Correlation between copy number variation genes and selected clinical features

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and selected clinical features.

Summary

Testing the association between copy number variation of 75 peak regions and 10 clinical features across 575 patients, 53 significant findings detected with Q value < 0.25.

Amp Peak 5(6p21.1) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Amp Peak 6(7p21.3) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Amp Peak 14(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Amp Peak 15(13q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Amp Peak 16(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
Amp Peak 18(16p11.2) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Amp Peak 24(20p11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 25(20q11.21) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
Amp Peak 26(20q12) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
Amp Peak 27(20q13.32) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
Del Peak 10(4p16.1) cnvs correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
Del Peak 18(8p23.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 19(8p22) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 30(14q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 34(16p13.3) cnvs correlated to 'Time to Death'.
Del Peak 36(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 38(18p11.31) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Del Peak 39(18q12.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 40(18q21.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 41(18q22.1) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 42(19p13.3) cnvs correlated to 'PATHOLOGY.N'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 75 regions and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 53 significant findings detected.


		Clinical Features	Time to Death	AGE	PRIMARY SITE OF DISEASE	GENDER	HISTOLOGICAL TYPE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact 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
Del Peak 18(8p23 2)	272 (47%)	303	0.619 (1.00)	0.205 (1.00)	2.4e-05 (0.0173)	0.18 (1.00)	2.8e-05 (0.0201)	0.0809 (1.00)	2.71e-05 (0.0195)	0.00989 (1.00)	3.34e-05 (0.0239)	0.0155 (1.00)
Del Peak 39(18q12 2)	386 (67%)	189	0.942 (1.00)	0.0817 (1.00)	1.57e-09 (1.16e-06)	0.477 (1.00)	5.64e-18 (4.23e-15)	0.424 (1.00)	0.000131 (0.0919)	0.00447 (1.00)	6.7e-05 (0.0477)	0.034 (1.00)
Del Peak 40(18q21 2)	403 (70%)	172	0.481 (1.00)	0.0823 (1.00)	1.07e-09 (7.94e-07)	0.145 (1.00)	2.57e-16 (1.92e-13)	0.314 (1.00)	2.01e-06 (0.00147)	0.00162 (1.00)	3.94e-07 (0.00029)	0.0637 (1.00)
Del Peak 41(18q22 1)	398 (69%)	177	0.332 (1.00)	0.221 (1.00)	1.94e-07 (0.000143)	0.239 (1.00)	1.41e-15 (1.05e-12)	0.443 (1.00)	1.1e-05 (0.00795)	0.00238 (1.00)	4.52e-06 (0.0033)	0.0632 (1.00)
Amp Peak 6(7p21 3)	337 (59%)	238	0.304 (1.00)	0.103 (1.00)	0.0292 (1.00)	0.734 (1.00)	0.000219 (0.153)	0.889 (1.00)	1.22e-05 (0.00884)	0.0274 (1.00)	4.31e-06 (0.00314)	0.0882 (1.00)
Amp Peak 14(13q12 13)	371 (65%)	204	0.126 (1.00)	0.314 (1.00)	0.00246 (1.00)	0.727 (1.00)	1.03e-09 (7.68e-07)	0.564 (1.00)	3.94e-05 (0.0281)	0.0101 (1.00)	7.37e-05 (0.0523)	1 (1.00)
Amp Peak 15(13q12 2)	366 (64%)	209	0.101 (1.00)	0.239 (1.00)	0.00188 (1.00)	0.543 (1.00)	2.33e-09 (1.72e-06)	0.53 (1.00)	9.29e-05 (0.0657)	0.023 (1.00)	0.000181 (0.127)	1 (1.00)
Amp Peak 25(20q11 21)	439 (76%)	136	0.317 (1.00)	0.823 (1.00)	9.13e-06 (0.00664)	0.376 (1.00)	5.89e-12 (4.39e-09)	0.513 (1.00)	0.00142 (0.946)	0.00533 (1.00)	0.000105 (0.0738)	0.693 (1.00)
Amp Peak 26(20q12)	441 (77%)	134	0.274 (1.00)	0.726 (1.00)	4.74e-06 (0.00345)	0.374 (1.00)	3.83e-13 (2.85e-10)	0.612 (1.00)	0.001 (0.683)	0.00129 (0.869)	4e-05 (0.0285)	0.692 (1.00)
Amp Peak 27(20q13 32)	444 (77%)	131	0.369 (1.00)	0.658 (1.00)	2.18e-05 (0.0158)	0.551 (1.00)	6.45e-12 (4.8e-09)	0.588 (1.00)	0.0016 (1.00)	0.00424 (1.00)	0.000128 (0.0901)	0.692 (1.00)
Del Peak 19(8p22)	285 (50%)	290	0.597 (1.00)	0.317 (1.00)	0.000379 (0.265)	0.403 (1.00)	0.000248 (0.173)	0.075 (1.00)	1.96e-06 (0.00144)	0.00381 (1.00)	1.22e-06 (0.000897)	0.0196 (1.00)
Del Peak 36(17p12)	343 (60%)	232	0.656 (1.00)	0.0983 (1.00)	0.00169 (1.00)	0.609 (1.00)	5.98e-08 (4.41e-05)	0.422 (1.00)	0.000119 (0.0839)	0.041 (1.00)	3.09e-05 (0.0222)	0.325 (1.00)
Amp Peak 5(6p21 1)	146 (25%)	429	0.489 (1.00)	0.682 (1.00)	0.0314 (1.00)	0.15 (1.00)	0.00234 (1.00)	0.214 (1.00)	3.15e-05 (0.0226)	0.109 (1.00)	0.000322 (0.225)	0.00136 (0.912)
Amp Peak 16(13q22 1)	371 (65%)	204	0.0454 (1.00)	0.444 (1.00)	0.0249 (1.00)	0.221 (1.00)	2.84e-08 (2.1e-05)	0.737 (1.00)	0.000126 (0.0887)	0.024 (1.00)	0.000595 (0.412)	0.503 (1.00)
Amp Peak 18(16p11 2)	161 (28%)	414	0.838 (1.00)	0.26 (1.00)	0.918 (1.00)	0.71 (1.00)	0.00229 (1.00)	0.721 (1.00)	5.86e-05 (0.0417)	0.111 (1.00)	8.31e-05 (0.0588)	0.715 (1.00)
Del Peak 38(18p11 31)	341 (59%)	234	0.98 (1.00)	0.059 (1.00)	1.82e-06 (0.00134)	1 (1.00)	1.11e-16 (8.35e-14)	0.886 (1.00)	0.0108 (1.00)	0.000584 (0.406)	0.000888 (0.607)	0.322 (1.00)
Amp Peak 24(20p11 21)	339 (59%)	236	0.808 (1.00)	0.709 (1.00)	0.00784 (1.00)	0.0413 (1.00)	1.08e-05 (0.00782)	0.886 (1.00)	0.381 (1.00)	0.00312 (1.00)	0.0517 (1.00)	0.32 (1.00)
Del Peak 10(4p16 1)	182 (32%)	393	0.0406 (1.00)	0.954 (1.00)	0.0561 (1.00)	0.128 (1.00)	0.0276 (1.00)	0.988 (1.00)	0.000554 (0.385)	0.0131 (1.00)	0.00162 (1.00)	2.78e-05 (0.02)
Del Peak 30(14q22 1)	185 (32%)	390	0.208 (1.00)	0.233 (1.00)	0.0212 (1.00)	0.421 (1.00)	1.08e-06 (0.000797)	0.777 (1.00)	0.00353 (1.00)	0.145 (1.00)	0.174 (1.00)	0.725 (1.00)
Del Peak 34(16p13 3)	58 (10%)	517	4.34e-05 (0.031)	0.254 (1.00)	0.359 (1.00)	0.89 (1.00)	0.422 (1.00)	0.0652 (1.00)	0.133 (1.00)	0.381 (1.00)	0.099 (1.00)	0.609 (1.00)
Del Peak 42(19p13 3)	92 (16%)	483	0.406 (1.00)	0.183 (1.00)	0.0305 (1.00)	0.733 (1.00)	0.0672 (1.00)	0.411 (1.00)	7.59e-05 (0.0538)	0.0275 (1.00)	0.00301 (1.00)	0.641 (1.00)
Amp Peak 1(1q31 1)	134 (23%)	441	0.466 (1.00)	0.292 (1.00)	0.0268 (1.00)	0.236 (1.00)	0.0928 (1.00)	0.381 (1.00)	0.0533 (1.00)	0.175 (1.00)	0.0341 (1.00)	0.0357 (1.00)
Amp Peak 2(2q33 1)	123 (21%)	452	0.135 (1.00)	0.385 (1.00)	0.031 (1.00)	1 (1.00)	0.00359 (1.00)	0.684 (1.00)	0.00128 (0.866)	0.541 (1.00)	0.0223 (1.00)	0.103 (1.00)
Amp Peak 3(5p12)	107 (19%)	468	0.0162 (1.00)	0.372 (1.00)	0.151 (1.00)	0.748 (1.00)	0.0551 (1.00)	0.398 (1.00)	0.0424 (1.00)	0.354 (1.00)	0.19 (1.00)	0.379 (1.00)
Amp Peak 4(5q22 3)	59 (10%)	516	0.75 (1.00)	0.865 (1.00)	0.445 (1.00)	0.891 (1.00)	0.315 (1.00)	0.908 (1.00)	0.174 (1.00)	0.032 (1.00)	0.118 (1.00)	1 (1.00)
Amp Peak 7(8p11 23)	196 (34%)	379	0.472 (1.00)	0.752 (1.00)	0.625 (1.00)	0.482 (1.00)	0.232 (1.00)	0.409 (1.00)	0.51 (1.00)	0.413 (1.00)	0.881 (1.00)	0.498 (1.00)
Amp Peak 8(8p11 21)	238 (41%)	337	0.633 (1.00)	0.597 (1.00)	0.636 (1.00)	0.204 (1.00)	0.12 (1.00)	0.504 (1.00)	0.337 (1.00)	0.305 (1.00)	0.479 (1.00)	0.742 (1.00)
Amp Peak 9(8q12 1)	309 (54%)	266	0.907 (1.00)	0.19 (1.00)	0.303 (1.00)	0.615 (1.00)	0.00904 (1.00)	0.127 (1.00)	0.0851 (1.00)	0.0256 (1.00)	0.0726 (1.00)	0.0423 (1.00)
Amp Peak 10(8q24 21)	345 (60%)	230	0.545 (1.00)	0.236 (1.00)	0.0863 (1.00)	0.394 (1.00)	0.0111 (1.00)	0.144 (1.00)	0.173 (1.00)	0.0551 (1.00)	0.234 (1.00)	0.0931 (1.00)
Amp Peak 11(10q22 3)	35 (6%)	540	0.819 (1.00)	0.303 (1.00)	1 (1.00)	0.487 (1.00)	0.952 (1.00)	0.137 (1.00)	0.00778 (1.00)	0.912 (1.00)	0.114 (1.00)	0.434 (1.00)
Amp Peak 12(11p15 5)	129 (22%)	446	0.709 (1.00)	0.0608 (1.00)	0.145 (1.00)	0.549 (1.00)	0.00139 (0.931)	0.296 (1.00)	0.71 (1.00)	0.385 (1.00)	0.817 (1.00)	0.12 (1.00)
Amp Peak 13(12p13 32)	144 (25%)	431	0.26 (1.00)	0.0696 (1.00)	0.829 (1.00)	0.5 (1.00)	0.353 (1.00)	0.383 (1.00)	0.0531 (1.00)	0.0859 (1.00)	0.0619 (1.00)	0.698 (1.00)
Amp Peak 17(15q26 1)	43 (7%)	532	0.0824 (1.00)	0.753 (1.00)	0.291 (1.00)	0.0582 (1.00)	0.435 (1.00)	0.281 (1.00)	0.00407 (1.00)	0.649 (1.00)	0.194 (1.00)	0.141 (1.00)
Amp Peak 19(17q12)	144 (25%)	431	0.489 (1.00)	0.363 (1.00)	0.591 (1.00)	0.101 (1.00)	0.459 (1.00)	0.42 (1.00)	0.151 (1.00)	0.0117 (1.00)	0.0157 (1.00)	0.462 (1.00)
Amp Peak 20(17q24 1)	128 (22%)	447	0.0431 (1.00)	0.245 (1.00)	0.911 (1.00)	0.617 (1.00)	0.087 (1.00)	0.774 (1.00)	0.896 (1.00)	0.0549 (1.00)	0.22 (1.00)	0.691 (1.00)
Amp Peak 21(19p13 2)	97 (17%)	478	0.144 (1.00)	0.493 (1.00)	0.216 (1.00)	0.182 (1.00)	0.0503 (1.00)	0.407 (1.00)	0.0341 (1.00)	0.233 (1.00)	0.125 (1.00)	1 (1.00)
Amp Peak 22(19q12)	122 (21%)	453	0.628 (1.00)	0.941 (1.00)	0.256 (1.00)	0.185 (1.00)	0.0289 (1.00)	0.662 (1.00)	0.0969 (1.00)	0.139 (1.00)	0.228 (1.00)	0.692 (1.00)
Amp Peak 23(20p11 23)	301 (52%)	274	0.699 (1.00)	0.921 (1.00)	0.0194 (1.00)	0.0364 (1.00)	0.000706 (0.485)	0.881 (1.00)	0.0369 (1.00)	0.00134 (0.901)	0.0111 (1.00)	0.181 (1.00)
Amp Peak 28(Xq28)	121 (21%)	454	0.245 (1.00)	0.209 (1.00)	0.421 (1.00)	0.838 (1.00)	0.0243 (1.00)	0.528 (1.00)	0.0168 (1.00)	0.219 (1.00)	0.0632 (1.00)	0.693 (1.00)
Del Peak 1(1p36 11)	222 (39%)	353	0.051 (1.00)	0.105 (1.00)	0.126 (1.00)	0.392 (1.00)	0.00635 (1.00)	0.238 (1.00)	0.00091 (0.622)	0.000615 (0.425)	0.000727 (0.498)	0.739 (1.00)
Del Peak 2(1p33)	156 (27%)	419	0.0178 (1.00)	0.836 (1.00)	0.401 (1.00)	0.851 (1.00)	0.0793 (1.00)	0.226 (1.00)	0.00497 (1.00)	0.0106 (1.00)	0.0156 (1.00)	0.709 (1.00)
Del Peak 3(1p13 2)	157 (27%)	418	0.0696 (1.00)	0.841 (1.00)	0.248 (1.00)	0.639 (1.00)	0.135 (1.00)	0.15 (1.00)	0.00208 (1.00)	0.00127 (0.86)	0.0161 (1.00)	0.265 (1.00)
Del Peak 4(2p12)	20 (3%)	555	0.796 (1.00)	0.179 (1.00)	0.00346 (1.00)	0.821 (1.00)	0.021 (1.00)	1 (1.00)	0.358 (1.00)	0.56 (1.00)	0.319 (1.00)	0.275 (1.00)
Del Peak 5(2q22 1)	33 (6%)	542	0.85 (1.00)	0.564 (1.00)	0.842 (1.00)	0.474 (1.00)	0.93 (1.00)	0.683 (1.00)	0.622 (1.00)	0.689 (1.00)	0.172 (1.00)	1 (1.00)
Del Peak 6(2q37 2)	30 (5%)	545	0.842 (1.00)	0.139 (1.00)	0.835 (1.00)	0.458 (1.00)	0.937 (1.00)	0.343 (1.00)	0.207 (1.00)	0.133 (1.00)	0.0403 (1.00)	1 (1.00)
Del Peak 7(3p26 3)	84 (15%)	491	0.000643 (0.443)	0.855 (1.00)	0.691 (1.00)	0.723 (1.00)	0.191 (1.00)	0.0365 (1.00)	0.0192 (1.00)	0.00105 (0.712)	0.000658 (0.453)	0.131 (1.00)
Del Peak 8(3p14 2)	104 (18%)	471	0.216 (1.00)	0.578 (1.00)	0.808 (1.00)	0.664 (1.00)	0.417 (1.00)	0.134 (1.00)	0.185 (1.00)	0.0317 (1.00)	0.0454 (1.00)	0.669 (1.00)
Del Peak 9(3q26 31)	56 (10%)	519	0.714 (1.00)	0.996 (1.00)	0.874 (1.00)	0.0931 (1.00)	0.0407 (1.00)	0.0132 (1.00)	0.366 (1.00)	0.327 (1.00)	0.00201 (1.00)	0.216 (1.00)
Del Peak 11(4q22 1)	198 (34%)	377	0.193 (1.00)	0.42 (1.00)	0.00417 (1.00)	0.187 (1.00)	0.00139 (0.931)	0.134 (1.00)	0.00178 (1.00)	0.369 (1.00)	0.0375 (1.00)	0.00114 (0.771)
Del Peak 12(4q35 1)	211 (37%)	364	0.277 (1.00)	0.303 (1.00)	0.0325 (1.00)	0.863 (1.00)	0.0209 (1.00)	0.708 (1.00)	0.00331 (1.00)	0.645 (1.00)	0.118 (1.00)	0.00185 (1.00)
Del Peak 13(5q11 2)	140 (24%)	435	0.164 (1.00)	0.0866 (1.00)	0.0389 (1.00)	1 (1.00)	0.0272 (1.00)	0.979 (1.00)	0.00769 (1.00)	0.0232 (1.00)	0.0341 (1.00)	0.00103 (0.701)
Del Peak 14(5q22 2)	172 (30%)	403	0.0866 (1.00)	0.359 (1.00)	0.155 (1.00)	0.648 (1.00)	0.0619 (1.00)	0.782 (1.00)	0.0166 (1.00)	0.0311 (1.00)	0.033 (1.00)	0.000382 (0.266)
Del Peak 15(6p25 3)	78 (14%)	497	0.611 (1.00)	0.0683 (1.00)	1 (1.00)	0.0876 (1.00)	0.539 (1.00)	0.256 (1.00)	0.551 (1.00)	0.326 (1.00)	0.22 (1.00)	0.351 (1.00)
Del Peak 16(6q26)	90 (16%)	485	0.029 (1.00)	0.9 (1.00)	0.368 (1.00)	0.301 (1.00)	0.0484 (1.00)	0.0565 (1.00)	0.0142 (1.00)	0.0389 (1.00)	0.594 (1.00)	0.637 (1.00)
Del Peak 17(7q31 1)	15 (3%)	560	1 (1.00)	0.329 (1.00)	1 (1.00)	0.307 (1.00)	0.503 (1.00)	0.525 (1.00)	0.673 (1.00)	0.33 (1.00)	0.348 (1.00)	1 (1.00)
Del Peak 20(8p11 21)	124 (22%)	451	0.598 (1.00)	0.329 (1.00)	0.031 (1.00)	0.542 (1.00)	0.164 (1.00)	0.539 (1.00)	0.00719 (1.00)	0.0823 (1.00)	0.027 (1.00)	0.414 (1.00)
Del Peak 21(8q11 1)	44 (8%)	531	0.889 (1.00)	0.382 (1.00)	0.16 (1.00)	0.208 (1.00)	0.42 (1.00)	0.722 (1.00)	0.0273 (1.00)	0.00202 (1.00)	0.0949 (1.00)	0.514 (1.00)
Del Peak 22(9p24 2)	78 (14%)	497	0.00207 (1.00)	0.12 (1.00)	0.496 (1.00)	0.0507 (1.00)	0.46 (1.00)	0.495 (1.00)	0.135 (1.00)	0.0231 (1.00)	0.289 (1.00)	0.351 (1.00)
Del Peak 23(10p15 3)	102 (18%)	473	0.577 (1.00)	0.0282 (1.00)	0.271 (1.00)	0.913 (1.00)	0.364 (1.00)	0.73 (1.00)	0.00724 (1.00)	0.181 (1.00)	0.00827 (1.00)	0.00145 (0.967)
Del Peak 24(10q21 1)	118 (21%)	457	0.869 (1.00)	0.0152 (1.00)	0.421 (1.00)	0.535 (1.00)	0.116 (1.00)	0.73 (1.00)	0.161 (1.00)	0.682 (1.00)	0.366 (1.00)	0.00326 (1.00)
Del Peak 25(10q23 31)	145 (25%)	430	0.566 (1.00)	0.00668 (1.00)	0.0408 (1.00)	0.923 (1.00)	0.0202 (1.00)	0.207 (1.00)	0.0137 (1.00)	0.0621 (1.00)	0.0973 (1.00)	0.0013 (0.874)
Del Peak 26(10q25 2)	140 (24%)	435	0.756 (1.00)	0.0715 (1.00)	0.128 (1.00)	0.846 (1.00)	0.0321 (1.00)	0.219 (1.00)	0.0136 (1.00)	0.43 (1.00)	0.115 (1.00)	0.00103 (0.701)
Del Peak 27(11q22 3)	104 (18%)	471	0.473 (1.00)	0.396 (1.00)	0.086 (1.00)	0.588 (1.00)	0.0526 (1.00)	0.391 (1.00)	0.0515 (1.00)	0.633 (1.00)	0.092 (1.00)	0.061 (1.00)
Del Peak 28(12p13 1)	77 (13%)	498	0.466 (1.00)	0.472 (1.00)	0.0256 (1.00)	0.327 (1.00)	0.0006 (0.415)	0.51 (1.00)	0.0317 (1.00)	0.1 (1.00)	0.206 (1.00)	0.344 (1.00)
Del Peak 29(12q21 2)	80 (14%)	495	0.636 (1.00)	0.709 (1.00)	0.0779 (1.00)	0.717 (1.00)	0.00778 (1.00)	0.682 (1.00)	0.0194 (1.00)	0.0916 (1.00)	0.239 (1.00)	0.117 (1.00)
Del Peak 31(15q11 2)	233 (41%)	342	0.771 (1.00)	0.618 (1.00)	0.216 (1.00)	0.496 (1.00)	0.0545 (1.00)	0.809 (1.00)	0.015 (1.00)	0.264 (1.00)	0.0412 (1.00)	0.035 (1.00)
Del Peak 32(15q21 1)	227 (39%)	348	0.434 (1.00)	0.603 (1.00)	0.0355 (1.00)	0.305 (1.00)	0.0246 (1.00)	0.852 (1.00)	0.0274 (1.00)	0.228 (1.00)	0.125 (1.00)	0.0327 (1.00)
Del Peak 33(15q22 33)	217 (38%)	358	0.555 (1.00)	0.327 (1.00)	0.012 (1.00)	0.667 (1.00)	0.00584 (1.00)	0.0961 (1.00)	0.00685 (1.00)	0.211 (1.00)	0.0233 (1.00)	0.00229 (1.00)
Del Peak 35(16q23 1)	72 (13%)	503	0.0014 (0.934)	0.264 (1.00)	0.402 (1.00)	0.167 (1.00)	0.513 (1.00)	0.251 (1.00)	0.76 (1.00)	0.951 (1.00)	0.469 (1.00)	1 (1.00)
Del Peak 37(17q24 3)	84 (15%)	491	0.731 (1.00)	0.305 (1.00)	0.793 (1.00)	0.0994 (1.00)	0.995 (1.00)	0.234 (1.00)	0.0072 (1.00)	0.352 (1.00)	0.0348 (1.00)	0.626 (1.00)
Del Peak 43(19q13 43)	68 (12%)	507	0.509 (1.00)	0.816 (1.00)	0.146 (1.00)	0.3 (1.00)	0.416 (1.00)	0.438 (1.00)	0.0155 (1.00)	0.0712 (1.00)	0.167 (1.00)	0.289 (1.00)
Del Peak 44(20p12 1)	179 (31%)	396	0.108 (1.00)	0.631 (1.00)	0.0445 (1.00)	0.321 (1.00)	0.142 (1.00)	0.47 (1.00)	0.317 (1.00)	0.827 (1.00)	0.192 (1.00)	0.0632 (1.00)
Del Peak 45(20p12 1)	179 (31%)	396	0.108 (1.00)	0.631 (1.00)	0.0445 (1.00)	0.321 (1.00)	0.142 (1.00)	0.47 (1.00)	0.317 (1.00)	0.827 (1.00)	0.192 (1.00)	0.0632 (1.00)
Del Peak 46(21q11 2)	195 (34%)	380	0.515 (1.00)	0.721 (1.00)	0.00555 (1.00)	0.66 (1.00)	0.000615 (0.425)	0.824 (1.00)	0.0459 (1.00)	0.614 (1.00)	0.326 (1.00)	0.175 (1.00)
Del Peak 47(22q13 32)	204 (35%)	371	0.04 (1.00)	0.672 (1.00)	0.173 (1.00)	0.93 (1.00)	0.0094 (1.00)	0.445 (1.00)	0.000796 (0.545)	0.0275 (1.00)	0.00928 (1.00)	0.727 (1.00)

'Amp Peak 5(6p21.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.15e-05 (Fisher's exact test), Q value = 0.023

Table S1. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 5(6P21.1) MUTATED	63	39	43
AMP PEAK 5(6P21.1) WILD-TYPE	265	101	60

Figure S1. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 5(6p21.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000322 (Fisher's exact test), Q value = 0.23

Table S2. Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 5(6P21.1) MUTATED	18	38	55	30
AMP PEAK 5(6P21.1) WILD-TYPE	79	169	111	51

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 6(7p21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000219 (Fisher's exact test), Q value = 0.15

Table S3. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 6(7P21.3) MUTATED	210	20	99	5
AMP PEAK 6(7P21.3) WILD-TYPE	146	34	44	8

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 6(7p21.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.22e-05 (Fisher's exact test), Q value = 0.0088

Table S4. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 6(7P21.3) MUTATED	164	100	69
AMP PEAK 6(7P21.3) WILD-TYPE	164	40	34

Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 6(7p21.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.31e-06 (Fisher's exact test), Q value = 0.0031

Table S5. Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 6(7P21.3) MUTATED	54	93	114	57
AMP PEAK 6(7P21.3) WILD-TYPE	43	114	52	24

Figure S5. Get High-res Image Gene #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 14(13q12.13) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-09 (Fisher's exact test), Q value = 7.7e-07

Table S6. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 14(13Q12.13) MUTATED	233	16	112	5
AMP PEAK 14(13Q12.13) WILD-TYPE	123	38	31	8

Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 14(13q12.13) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.94e-05 (Fisher's exact test), Q value = 0.028

Table S7. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 14(13Q12.13) MUTATED	186	105	77
AMP PEAK 14(13Q12.13) WILD-TYPE	142	35	26

Figure S7. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 14(13q12.13) mutation analysis' versus 'TUMOR.STAGE'

P value = 7.37e-05 (Fisher's exact test), Q value = 0.052

Table S8. Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 14(13Q12.13) MUTATED	60	112	117	65
AMP PEAK 14(13Q12.13) WILD-TYPE	37	95	49	16

Figure S8. Get High-res Image Gene #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 15(13q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.33e-09 (Fisher's exact test), Q value = 1.7e-06

Table S9. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 15(13Q12.2) MUTATED	229	16	111	5
AMP PEAK 15(13Q12.2) WILD-TYPE	127	38	32	8

Figure S9. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(13q12.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 9.29e-05 (Fisher's exact test), Q value = 0.066

Table S10. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 15(13Q12.2) MUTATED	184	103	76
AMP PEAK 15(13Q12.2) WILD-TYPE	144	37	27

Figure S10. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 15(13q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000181 (Fisher's exact test), Q value = 0.13

Table S11. Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 15(13Q12.2) MUTATED	60	110	116	63
AMP PEAK 15(13Q12.2) WILD-TYPE	37	97	50	18

Figure S11. Get High-res Image Gene #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 16(13q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.84e-08 (Fisher's exact test), Q value = 2.1e-05

Table S12. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 16(13Q22.1) MUTATED	235	18	109	4
AMP PEAK 16(13Q22.1) WILD-TYPE	121	36	34	9

Figure S12. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(13q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000126 (Fisher's exact test), Q value = 0.089

Table S13. Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 16(13Q22.1) MUTATED	187	105	75
AMP PEAK 16(13Q22.1) WILD-TYPE	141	35	28

Figure S13. Get High-res Image Gene #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.86e-05 (Fisher's exact test), Q value = 0.042

Table S14. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
AMP PEAK 18(16P11.2) MUTATED	68	52	39
AMP PEAK 18(16P11.2) WILD-TYPE	260	88	64

Figure S14. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 18(16p11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 8.31e-05 (Fisher's exact test), Q value = 0.059

Table S15. Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 18(16P11.2) MUTATED	19	40	64	27
AMP PEAK 18(16P11.2) WILD-TYPE	78	167	102	54

Figure S15. Get High-res Image Gene #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 24(20p11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.0078

Table S16. Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 24(20P11.21) MUTATED	207	20	103	4
AMP PEAK 24(20P11.21) WILD-TYPE	149	34	40	9

Figure S16. Get High-res Image Gene #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.13e-06 (Fisher's exact test), Q value = 0.0066

Table S17. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
AMP PEAK 25(20Q11.21) MUTATED	295	141
AMP PEAK 25(20Q11.21) WILD-TYPE	117	18

Figure S17. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.89e-12 (Fisher's exact test), Q value = 4.4e-09

Table S18. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 25(20Q11.21) MUTATED	269	24	132	7
AMP PEAK 25(20Q11.21) WILD-TYPE	87	30	11	6

Figure S18. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(20q11.21) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000105 (Fisher's exact test), Q value = 0.074

Table S19. Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 25(20Q11.21) MUTATED	74	136	136	71
AMP PEAK 25(20Q11.21) WILD-TYPE	23	71	30	10

Figure S19. Get High-res Image Gene #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 26(20q12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.74e-06 (Fisher's exact test), Q value = 0.0034

Table S20. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
AMP PEAK 26(20Q12) MUTATED	296	142
AMP PEAK 26(20Q12) WILD-TYPE	116	17

Figure S20. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 26(20q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.83e-13 (Fisher's exact test), Q value = 2.9e-10

Table S21. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 26(20Q12) MUTATED	271	23	133	7
AMP PEAK 26(20Q12) WILD-TYPE	85	31	10	6

Figure S21. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(20q12) mutation analysis' versus 'TUMOR.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.029

Table S22. Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 26(20Q12) MUTATED	74	137	135	73
AMP PEAK 26(20Q12) WILD-TYPE	23	70	31	8

Figure S22. Get High-res Image Gene #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.18e-05 (Fisher's exact test), Q value = 0.016

Table S23. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
AMP PEAK 27(20Q13.32) MUTATED	299	141
AMP PEAK 27(20Q13.32) WILD-TYPE	113	18

Figure S23. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.45e-12 (Fisher's exact test), Q value = 4.8e-09

Table S24. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
AMP PEAK 27(20Q13.32) MUTATED	273	24	132	7
AMP PEAK 27(20Q13.32) WILD-TYPE	83	30	11	6

Figure S24. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 27(20q13.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000128 (Fisher's exact test), Q value = 0.09

Table S25. Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
AMP PEAK 27(20Q13.32) MUTATED	74	139	137	72
AMP PEAK 27(20Q13.32) WILD-TYPE	23	68	29	9

Figure S25. Get High-res Image Gene #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 10(4p16.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.78e-05 (Fisher's exact test), Q value = 0.02

Table S26. Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients	NO	YES
ALL	566	9
DEL PEAK 10(4P16.1) MUTATED	173	9
DEL PEAK 10(4P16.1) WILD-TYPE	393	0

Figure S26. Get High-res Image Gene #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 18(8p23.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.4e-05 (Fisher's exact test), Q value = 0.017

Table S27. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
DEL PEAK 18(8P23.2) MUTATED	172	98
DEL PEAK 18(8P23.2) WILD-TYPE	240	61

Figure S27. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 18(8p23.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.8e-05 (Fisher's exact test), Q value = 0.02

Table S28. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 18(8P23.2) MUTATED	156	15	89	7
DEL PEAK 18(8P23.2) WILD-TYPE	200	39	54	6

Figure S28. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.71e-05 (Fisher's exact test), Q value = 0.02

Table S29. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 18(8P23.2) MUTATED	129	75	65
DEL PEAK 18(8P23.2) WILD-TYPE	199	65	38

Figure S29. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 18(8p23.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.024

Table S30. Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 18(8P23.2) MUTATED	39	78	92	52
DEL PEAK 18(8P23.2) WILD-TYPE	58	129	74	29

Figure S30. Get High-res Image Gene #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 19(8p22) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000248 (Fisher's exact test), Q value = 0.17

Table S31. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 19(8P22) MUTATED	168	16	89	7
DEL PEAK 19(8P22) WILD-TYPE	188	38	54	6

Figure S31. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 19(8p22) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.96e-06 (Fisher's exact test), Q value = 0.0014

Table S32. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 19(8P22) MUTATED	134	78	70
DEL PEAK 19(8P22) WILD-TYPE	194	62	33

Figure S32. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 19(8p22) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.22e-06 (Fisher's exact test), Q value = 9e-04

Table S33. Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 19(8P22) MUTATED	39	81	99	55
DEL PEAK 19(8P22) WILD-TYPE	58	126	67	26

Figure S33. Get High-res Image Gene #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 30(14q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.08e-06 (Fisher's exact test), Q value = 8e-04

Table S34. Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 30(14Q22.1) MUTATED	115	4	62	1
DEL PEAK 30(14Q22.1) WILD-TYPE	241	50	81	12

Figure S34. Get High-res Image Gene #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 34(16p13.3) mutation analysis' versus 'Time to Death'

P value = 4.34e-05 (logrank test), Q value = 0.031

Table S35. Gene #62: 'Del Peak 34(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	444	60	0.1 - 135.5 (7.0)
DEL PEAK 34(16P13.3) MUTATED	42	13	0.2 - 49.9 (7.6)
DEL PEAK 34(16P13.3) WILD-TYPE	402	47	0.1 - 135.5 (7.0)

Figure S35. Get High-res Image Gene #62: 'Del Peak 34(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 36(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.98e-08 (Fisher's exact test), Q value = 4.4e-05

Table S36. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 36(17P12) MUTATED	213	14	103	6
DEL PEAK 36(17P12) WILD-TYPE	143	40	40	7

Figure S36. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 36(17p12) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000119 (Fisher's exact test), Q value = 0.084

Table S37. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 36(17P12) MUTATED	171	95	74
DEL PEAK 36(17P12) WILD-TYPE	157	45	29

Figure S37. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 36(17p12) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.09e-05 (Fisher's exact test), Q value = 0.022

Table S38. Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 36(17P12) MUTATED	50	104	116	59
DEL PEAK 36(17P12) WILD-TYPE	47	103	50	22

Figure S38. Get High-res Image Gene #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 38(18p11.31) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.82e-06 (Fisher's exact test), Q value = 0.0013

Table S39. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
DEL PEAK 38(18P11.31) MUTATED	219	119
DEL PEAK 38(18P11.31) WILD-TYPE	193	40

Figure S39. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 38(18p11.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.11e-16 (Fisher's exact test), Q value = 8.3e-14

Table S40. Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 38(18P11.31) MUTATED	211	7	113	6
DEL PEAK 38(18P11.31) WILD-TYPE	145	47	30	7

Figure S40. Get High-res Image Gene #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.57e-09 (Fisher's exact test), Q value = 1.2e-06

Table S41. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
DEL PEAK 39(18Q12.2) MUTATED	247	136
DEL PEAK 39(18Q12.2) WILD-TYPE	165	23

Figure S41. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 39(18q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.64e-18 (Fisher's exact test), Q value = 4.2e-15

Table S42. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 39(18Q12.2) MUTATED	235	11	125	10
DEL PEAK 39(18Q12.2) WILD-TYPE	121	43	18	3

Figure S42. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q12.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000131 (Fisher's exact test), Q value = 0.092

Table S43. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 39(18Q12.2) MUTATED	196	107	79
DEL PEAK 39(18Q12.2) WILD-TYPE	132	33	24

Figure S43. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 39(18q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.7e-05 (Fisher's exact test), Q value = 0.048

Table S44. Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 39(18Q12.2) MUTATED	56	122	121	67
DEL PEAK 39(18Q12.2) WILD-TYPE	41	85	45	14

Figure S44. Get High-res Image Gene #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 40(18q21.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.07e-09 (Fisher's exact test), Q value = 7.9e-07

Table S45. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
DEL PEAK 40(18Q21.2) MUTATED	260	140
DEL PEAK 40(18Q21.2) WILD-TYPE	152	19

Figure S45. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.57e-16 (Fisher's exact test), Q value = 1.9e-13

Table S46. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 40(18Q21.2) MUTATED	245	14	126	12
DEL PEAK 40(18Q21.2) WILD-TYPE	111	40	17	1

Figure S46. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.01e-06 (Fisher's exact test), Q value = 0.0015

Table S47. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 40(18Q21.2) MUTATED	202	111	86
DEL PEAK 40(18Q21.2) WILD-TYPE	126	29	17

Figure S47. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 40(18q21.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.94e-07 (Fisher's exact test), Q value = 0.00029

Table S48. Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 40(18Q21.2) MUTATED	58	126	128	72
DEL PEAK 40(18Q21.2) WILD-TYPE	39	81	38	9

Figure S48. Get High-res Image Gene #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 41(18q22.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00014

Table S49. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	159
DEL PEAK 41(18Q22.1) MUTATED	260	135
DEL PEAK 41(18Q22.1) WILD-TYPE	152	24

Figure S49. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(18q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.41e-15 (Fisher's exact test), Q value = 1.1e-12

Table S50. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	143	13
DEL PEAK 41(18Q22.1) MUTATED	246	13	124	10
DEL PEAK 41(18Q22.1) WILD-TYPE	110	41	19	3

Figure S50. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 41(18q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.1e-05 (Fisher's exact test), Q value = 0.008

Table S51. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 41(18Q22.1) MUTATED	201	108	85
DEL PEAK 41(18Q22.1) WILD-TYPE	127	32	18

Figure S51. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 41(18q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.52e-06 (Fisher's exact test), Q value = 0.0033

Table S52. Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	97	207	166	81
DEL PEAK 41(18Q22.1) MUTATED	58	126	124	71
DEL PEAK 41(18Q22.1) WILD-TYPE	39	81	42	10

Figure S52. Get High-res Image Gene #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

'Del Peak 42(19p13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 7.59e-05 (Fisher's exact test), Q value = 0.054

Table S53. Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	328	140	103
DEL PEAK 42(19P13.3) MUTATED	36	26	30
DEL PEAK 42(19P13.3) WILD-TYPE	292	114	73

Figure S53. Get High-res Image Gene #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Clinical data file = COADREAD-TP.clin.merged.picked.txt
Number of patients = 575
Number of copy number variation regions = 75
Number of selected clinical features = 10
Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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.

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)

[6] GISTIC_version2

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