (1.00)	0.249 (1.00)	0.431 (1.00)	0.059 (1.00)	0.105 (1.00)
2P GAIN MUTATION ANALYSIS	71 (17%)	350	0.326 (1.00)	0.662 (1.00)	0.268 (1.00)	0.576 (1.00)	0.366 (1.00)	0.681 (1.00)	0.605 (1.00)	0.0517 (1.00)	0.426 (1.00)	0.0959 (1.00)	0.718 (1.00)
2Q GAIN MUTATION ANALYSIS	67 (16%)	354	0.157 (1.00)	0.239 (1.00)	0.135 (1.00)	0.47 (1.00)	0.147 (1.00)	0.544 (1.00)	0.79 (1.00)	0.0739 (1.00)	0.406 (1.00)	0.146 (1.00)	0.535 (1.00)
3Q GAIN MUTATION ANALYSIS	56 (13%)	365	0.0714 (1.00)	0.213 (1.00)	0.0207 (1.00)	0.913 (1.00)	0.0896 (1.00)	0.00168 (1.00)	1 (1.00)	0.202 (1.00)	1 (1.00)	0.621 (1.00)	0.172 (1.00)
4P GAIN MUTATION ANALYSIS	6 (1%)	415	0.773 (1.00)	0.725 (1.00)	0.844 (1.00)	1 (1.00)	0.204 (1.00)	0.0553 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.794 (1.00)
4Q GAIN MUTATION ANALYSIS	11 (3%)	410	0.421 (1.00)	0.661 (1.00)	0.8 (1.00)	0.722 (1.00)	0.158 (1.00)	0.622 (1.00)	0.761 (1.00)	0.373 (1.00)	1 (1.00)	0.298 (1.00)	0.654 (1.00)
5P GAIN MUTATION ANALYSIS	62 (15%)	359	0.967 (1.00)	0.142 (1.00)	0.252 (1.00)	0.898 (1.00)	0.105 (1.00)	0.841 (1.00)	0.17 (1.00)	0.838 (1.00)	1 (1.00)	0.445 (1.00)	0.321 (1.00)
5Q GAIN MUTATION ANALYSIS	38 (9%)	383	0.598 (1.00)	0.931 (1.00)	0.825 (1.00)	0.894 (1.00)	0.529 (1.00)	0.952 (1.00)	0.734 (1.00)	0.451 (1.00)	1 (1.00)	0.368 (1.00)	0.996 (1.00)
6P GAIN MUTATION ANALYSIS	79 (19%)	342	0.444 (1.00)	0.715 (1.00)	0.247 (1.00)	0.831 (1.00)	0.0166 (1.00)	0.806 (1.00)	0.382 (1.00)	0.269 (1.00)	0.0064 (1.00)	0.54 (1.00)	0.0519 (1.00)
6Q GAIN MUTATION ANALYSIS	71 (17%)	350	0.577 (1.00)	0.442 (1.00)	0.123 (1.00)	1 (1.00)	0.02 (1.00)	0.645 (1.00)	0.796 (1.00)	0.25 (1.00)	0.00463 (1.00)	0.641 (1.00)	0.0801 (1.00)
7P GAIN MUTATION ANALYSIS	233 (55%)	188	0.777 (1.00)	0.208 (1.00)	0.000899 (0.761)	0.357 (1.00)	0.000337 (0.289)	0.0246 (1.00)	1 (1.00)	0.0193 (1.00)	0.257 (1.00)	0.202 (1.00)	0.0707 (1.00)
7Q GAIN MUTATION ANALYSIS	210 (50%)	211	0.607 (1.00)	0.103 (1.00)	0.0461 (1.00)	0.179 (1.00)	0.0281 (1.00)	0.0234 (1.00)	1 (1.00)	0.0421 (1.00)	0.623 (1.00)	0.36 (1.00)	0.209 (1.00)
8P GAIN MUTATION ANALYSIS	118 (28%)	303	0.384 (1.00)	0.503 (1.00)	0.504 (1.00)	0.93 (1.00)	0.7 (1.00)	0.871 (1.00)	0.829 (1.00)	0.198 (1.00)	0.191 (1.00)	0.565 (1.00)	0.219 (1.00)
8Q GAIN MUTATION ANALYSIS	206 (49%)	215	0.919 (1.00)	0.146 (1.00)	0.748 (1.00)	0.285 (1.00)	0.624 (1.00)	0.485 (1.00)	0.769 (1.00)	0.0293 (1.00)	0.116 (1.00)	0.273 (1.00)	0.554 (1.00)
9P GAIN MUTATION ANALYSIS	73 (17%)	348	0.0882 (1.00)	0.453 (1.00)	0.0542 (1.00)	0.626 (1.00)	0.0923 (1.00)	0.274 (1.00)	1 (1.00)	0.0545 (1.00)	1 (1.00)	0.772 (1.00)	0.145 (1.00)
9Q GAIN MUTATION ANALYSIS	65 (15%)	356	0.183 (1.00)	0.576 (1.00)	0.15 (1.00)	0.435 (1.00)	0.271 (1.00)	0.789 (1.00)	0.788 (1.00)	0.107 (1.00)	1 (1.00)	0.836 (1.00)	0.219 (1.00)
10P GAIN MUTATION ANALYSIS	31 (7%)	390	0.0945 (1.00)	0.395 (1.00)	0.723 (1.00)	0.297 (1.00)	0.0835 (1.00)	0.187 (1.00)	1 (1.00)	0.783 (1.00)	1 (1.00)	0.283 (1.00)	0.108 (1.00)
10Q GAIN MUTATION ANALYSIS	18 (4%)	403	0.629 (1.00)	0.0496 (1.00)	0.734 (1.00)	0.878 (1.00)	0.0528 (1.00)	0.433 (1.00)	0.631 (1.00)	0.718 (1.00)	1 (1.00)	0.561 (1.00)	0.111 (1.00)
11P GAIN MUTATION ANALYSIS	49 (12%)	372	0.933 (1.00)	0.0402 (1.00)	0.234 (1.00)	0.141 (1.00)	0.134 (1.00)	0.0619 (1.00)	1 (1.00)	0.0115 (1.00)	0.0369 (1.00)	0.379 (1.00)	0.243 (1.00)
11Q GAIN MUTATION ANALYSIS	48 (11%)	373	0.729 (1.00)	0.00295 (1.00)	0.16 (1.00)	0.403 (1.00)	0.0778 (1.00)	0.072 (1.00)	0.879 (1.00)	0.00112 (0.938)	0.0355 (1.00)	0.405 (1.00)	0.325 (1.00)
12P GAIN MUTATION ANALYSIS	87 (21%)	334	0.481 (1.00)	0.0818 (1.00)	0.148 (1.00)	0.375 (1.00)	0.154 (1.00)	0.0776 (1.00)	1 (1.00)	0.859 (1.00)	1 (1.00)	0.544 (1.00)	0.0402 (1.00)
15Q GAIN MUTATION ANALYSIS	12 (3%)	409	0.427 (1.00)	0.167 (1.00)	0.742 (1.00)	0.125 (1.00)	0.424 (1.00)	0.179 (1.00)	0.0743 (1.00)	1 (1.00)	1 (1.00)	0.056 (1.00)	0.527 (1.00)
16P GAIN MUTATION ANALYSIS	100 (24%)	321	0.696 (1.00)	0.0797 (1.00)	0.00677 (1.00)	0.986 (1.00)	0.00274 (1.00)	0.286 (1.00)	0.819 (1.00)	0.00587 (1.00)	0.558 (1.00)	0.939 (1.00)	0.13 (1.00)
16Q GAIN MUTATION ANALYSIS	96 (23%)	325	0.648 (1.00)	0.0287 (1.00)	0.00167 (1.00)	1 (1.00)	0.0032 (1.00)	0.313 (1.00)	0.485 (1.00)	0.00898 (1.00)	0.541 (1.00)	0.823 (1.00)	0.199 (1.00)
17P GAIN MUTATION ANALYSIS	21 (5%)	400	0.127 (1.00)	0.646 (1.00)	0.366 (1.00)	0.53 (1.00)	0.219 (1.00)	0.0266 (1.00)	0.373 (1.00)	0.747 (1.00)	1 (1.00)	0.451 (1.00)	0.695 (1.00)
17Q GAIN MUTATION ANALYSIS	67 (16%)	354	0.377 (1.00)	0.349 (1.00)	0.135 (1.00)	0.677 (1.00)	0.116 (1.00)	0.0039 (1.00)	0.689 (1.00)	0.168 (1.00)	0.406 (1.00)	0.513 (1.00)	0.678 (1.00)
18P GAIN MUTATION ANALYSIS	21 (5%)	400	0.971 (1.00)	0.505 (1.00)	0.0071 (1.00)	1 (1.00)	0.0623 (1.00)	0.00038 (0.325)	0.504 (1.00)	0.0122 (1.00)	1 (1.00)	0.524 (1.00)	0.114 (1.00)
18Q GAIN MUTATION ANALYSIS	13 (3%)	408	0.441 (1.00)	0.0604 (1.00)	0.807 (1.00)	0.763 (1.00)	0.275 (1.00)	0.976 (1.00)	0.587 (1.00)	0.0183 (1.00)	1 (1.00)	1 (1.00)	0.711 (1.00)
19P GAIN MUTATION ANALYSIS	65 (15%)	356	0.298 (1.00)	0.672 (1.00)	0.359 (1.00)	0.833 (1.00)	0.0755 (1.00)	0.00298 (1.00)	0.0303 (1.00)	0.0741 (1.00)	0.396 (1.00)	0.204 (1.00)	0.348 (1.00)
19Q GAIN MUTATION ANALYSIS	70 (17%)	351	0.331 (1.00)	0.644 (1.00)	0.606 (1.00)	0.993 (1.00)	0.373 (1.00)	0.00629 (1.00)	0.0894 (1.00)	0.846 (1.00)	0.421 (1.00)	0.207 (1.00)	0.884 (1.00)
20P GAIN MUTATION ANALYSIS	225 (53%)	196	0.304 (1.00)	0.715 (1.00)	0.000434 (0.371)	0.85 (1.00)	0.191 (1.00)	0.00141 (1.00)	0.142 (1.00)	0.00131 (1.00)	0.252 (1.00)	0.0693 (1.00)	0.252 (1.00)
21Q GAIN MUTATION ANALYSIS	21 (5%)	400	0.155 (1.00)	0.00097 (0.816)	0.722 (1.00)	0.137 (1.00)	0.472 (1.00)	0.735 (1.00)	1 (1.00)	0.736 (1.00)	1 (1.00)	0.39 (1.00)	0.944 (1.00)
22Q GAIN MUTATION ANALYSIS	12 (3%)	409	0.362 (1.00)	0.427 (1.00)	0.882 (1.00)	0.694 (1.00)	1 (1.00)	0.186 (1.00)	0.778 (1.00)	0.38 (1.00)	0.0833 (1.00)	0.345 (1.00)	0.375 (1.00)
XQ GAIN MUTATION ANALYSIS	73 (17%)	348	0.98 (1.00)	0.571 (1.00)	0.311 (1.00)	0.0189 (1.00)	0.69 (1.00)	0.205 (1.00)	0.798 (1.00)	0.251 (1.00)	0.436 (1.00)	0.559 (1.00)	0.891 (1.00)
1P LOSS MUTATION ANALYSIS	86 (20%)	335	0.0256 (1.00)	0.496 (1.00)	0.0116 (1.00)	0.796 (1.00)	0.000514 (0.438)	0.00137 (1.00)	1 (1.00)	0.285 (1.00)	1 (1.00)	0.247 (1.00)	0.00821 (1.00)
1Q LOSS MUTATION ANALYSIS	49 (12%)	372	0.121 (1.00)	0.752 (1.00)	0.12 (1.00)	1 (1.00)	0.0112 (1.00)	0.159 (1.00)	0.447 (1.00)	1 (1.00)	1 (1.00)	0.483 (1.00)	0.0443 (1.00)
2P LOSS MUTATION ANALYSIS	6 (1%)	415	0.000958 (0.807)	0.756 (1.00)	0.711 (1.00)	0.837 (1.00)	0.85 (1.00)	0.761 (1.00)	0.222 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.796 (1.00)
2Q LOSS MUTATION ANALYSIS	7 (2%)	414	0.000958 (0.807)	0.745 (1.00)	0.761 (1.00)	0.869 (1.00)	1 (1.00)	0.703 (1.00)	0.128 (1.00)	0.601 (1.00)	1 (1.00)	1 (1.00)	0.527 (1.00)
3P LOSS MUTATION ANALYSIS	46 (11%)	375	0.162 (1.00)	0.831 (1.00)	0.353 (1.00)	0.115 (1.00)	0.144 (1.00)	0.0107 (1.00)	0.877 (1.00)	0.244 (1.00)	1 (1.00)	0.77 (1.00)	0.629 (1.00)
3Q LOSS MUTATION ANALYSIS	28 (7%)	393	0.846 (1.00)	0.518 (1.00)	0.718 (1.00)	0.388 (1.00)	0.963 (1.00)	0.595 (1.00)	0.701 (1.00)	0.56 (1.00)	1 (1.00)	0.92 (1.00)	0.289 (1.00)
4Q LOSS MUTATION ANALYSIS	110 (26%)	311	0.0743 (1.00)	0.673 (1.00)	0.0541 (1.00)	0.651 (1.00)	0.00244 (1.00)	0.0534 (1.00)	0.739 (1.00)	0.0986 (1.00)	0.0175 (1.00)	0.526 (1.00)	0.0249 (1.00)
5P LOSS MUTATION ANALYSIS	51 (12%)	370	0.643 (1.00)	0.252 (1.00)	0.00851 (1.00)	0.426 (1.00)	0.00376 (1.00)	0.129 (1.00)	0.882 (1.00)	0.276 (1.00)	0.0399 (1.00)	0.509 (1.00)	0.0474 (1.00)
6P LOSS MUTATION ANALYSIS	34 (8%)	387	0.394 (1.00)	0.204 (1.00)	0.967 (1.00)	0.0261 (1.00)	0.683 (1.00)	0.314 (1.00)	0.371 (1.00)	0.791 (1.00)	1 (1.00)	0.121 (1.00)	0.804 (1.00)
6Q LOSS MUTATION ANALYSIS	45 (11%)	376	0.22 (1.00)	0.712 (1.00)	0.395 (1.00)	0.0804 (1.00)	0.145 (1.00)	0.0125 (1.00)	0.636 (1.00)	0.64 (1.00)	1 (1.00)	0.173 (1.00)	0.0883 (1.00)
7Q LOSS MUTATION ANALYSIS	3 (1%)	418	0.568 (1.00)	0.131 (1.00)	0.421 (1.00)	0.675 (1.00)	1 (1.00)	0.921 (1.00)	0.6 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.011 (1.00)
8P LOSS MUTATION ANALYSIS	134 (32%)	287	0.474 (1.00)	0.466 (1.00)	0.0255 (1.00)	0.274 (1.00)	0.000828 (0.701)	0.0208 (1.00)	0.294 (1.00)	0.119 (1.00)	1 (1.00)	0.0774 (1.00)	0.00262 (1.00)
8Q LOSS MUTATION ANALYSIS	25 (6%)	396	0.54 (1.00)	0.643 (1.00)	0.126 (1.00)	0.0355 (1.00)	0.0434 (1.00)	0.0728 (1.00)	0.839 (1.00)	0.555 (1.00)	1 (1.00)	0.683 (1.00)	0.187 (1.00)
9P LOSS MUTATION ANALYSIS	48 (11%)	373	0.205 (1.00)	0.273 (1.00)	0.975 (1.00)	0.164 (1.00)	0.291 (1.00)	0.614 (1.00)	0.54 (1.00)	0.173 (1.00)	1 (1.00)	0.509 (1.00)	0.411 (1.00)
9Q LOSS MUTATION ANALYSIS	47 (11%)	374	0.0794 (1.00)	0.0394 (1.00)	0.845 (1.00)	0.175 (1.00)	0.196 (1.00)	0.382 (1.00)	0.758 (1.00)	0.0652 (1.00)	1 (1.00)	0.495 (1.00)	0.605 (1.00)
10P LOSS MUTATION ANALYSIS	62 (15%)	359	0.908 (1.00)	0.24 (1.00)	0.000771 (0.655)	0.992 (1.00)	0.00399 (1.00)	0.00188 (1.00)	0.583 (1.00)	0.838 (1.00)	0.058 (1.00)	0.403 (1.00)	0.0844 (1.00)
10Q LOSS MUTATION ANALYSIS	65 (15%)	356	0.658 (1.00)	0.118 (1.00)	0.0136 (1.00)	0.91 (1.00)	0.0245 (1.00)	0.0181 (1.00)	0.5 (1.00)	0.69 (1.00)	0.0635 (1.00)	0.157 (1.00)	0.2 (1.00)
11P LOSS MUTATION ANALYSIS	47 (11%)	374	0.87 (1.00)	0.635 (1.00)	0.691 (1.00)	0.439 (1.00)	0.0175 (1.00)	0.0337 (1.00)	0.877 (1.00)	1 (1.00)	0.3 (1.00)	0.21 (1.00)	0.121 (1.00)
11Q LOSS MUTATION ANALYSIS	56 (13%)	365	0.581 (1.00)	0.573 (1.00)	0.456 (1.00)	0.0454 (1.00)	0.02 (1.00)	0.0357 (1.00)	0.666 (1.00)	1 (1.00)	0.349 (1.00)	0.405 (1.00)	0.248 (1.00)
12P LOSS MUTATION ANALYSIS	36 (9%)	385	0.691 (1.00)	0.621 (1.00)	0.457 (1.00)	0.639 (1.00)	0.0824 (1.00)	0.312 (1.00)	0.728 (1.00)	0.00827 (1.00)	0.236 (1.00)	0.84 (1.00)	0.554 (1.00)
12Q LOSS MUTATION ANALYSIS	39 (9%)	382	0.986 (1.00)	0.582 (1.00)	0.318 (1.00)	0.632 (1.00)	0.0542 (1.00)	0.175 (1.00)	0.4 (1.00)	0.0437 (1.00)	1 (1.00)	0.851 (1.00)	0.427 (1.00)
13Q LOSS MUTATION ANALYSIS	10 (2%)	411	0.901 (1.00)	0.641 (1.00)	0.487 (1.00)	0.364 (1.00)	0.0135 (1.00)	0.542 (1.00)	0.757 (1.00)	0.101 (1.00)	1 (1.00)	0.726 (1.00)	0.133 (1.00)
15Q LOSS MUTATION ANALYSIS	139 (33%)	282	0.351 (1.00)	0.906 (1.00)	0.128 (1.00)	0.647 (1.00)	0.0548 (1.00)	0.0673 (1.00)	0.836 (1.00)	0.00526 (1.00)	0.0355 (1.00)	0.571 (1.00)	0.494 (1.00)
16P LOSS MUTATION ANALYSIS	22 (5%)	399	0.269 (1.00)	0.737 (1.00)	0.399 (1.00)	0.481 (1.00)	0.565 (1.00)	0.696 (1.00)	0.274 (1.00)	0.189 (1.00)	1 (1.00)	0.876 (1.00)	0.759 (1.00)
16Q LOSS MUTATION ANALYSIS	22 (5%)	399	0.548 (1.00)	0.552 (1.00)	0.761 (1.00)	0.702 (1.00)	0.361 (1.00)	0.5 (1.00)	0.828 (1.00)	0.512 (1.00)	1 (1.00)	1 (1.00)	0.714 (1.00)
17Q LOSS MUTATION ANALYSIS	63 (15%)	358	0.753 (1.00)	0.85 (1.00)	0.0409 (1.00)	0.947 (1.00)	0.016 (1.00)	0.234 (1.00)	0.412 (1.00)	1 (1.00)	1 (1.00)	0.403 (1.00)	0.0484 (1.00)
19P LOSS MUTATION ANALYSIS	37 (9%)	384	0.516 (1.00)	0.376 (1.00)	0.00263 (1.00)	0.956 (1.00)	0.00354 (1.00)	0.000726 (0.617)	0.606 (1.00)	0.449 (1.00)	0.242 (1.00)	0.266 (1.00)	0.00569 (1.00)
19Q LOSS MUTATION ANALYSIS	34 (8%)	387	0.938 (1.00)	0.463 (1.00)	0.00518 (1.00)	1 (1.00)	0.00839 (1.00)	0.000791 (0.67)	0.285 (1.00)	0.787 (1.00)	0.224 (1.00)	0.146 (1.00)	0.00997 (1.00)
20P LOSS MUTATION ANALYSIS	43 (10%)	378	0.963 (1.00)	0.844 (1.00)	0.247 (1.00)	0.803 (1.00)	0.389 (1.00)	0.854 (1.00)	0.75 (1.00)	0.633 (1.00)	1 (1.00)	0.945 (1.00)	0.217 (1.00)
20Q LOSS MUTATION ANALYSIS	6 (1%)	415	0.11 (1.00)	0.025 (1.00)	0.871 (1.00)	0.496 (1.00)	0.367 (1.00)	0.873 (1.00)	0.69 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.915 (1.00)
21Q LOSS MUTATION ANALYSIS	113 (27%)	308	0.578 (1.00)	0.847 (1.00)	0.585 (1.00)	0.457 (1.00)	0.0266 (1.00)	0.195 (1.00)	1 (1.00)	0.033 (1.00)	1 (1.00)	0.766 (1.00)	0.0144 (1.00)
XQ LOSS MUTATION ANALYSIS	50 (12%)	371	0.987 (1.00)	0.225 (1.00)	0.0988 (1.00)	0.553 (1.00)	0.0277 (1.00)	0.0194 (1.00)	0.366 (1.00)	0.656 (1.00)	1 (1.00)	0.0987 (1.00)	0.186 (1.00)

'3P GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 5.57e-05 (Chi-square test), Q value = 0.048

Table S1. Gene #5: '3P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	M1A	M1B	MX
ALL	317	50	7	1	39
3P GAIN MUTATED	22	4	1	1	10
3P GAIN WILD-TYPE	295	46	6	0	29

Figure S1. Get High-res Image Gene #5: '3P GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'12Q GAIN MUTATION STATUS' versus 'NUMBER.OF.LYMPH.NODES'

P value = 6.71e-05 (t-test), Q value = 0.058

Table S2. Gene #24: '12Q GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

	nPatients	Mean (Std.Dev)
ALL	397	2.1 (4.5)
12Q GAIN MUTATED	76	0.9 (1.8)
12Q GAIN WILD-TYPE	321	2.3 (4.9)

Figure S2. Get High-res Image Gene #24: '12Q GAIN MUTATION STATUS' versus Clinical Feature #11: 'NUMBER.OF.LYMPH.NODES'

'13Q GAIN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.46e-06 (Fisher's exact test), Q value = 0.0013

Table S3. Gene #25: '13Q GAIN MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
13Q GAIN MUTATED	227	15
13Q GAIN WILD-TYPE	137	40

Figure S3. Get High-res Image Gene #25: '13Q GAIN MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'14Q GAIN MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 6.56e-05 (Chi-square test), Q value = 0.057

Table S4. Gene #26: '14Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	M1A	M1B	MX
ALL	317	50	7	1	39
14Q GAIN MUTATED	22	3	4	0	5
14Q GAIN WILD-TYPE	295	47	3	1	34

Figure S4. Get High-res Image Gene #26: '14Q GAIN MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'20Q GAIN MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 9.79e-06 (Fisher's exact test), Q value = 0.0085

Table S5. Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
20Q GAIN MUTATED	272	24
20Q GAIN WILD-TYPE	92	31

Figure S5. Get High-res Image Gene #37: '20Q GAIN MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'4P LOSS MUTATION STATUS' versus 'PATHOLOGY.M.STAGE'

P value = 0.000157 (Chi-square test), Q value = 0.14

Table S6. Gene #47: '4P LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

nPatients	M0	M1	M1A	M1B	MX
ALL	317	50	7	1	39
4P LOSS MUTATED	76	27	3	1	13
4P LOSS WILD-TYPE	241	23	4	0	26

Figure S6. Get High-res Image Gene #47: '4P LOSS MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY.M.STAGE'

'5Q LOSS MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000197 (Fisher's exact test), Q value = 0.17

Table S7. Gene #50: '5Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients	N0	N1	N2
ALL	246	100	74
5Q LOSS MUTATED	28	18	24
5Q LOSS WILD-TYPE	218	82	50

Figure S7. Get High-res Image Gene #50: '5Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'14Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 4.7e-05 (Fisher's exact test), Q value = 0.041

Table S8. Gene #65: '14Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
14Q LOSS MUTATED	118	4
14Q LOSS WILD-TYPE	246	51

Figure S8. Get High-res Image Gene #65: '14Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'17P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0094

Table S9. Gene #69: '17P LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
17P LOSS MUTATED	201	13
17P LOSS WILD-TYPE	163	42

Figure S9. Get High-res Image Gene #69: '17P LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18P LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 3.8e-10 (Fisher's exact test), Q value = 3.3e-07

Table S10. Gene #71: '18P LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
18P LOSS MUTATED	222	9
18P LOSS WILD-TYPE	142	46

Figure S10. Get High-res Image Gene #71: '18P LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'18Q LOSS MUTATION STATUS' versus 'HISTOLOGICAL.TYPE'

P value = 1.74e-09 (Fisher's exact test), Q value = 1.5e-06

Table S11. Gene #72: '18Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	364	55
18Q LOSS MUTATED	237	12
18Q LOSS WILD-TYPE	127	43

Figure S11. Get High-res Image Gene #72: '18Q LOSS MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'

'22Q LOSS MUTATION STATUS' versus 'PATHOLOGY.N.STAGE'

P value = 0.000273 (Fisher's exact test), Q value = 0.23

Table S12. Gene #78: '22Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients	N0	N1	N2
ALL	246	100	74
22Q LOSS MUTATED	58	40	33
22Q LOSS WILD-TYPE	188	60	41

Figure S12. Get High-res Image Gene #78: '22Q LOSS MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = COAD-TP.clin.merged.picked.txt
Number of patients = 421
Number of significantly arm-level cnvs = 79
Number of selected clinical features = 11
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

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

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

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

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

[4] 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)

[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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