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 78 peak regions and 10 clinical features across 574 patients, 34 significant findings detected with Q value < 0.25.

Amp Peak 5(6p21.1) cnvs correlated to 'PATHOLOGY.N'.
Amp Peak 6(7p11.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 11(9p13.3) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE'.
Amp Peak 15(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 16(13q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 17(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
Amp Peak 26(20p11.23) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 27(20p11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 28(20q11.21) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Amp Peak 29(20q13.12) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Amp Peak 30(20q13.32) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Del Peak 2(1p36.11) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 14(4q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 22(8p23.2) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
Del Peak 23(8p22) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
Del Peak 32(14q11.2) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 35(15q22.33) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 38(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 40(18p11.31) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Del Peak 41(18q12.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
Del Peak 42(18q21.2) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.N'.
Del Peak 43(18q22.1) cnvs correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.N'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 78 regions and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 34 significant findings detected.


		Clinical Features	Time to Death	AGE	PRIMARY SITE OF DISEASE	GENDER	HISTOLOGICAL TYPE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	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	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test
Del Peak 42(18q21 2)	374 (65%)	200	0.295 (1.00)	0.22 (1.00)	4.62e-07 (0.000355)	0.254 (1.00)	6.42e-12 (4.97e-09)	0.158 (1.00)	4.08e-06 (0.00312)	0.000966 (0.708)	0.507 (1.00)	0.802 (1.00)
Del Peak 43(18q22 1)	369 (64%)	205	0.19 (1.00)	0.487 (1.00)	9.83e-06 (0.00751)	0.433 (1.00)	1.25e-12 (9.72e-10)	0.203 (1.00)	2.06e-05 (0.0157)	0.00323 (1.00)	0.501 (1.00)	1 (1.00)
Amp Peak 17(13q22 1)	336 (59%)	238	0.255 (1.00)	0.756 (1.00)	0.00803 (1.00)	0.174 (1.00)	1.05e-07 (8.1e-05)	0.745 (1.00)	0.000212 (0.159)	0.116 (1.00)	0.318 (1.00)	0.545 (1.00)
Amp Peak 28(20q11 21)	403 (70%)	171	0.84 (1.00)	0.683 (1.00)	2.57e-05 (0.0195)	0.36 (1.00)	2.31e-15 (1.8e-12)	0.262 (1.00)	0.0217 (1.00)	0.135 (1.00)	0.73 (1.00)	0.516 (1.00)
Amp Peak 29(20q13 12)	412 (72%)	162	0.424 (1.00)	0.972 (1.00)	7.52e-05 (0.0569)	0.516 (1.00)	1.44e-13 (1.12e-10)	0.465 (1.00)	0.00756 (1.00)	0.0333 (1.00)	0.717 (1.00)	0.508 (1.00)
Amp Peak 30(20q13 32)	414 (72%)	160	0.409 (1.00)	0.701 (1.00)	0.000157 (0.118)	0.642 (1.00)	1.34e-13 (1.04e-10)	0.469 (1.00)	0.00522 (1.00)	0.0254 (1.00)	0.714 (1.00)	0.595 (1.00)
Del Peak 22(8p23 2)	244 (43%)	330	0.397 (1.00)	0.656 (1.00)	0.000444 (0.329)	0.31 (1.00)	8.34e-05 (0.063)	0.207 (1.00)	0.000169 (0.127)	0.0413 (1.00)	0.505 (1.00)	0.336 (1.00)
Del Peak 23(8p22)	256 (45%)	318	0.246 (1.00)	0.717 (1.00)	0.000996 (0.727)	0.614 (1.00)	1.88e-05 (0.0143)	0.106 (1.00)	2.41e-05 (0.0183)	0.043 (1.00)	0.521 (1.00)	0.472 (1.00)
Del Peak 40(18p11 31)	312 (54%)	262	0.822 (1.00)	0.319 (1.00)	1.41e-05 (0.0107)	0.675 (1.00)	9.2e-15 (7.17e-12)	0.685 (1.00)	0.00512 (1.00)	0.00948 (1.00)	0.738 (1.00)	1 (1.00)
Del Peak 41(18q12 2)	356 (62%)	218	0.86 (1.00)	0.303 (1.00)	8.03e-07 (0.000616)	0.547 (1.00)	5.73e-14 (4.46e-11)	0.215 (1.00)	0.000453 (0.335)	0.025 (1.00)	0.494 (1.00)	0.807 (1.00)
Amp Peak 5(6p21 1)	102 (18%)	472	0.349 (1.00)	0.535 (1.00)	0.00681 (1.00)	0.512 (1.00)	0.00171 (1.00)	0.318 (1.00)	0.000301 (0.225)	0.124 (1.00)	0.204 (1.00)	0.755 (1.00)
Amp Peak 6(7p11 2)	282 (49%)	292	0.118 (1.00)	0.709 (1.00)	0.261 (1.00)	0.558 (1.00)	0.000102 (0.077)	0.796 (1.00)	0.00877 (1.00)	0.0479 (1.00)	0.748 (1.00)	0.905 (1.00)
Amp Peak 11(9p13 3)	87 (15%)	487	0.407 (1.00)	0.565 (1.00)	7.82e-05 (0.0591)	1 (1.00)	0.000405 (0.301)	0.793 (1.00)	0.684 (1.00)	0.777 (1.00)	1 (1.00)	0.319 (1.00)
Amp Peak 15(13q12 13)	339 (59%)	235	0.589 (1.00)	0.636 (1.00)	0.00121 (0.877)	0.932 (1.00)	5.34e-10 (4.13e-07)	0.692 (1.00)	0.000574 (0.423)	0.036 (1.00)	0.744 (1.00)	0.547 (1.00)
Amp Peak 16(13q12 2)	333 (58%)	241	0.516 (1.00)	0.499 (1.00)	0.00173 (1.00)	0.799 (1.00)	2.15e-09 (1.66e-06)	0.622 (1.00)	0.000796 (0.584)	0.0607 (1.00)	0.741 (1.00)	0.629 (1.00)
Amp Peak 26(20p11 23)	257 (45%)	317	0.932 (1.00)	0.32 (1.00)	0.00487 (1.00)	0.078 (1.00)	1.09e-06 (0.000835)	0.709 (1.00)	0.0774 (1.00)	0.0715 (1.00)	0.523 (1.00)	0.15 (1.00)
Amp Peak 27(20p11 21)	294 (51%)	280	0.82 (1.00)	0.67 (1.00)	0.00888 (1.00)	0.0789 (1.00)	1.71e-08 (1.32e-05)	0.309 (1.00)	0.823 (1.00)	0.102 (1.00)	1 (1.00)	0.721 (1.00)
Del Peak 2(1p36 11)	166 (29%)	408	0.0371 (1.00)	0.351 (1.00)	0.351 (1.00)	0.58 (1.00)	0.000257 (0.193)	0.283 (1.00)	0.00848 (1.00)	0.0013 (0.942)	1 (1.00)	0.149 (1.00)
Del Peak 14(4q22 1)	140 (24%)	434	0.196 (1.00)	0.959 (1.00)	0.0043 (1.00)	0.244 (1.00)	0.000137 (0.103)	0.472 (1.00)	0.0327 (1.00)	0.343 (1.00)	0.043 (1.00)	0.211 (1.00)
Del Peak 32(14q11 2)	149 (26%)	425	0.151 (1.00)	0.465 (1.00)	0.0181 (1.00)	0.775 (1.00)	1.45e-05 (0.011)	0.642 (1.00)	0.0342 (1.00)	0.556 (1.00)	0.702 (1.00)	0.892 (1.00)
Del Peak 35(15q22 33)	160 (28%)	414	0.343 (1.00)	0.912 (1.00)	0.000775 (0.57)	0.78 (1.00)	0.000171 (0.128)	0.0449 (1.00)	0.0684 (1.00)	0.32 (1.00)	0.273 (1.00)	0.791 (1.00)
Del Peak 38(17p12)	300 (52%)	274	0.524 (1.00)	0.301 (1.00)	0.00367 (1.00)	0.452 (1.00)	1.84e-07 (0.000142)	0.699 (1.00)	0.00777 (1.00)	0.0611 (1.00)	0.18 (1.00)	0.72 (1.00)
Amp Peak 1(1q21 3)	100 (17%)	474	0.897 (1.00)	0.682 (1.00)	0.107 (1.00)	0.0618 (1.00)	0.195 (1.00)	0.317 (1.00)	0.229 (1.00)	0.377 (1.00)	0.66 (1.00)	0.875 (1.00)
Amp Peak 2(2q33 1)	76 (13%)	498	0.933 (1.00)	0.636 (1.00)	0.129 (1.00)	0.109 (1.00)	0.0143 (1.00)	0.909 (1.00)	0.0404 (1.00)	0.933 (1.00)	1 (1.00)	0.29 (1.00)
Amp Peak 3(4q28 3)	19 (3%)	555	0.341 (1.00)	0.35 (1.00)	0.191 (1.00)	0.243 (1.00)	0.238 (1.00)	0.217 (1.00)	0.768 (1.00)	0.0962 (1.00)	0.263 (1.00)	1 (1.00)
Amp Peak 4(5p13 2)	84 (15%)	490	0.181 (1.00)	0.91 (1.00)	0.356 (1.00)	0.906 (1.00)	0.234 (1.00)	0.401 (1.00)	0.532 (1.00)	0.948 (1.00)	0.626 (1.00)	0.613 (1.00)
Amp Peak 7(8p11 23)	155 (27%)	419	0.37 (1.00)	0.993 (1.00)	0.916 (1.00)	0.347 (1.00)	0.524 (1.00)	0.359 (1.00)	0.672 (1.00)	0.616 (1.00)	0.708 (1.00)	0.687 (1.00)
Amp Peak 8(8p11 21)	195 (34%)	379	0.781 (1.00)	0.624 (1.00)	0.375 (1.00)	0.134 (1.00)	0.264 (1.00)	0.376 (1.00)	0.493 (1.00)	0.501 (1.00)	0.725 (1.00)	0.9 (1.00)
Amp Peak 9(8q11 23)	239 (42%)	335	0.702 (1.00)	0.235 (1.00)	0.0717 (1.00)	0.498 (1.00)	0.0171 (1.00)	0.386 (1.00)	0.0999 (1.00)	0.209 (1.00)	0.742 (1.00)	0.717 (1.00)
Amp Peak 10(8q24 21)	293 (51%)	281	0.467 (1.00)	0.128 (1.00)	0.0754 (1.00)	0.503 (1.00)	0.0302 (1.00)	0.455 (1.00)	0.0267 (1.00)	0.0262 (1.00)	0.747 (1.00)	0.635 (1.00)
Amp Peak 12(10q23 1)	25 (4%)	549	0.603 (1.00)	0.0542 (1.00)	0.363 (1.00)	0.683 (1.00)	0.502 (1.00)	0.0806 (1.00)	0.0148 (1.00)	0.533 (1.00)	1 (1.00)	0.77 (1.00)
Amp Peak 13(11p15 5)	102 (18%)	472	0.814 (1.00)	0.217 (1.00)	0.00977 (1.00)	0.446 (1.00)	0.000538 (0.397)	0.218 (1.00)	0.186 (1.00)	0.125 (1.00)	0.665 (1.00)	0.532 (1.00)
Amp Peak 14(12p13 32)	115 (20%)	459	0.599 (1.00)	0.00701 (1.00)	0.907 (1.00)	1 (1.00)	0.59 (1.00)	0.746 (1.00)	0.00879 (1.00)	0.27 (1.00)	1 (1.00)	0.372 (1.00)
Amp Peak 18(15q26 1)	25 (4%)	549	0.187 (1.00)	0.732 (1.00)	1 (1.00)	0.683 (1.00)	0.794 (1.00)	0.979 (1.00)	0.0312 (1.00)	0.414 (1.00)	1 (1.00)	0.77 (1.00)
Amp Peak 19(16p11 2)	123 (21%)	451	0.988 (1.00)	0.748 (1.00)	0.82 (1.00)	0.476 (1.00)	0.005 (1.00)	0.758 (1.00)	0.000427 (0.317)	0.337 (1.00)	0.412 (1.00)	0.145 (1.00)
Amp Peak 20(16q12 1)	108 (19%)	466	0.779 (1.00)	0.238 (1.00)	0.472 (1.00)	0.593 (1.00)	0.00561 (1.00)	0.66 (1.00)	0.000664 (0.488)	0.449 (1.00)	0.381 (1.00)	0.0315 (1.00)
Amp Peak 21(17q12)	99 (17%)	475	0.271 (1.00)	0.391 (1.00)	0.538 (1.00)	0.0271 (1.00)	0.0151 (1.00)	0.6 (1.00)	0.286 (1.00)	0.0438 (1.00)	1 (1.00)	0.0175 (1.00)
Amp Peak 22(17q24 1)	92 (16%)	482	0.0245 (1.00)	0.197 (1.00)	0.702 (1.00)	0.733 (1.00)	0.0846 (1.00)	0.687 (1.00)	0.723 (1.00)	0.121 (1.00)	1 (1.00)	0.00845 (1.00)
Amp Peak 23(19q12)	82 (14%)	492	0.911 (1.00)	0.75 (1.00)	0.109 (1.00)	0.634 (1.00)	0.0209 (1.00)	0.937 (1.00)	0.222 (1.00)	0.642 (1.00)	0.371 (1.00)	0.495 (1.00)
Amp Peak 24(19q13 12)	78 (14%)	496	0.135 (1.00)	0.974 (1.00)	0.173 (1.00)	0.903 (1.00)	0.115 (1.00)	0.911 (1.00)	0.58 (1.00)	0.855 (1.00)	0.617 (1.00)	0.301 (1.00)
Amp Peak 25(20p12 1)	213 (37%)	361	0.764 (1.00)	0.179 (1.00)	0.148 (1.00)	0.00947 (1.00)	0.000393 (0.292)	0.305 (1.00)	0.33 (1.00)	0.0304 (1.00)	0.303 (1.00)	1 (1.00)
Del Peak 1(1p36 21)	151 (26%)	423	0.106 (1.00)	0.591 (1.00)	0.0423 (1.00)	0.343 (1.00)	0.00385 (1.00)	0.868 (1.00)	0.0264 (1.00)	0.00933 (1.00)	1 (1.00)	0.139 (1.00)
Del Peak 3(1p33)	103 (18%)	471	0.00682 (1.00)	0.561 (1.00)	0.542 (1.00)	0.664 (1.00)	0.251 (1.00)	0.173 (1.00)	0.0469 (1.00)	0.0187 (1.00)	1 (1.00)	0.163 (1.00)
Del Peak 4(1p13 2)	103 (18%)	471	0.11 (1.00)	0.567 (1.00)	0.714 (1.00)	0.586 (1.00)	0.172 (1.00)	0.141 (1.00)	0.153 (1.00)	0.00224 (1.00)	0.667 (1.00)	0.0871 (1.00)
Del Peak 5(1q42 3)	28 (5%)	546	0.96 (1.00)	0.75 (1.00)	0.832 (1.00)	1 (1.00)	1 (1.00)	0.505 (1.00)	0.146 (1.00)	0.867 (1.00)	1 (1.00)	0.406 (1.00)
Del Peak 6(2p21)	21 (4%)	553	0.767 (1.00)	0.83 (1.00)	0.0219 (1.00)	0.183 (1.00)	0.0649 (1.00)	0.739 (1.00)	0.393 (1.00)	0.794 (1.00)	0.287 (1.00)	0.754 (1.00)
Del Peak 7(2p12)	23 (4%)	551	0.822 (1.00)	0.499 (1.00)	0.00117 (0.856)	0.833 (1.00)	0.00976 (1.00)	0.265 (1.00)	0.538 (1.00)	0.789 (1.00)	0.31 (1.00)	1 (1.00)
Del Peak 8(2q22 1)	20 (3%)	554	0.754 (1.00)	0.987 (1.00)	1 (1.00)	0.364 (1.00)	0.487 (1.00)	0.481 (1.00)	0.704 (1.00)	0.184 (1.00)	1 (1.00)	0.754 (1.00)
Del Peak 9(2q37 2)	21 (4%)	553	0.55 (1.00)	0.504 (1.00)	0.807 (1.00)	0.659 (1.00)	0.927 (1.00)	0.329 (1.00)	0.46 (1.00)	0.368 (1.00)	1 (1.00)	0.0572 (1.00)
Del Peak 10(3p26 3)	58 (10%)	516	0.000381 (0.284)	0.306 (1.00)	0.643 (1.00)	0.331 (1.00)	0.0449 (1.00)	0.0245 (1.00)	0.0184 (1.00)	0.000487 (0.36)	1 (1.00)	1 (1.00)
Del Peak 11(3p14 2)	80 (14%)	494	0.276 (1.00)	0.749 (1.00)	1 (1.00)	0.63 (1.00)	0.507 (1.00)	0.182 (1.00)	0.292 (1.00)	0.0125 (1.00)	1 (1.00)	0.302 (1.00)
Del Peak 12(3q26 31)	35 (6%)	539	0.641 (1.00)	0.843 (1.00)	0.435 (1.00)	0.035 (1.00)	0.0209 (1.00)	0.357 (1.00)	0.516 (1.00)	0.233 (1.00)	1 (1.00)	0.209 (1.00)
Del Peak 13(4p16 2)	131 (23%)	443	0.00429 (1.00)	0.379 (1.00)	0.094 (1.00)	0.135 (1.00)	0.0225 (1.00)	0.901 (1.00)	0.00517 (1.00)	0.0173 (1.00)	0.00581 (1.00)	0.0323 (1.00)
Del Peak 15(4q35 1)	151 (26%)	423	0.695 (1.00)	0.579 (1.00)	0.134 (1.00)	0.85 (1.00)	0.00241 (1.00)	0.864 (1.00)	0.0876 (1.00)	0.856 (1.00)	0.0124 (1.00)	0.416 (1.00)
Del Peak 16(5q11 2)	95 (17%)	479	0.791 (1.00)	0.74 (1.00)	0.0173 (1.00)	0.261 (1.00)	0.0173 (1.00)	0.976 (1.00)	0.0725 (1.00)	0.223 (1.00)	0.00098 (0.716)	0.425 (1.00)
Del Peak 17(5q21 1)	112 (20%)	462	0.571 (1.00)	0.943 (1.00)	0.815 (1.00)	0.141 (1.00)	0.615 (1.00)	0.919 (1.00)	0.127 (1.00)	0.223 (1.00)	0.0168 (1.00)	0.549 (1.00)
Del Peak 18(5q22 2)	124 (22%)	450	0.53 (1.00)	0.632 (1.00)	0.308 (1.00)	0.0843 (1.00)	0.161 (1.00)	0.934 (1.00)	0.416 (1.00)	0.831 (1.00)	0.00431 (1.00)	0.472 (1.00)
Del Peak 19(6p25 3)	47 (8%)	527	0.862 (1.00)	0.164 (1.00)	0.227 (1.00)	0.169 (1.00)	0.147 (1.00)	0.138 (1.00)	0.709 (1.00)	0.614 (1.00)	0.539 (1.00)	0.284 (1.00)
Del Peak 20(6q26)	48 (8%)	526	0.00253 (1.00)	0.675 (1.00)	0.302 (1.00)	0.547 (1.00)	0.0618 (1.00)	0.14 (1.00)	0.00236 (1.00)	0.00123 (0.89)	0.547 (1.00)	0.523 (1.00)
Del Peak 21(7q31 1)	12 (2%)	562	0.891 (1.00)	0.313 (1.00)	0.745 (1.00)	0.561 (1.00)	0.417 (1.00)	0.681 (1.00)	0.0907 (1.00)	0.452 (1.00)	1 (1.00)	1 (1.00)
Del Peak 24(8p11 21)	96 (17%)	478	0.0894 (1.00)	0.771 (1.00)	0.259 (1.00)	0.37 (1.00)	0.254 (1.00)	0.914 (1.00)	0.0198 (1.00)	0.479 (1.00)	1 (1.00)	0.749 (1.00)
Del Peak 25(8p11 21)	49 (9%)	525	0.14 (1.00)	0.219 (1.00)	0.866 (1.00)	0.881 (1.00)	0.641 (1.00)	0.677 (1.00)	0.0413 (1.00)	0.0728 (1.00)	0.555 (1.00)	0.523 (1.00)
Del Peak 26(10q21 1)	68 (12%)	506	0.449 (1.00)	0.159 (1.00)	0.0214 (1.00)	0.898 (1.00)	0.0251 (1.00)	0.815 (1.00)	0.418 (1.00)	0.53 (1.00)	1 (1.00)	0.712 (1.00)
Del Peak 27(10q23 31)	86 (15%)	488	0.331 (1.00)	0.0655 (1.00)	0.00571 (1.00)	0.641 (1.00)	0.0144 (1.00)	0.219 (1.00)	0.149 (1.00)	0.0227 (1.00)	0.63 (1.00)	0.403 (1.00)
Del Peak 28(10q25 2)	81 (14%)	493	0.722 (1.00)	0.164 (1.00)	0.0153 (1.00)	0.631 (1.00)	0.0257 (1.00)	0.301 (1.00)	0.1 (1.00)	0.363 (1.00)	0.37 (1.00)	0.732 (1.00)
Del Peak 29(11q22 3)	72 (13%)	502	0.905 (1.00)	0.85 (1.00)	0.00157 (1.00)	0.531 (1.00)	0.000973 (0.712)	0.522 (1.00)	0.312 (1.00)	0.968 (1.00)	0.0911 (1.00)	1 (1.00)
Del Peak 30(12p13 1)	47 (8%)	527	0.0244 (1.00)	0.669 (1.00)	0.0141 (1.00)	0.224 (1.00)	0.00338 (1.00)	0.31 (1.00)	0.0243 (1.00)	0.185 (1.00)	0.163 (1.00)	0.284 (1.00)
Del Peak 31(12q21 2)	40 (7%)	534	0.841 (1.00)	0.889 (1.00)	0.278 (1.00)	0.324 (1.00)	0.0609 (1.00)	0.497 (1.00)	0.0894 (1.00)	0.0012 (0.873)	0.48 (1.00)	1 (1.00)
Del Peak 33(15q11 2)	178 (31%)	396	0.986 (1.00)	0.481 (1.00)	0.0676 (1.00)	0.857 (1.00)	0.00259 (1.00)	0.468 (1.00)	0.0486 (1.00)	0.334 (1.00)	0.469 (1.00)	0.52 (1.00)
Del Peak 34(15q21 1)	174 (30%)	400	0.36 (1.00)	0.973 (1.00)	0.00799 (1.00)	0.785 (1.00)	0.0025 (1.00)	0.513 (1.00)	0.126 (1.00)	0.245 (1.00)	0.465 (1.00)	0.604 (1.00)
Del Peak 36(16p13 3)	43 (7%)	531	0.00619 (1.00)	0.546 (1.00)	0.597 (1.00)	0.874 (1.00)	0.296 (1.00)	0.119 (1.00)	0.388 (1.00)	0.562 (1.00)	1 (1.00)	0.821 (1.00)
Del Peak 37(16q23 1)	54 (9%)	520	0.0199 (1.00)	0.075 (1.00)	0.34 (1.00)	0.197 (1.00)	0.379 (1.00)	0.527 (1.00)	0.618 (1.00)	0.857 (1.00)	0.592 (1.00)	1 (1.00)
Del Peak 39(17q24 3)	59 (10%)	515	0.278 (1.00)	0.356 (1.00)	0.283 (1.00)	0.409 (1.00)	0.619 (1.00)	0.392 (1.00)	0.0188 (1.00)	0.121 (1.00)	0.234 (1.00)	0.113 (1.00)
Del Peak 44(19p13 3)	50 (9%)	524	0.465 (1.00)	0.74 (1.00)	0.322 (1.00)	0.138 (1.00)	0.0487 (1.00)	0.94 (1.00)	0.108 (1.00)	0.54 (1.00)	1 (1.00)	0.832 (1.00)
Del Peak 45(20p12 1)	107 (19%)	467	0.921 (1.00)	0.599 (1.00)	0.0157 (1.00)	0.668 (1.00)	0.0127 (1.00)	0.809 (1.00)	0.527 (1.00)	0.376 (1.00)	0.221 (1.00)	0.646 (1.00)
Del Peak 46(21q11 2)	137 (24%)	437	0.973 (1.00)	0.741 (1.00)	0.0203 (1.00)	1 (1.00)	0.00287 (1.00)	0.657 (1.00)	0.273 (1.00)	0.496 (1.00)	0.452 (1.00)	0.576 (1.00)
Del Peak 47(21q22 2)	123 (21%)	451	0.29 (1.00)	0.668 (1.00)	0.00195 (1.00)	0.262 (1.00)	0.00138 (1.00)	0.402 (1.00)	0.278 (1.00)	0.75 (1.00)	1 (1.00)	0.771 (1.00)
Del Peak 48(22q13 31)	141 (25%)	433	0.333 (1.00)	0.0663 (1.00)	0.0163 (1.00)	0.498 (1.00)	0.000375 (0.28)	0.505 (1.00)	0.00211 (1.00)	0.0457 (1.00)	0.234 (1.00)	0.168 (1.00)

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

P value = 0.000301 (Fisher's exact test), Q value = 0.22

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

nPatients	N0	N1	N2
ALL	327	140	103
AMP PEAK 5(6P21.1) MUTATED	43	26	32
AMP PEAK 5(6P21.1) WILD-TYPE	284	114	71

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

'Amp Peak 6(7p11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000102 (Fisher's exact test), Q value = 0.077

Table S2. Gene #6: 'Amp Peak 6(7p11.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 6(7P11.2) MUTATED	181	15	82	2
AMP PEAK 6(7P11.2) WILD-TYPE	175	39	60	11

Figure S2. Get High-res Image Gene #6: 'Amp Peak 6(7p11.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 11(9p13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.82e-05 (Fisher's exact test), Q value = 0.059

Table S3. Gene #11: 'Amp Peak 11(9p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
AMP PEAK 11(9P13.3) MUTATED	47	40
AMP PEAK 11(9P13.3) WILD-TYPE	365	118

Figure S3. Get High-res Image Gene #11: 'Amp Peak 11(9p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 5.34e-10 (Fisher's exact test), Q value = 4.1e-07

Table S4. Gene #15: 'Amp Peak 15(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 15(13Q12.13) MUTATED	212	13	105	4
AMP PEAK 15(13Q12.13) WILD-TYPE	144	41	37	9

Figure S4. Get High-res Image Gene #15: 'Amp Peak 15(13q12.13) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(13q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.15e-09 (Fisher's exact test), Q value = 1.7e-06

Table S5. Gene #16: 'Amp Peak 16(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 16(13Q12.2) MUTATED	208	13	103	4
AMP PEAK 16(13Q12.2) WILD-TYPE	148	41	39	9

Figure S5. Get High-res Image Gene #16: 'Amp Peak 16(13q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 17(13q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.05e-07 (Fisher's exact test), Q value = 8.1e-05

Table S6. Gene #17: 'Amp Peak 17(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 17(13Q22.1) MUTATED	211	15	101	4
AMP PEAK 17(13Q22.1) WILD-TYPE	145	39	41	9

Figure S6. Get High-res Image Gene #17: 'Amp Peak 17(13q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 17(13q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000212 (Fisher's exact test), Q value = 0.16

Table S7. Gene #17: 'Amp Peak 17(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	327	140	103
AMP PEAK 17(13Q22.1) MUTATED	167	98	67
AMP PEAK 17(13Q22.1) WILD-TYPE	160	42	36

Figure S7. Get High-res Image Gene #17: 'Amp Peak 17(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Amp Peak 26(20p11.23) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.09e-06 (Fisher's exact test), Q value = 0.00083

Table S8. Gene #26: 'Amp Peak 26(20p11.23) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 26(20P11.23) MUTATED	159	9	81	3
AMP PEAK 26(20P11.23) WILD-TYPE	197	45	61	10

Figure S8. Get High-res Image Gene #26: 'Amp Peak 26(20p11.23) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 27(20p11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.71e-08 (Fisher's exact test), Q value = 1.3e-05

Table S9. Gene #27: 'Amp Peak 27(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 27(20P11.21) MUTATED	185	10	91	3
AMP PEAK 27(20P11.21) WILD-TYPE	171	44	51	10

Figure S9. Get High-res Image Gene #27: 'Amp Peak 27(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 28(20q11.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.57e-05 (Fisher's exact test), Q value = 0.019

Table S10. Gene #28: 'Amp Peak 28(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
AMP PEAK 28(20Q11.21) MUTATED	269	131
AMP PEAK 28(20Q11.21) WILD-TYPE	143	27

Figure S10. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 28(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.31e-15 (Fisher's exact test), Q value = 1.8e-12

Table S11. Gene #28: 'Amp Peak 28(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 28(20Q11.21) MUTATED	253	14	123	6
AMP PEAK 28(20Q11.21) WILD-TYPE	103	40	19	7

Figure S11. Get High-res Image Gene #28: 'Amp Peak 28(20q11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 29(20q13.12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.52e-05 (Fisher's exact test), Q value = 0.057

Table S12. Gene #29: 'Amp Peak 29(20q13.12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
AMP PEAK 29(20Q13.12) MUTATED	277	132
AMP PEAK 29(20Q13.12) WILD-TYPE	135	26

Figure S12. Get High-res Image Gene #29: 'Amp Peak 29(20q13.12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 29(20q13.12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.44e-13 (Fisher's exact test), Q value = 1.1e-10

Table S13. Gene #29: 'Amp Peak 29(20q13.12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 29(20Q13.12) MUTATED	258	17	124	6
AMP PEAK 29(20Q13.12) WILD-TYPE	98	37	18	7

Figure S13. Get High-res Image Gene #29: 'Amp Peak 29(20q13.12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Amp Peak 30(20q13.32) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0.000157 (Fisher's exact test), Q value = 0.12

Table S14. Gene #30: 'Amp Peak 30(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
AMP PEAK 30(20Q13.32) MUTATED	279	132
AMP PEAK 30(20Q13.32) WILD-TYPE	133	26

Figure S14. Get High-res Image Gene #30: 'Amp Peak 30(20q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 30(20q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.34e-13 (Fisher's exact test), Q value = 1e-10

Table S15. Gene #30: 'Amp Peak 30(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
AMP PEAK 30(20Q13.32) MUTATED	260	17	124	6
AMP PEAK 30(20Q13.32) WILD-TYPE	96	37	18	7

Figure S15. Get High-res Image Gene #30: 'Amp Peak 30(20q13.32) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p36.11) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000257 (Fisher's exact test), Q value = 0.19

Table S16. Gene #32: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 2(1P36.11) MUTATED	108	4	42	7
DEL PEAK 2(1P36.11) WILD-TYPE	248	50	100	6

Figure S16. Get High-res Image Gene #32: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 14(4q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000137 (Fisher's exact test), Q value = 0.1

Table S17. Gene #44: 'Del Peak 14(4q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 14(4Q22.1) MUTATED	82	3	48	2
DEL PEAK 14(4Q22.1) WILD-TYPE	274	51	94	11

Figure S17. Get High-res Image Gene #44: 'Del Peak 14(4q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 22(8p23.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.34e-05 (Fisher's exact test), Q value = 0.063

Table S18. Gene #52: 'Del Peak 22(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 22(8P23.2) MUTATED	144	11	78	6
DEL PEAK 22(8P23.2) WILD-TYPE	212	43	64	7

Figure S18. Get High-res Image Gene #52: 'Del Peak 22(8p23.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 22(8p23.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000169 (Fisher's exact test), Q value = 0.13

Table S19. Gene #52: 'Del Peak 22(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	327	140	103
DEL PEAK 22(8P23.2) MUTATED	115	68	58
DEL PEAK 22(8P23.2) WILD-TYPE	212	72	45

Figure S19. Get High-res Image Gene #52: 'Del Peak 22(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 23(8p22) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.88e-05 (Fisher's exact test), Q value = 0.014

Table S20. Gene #53: 'Del Peak 23(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 23(8P22) MUTATED	155	10	80	6
DEL PEAK 23(8P22) WILD-TYPE	201	44	62	7

Figure S20. Get High-res Image Gene #53: 'Del Peak 23(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 23(8p22) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.018

Table S21. Gene #53: 'Del Peak 23(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	327	140	103
DEL PEAK 23(8P22) MUTATED	120	70	63
DEL PEAK 23(8P22) WILD-TYPE	207	70	40

Figure S21. Get High-res Image Gene #53: 'Del Peak 23(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 32(14q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.45e-05 (Fisher's exact test), Q value = 0.011

Table S22. Gene #62: 'Del Peak 32(14q11.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 32(14Q11.2) MUTATED	90	4	52	0
DEL PEAK 32(14Q11.2) WILD-TYPE	266	50	90	13

Figure S22. Get High-res Image Gene #62: 'Del Peak 32(14q11.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 35(15q22.33) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 0.000171 (Fisher's exact test), Q value = 0.13

Table S23. Gene #65: 'Del Peak 35(15q22.33) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 35(15Q22.33) MUTATED	92	5	55	4
DEL PEAK 35(15Q22.33) WILD-TYPE	264	49	87	9

Figure S23. Get High-res Image Gene #65: 'Del Peak 35(15q22.33) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 38(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.84e-07 (Fisher's exact test), Q value = 0.00014

Table S24. Gene #68: 'Del Peak 38(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 38(17P12) MUTATED	188	10	90	6
DEL PEAK 38(17P12) WILD-TYPE	168	44	52	7

Figure S24. Get High-res Image Gene #68: 'Del Peak 38(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18p11.31) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.41e-05 (Fisher's exact test), Q value = 0.011

Table S25. Gene #70: 'Del Peak 40(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
DEL PEAK 40(18P11.31) MUTATED	200	109
DEL PEAK 40(18P11.31) WILD-TYPE	212	49

Figure S25. Get High-res Image Gene #70: 'Del Peak 40(18p11.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(18p11.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.2e-15 (Fisher's exact test), Q value = 7.2e-12

Table S26. Gene #70: 'Del Peak 40(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 40(18P11.31) MUTATED	193	6	104	5
DEL PEAK 40(18P11.31) WILD-TYPE	163	48	38	8

Figure S26. Get High-res Image Gene #70: 'Del Peak 40(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 41(18q12.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.03e-07 (Fisher's exact test), Q value = 0.00062

Table S27. Gene #71: 'Del Peak 41(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
DEL PEAK 41(18Q12.2) MUTATED	230	123
DEL PEAK 41(18Q12.2) WILD-TYPE	182	35

Figure S27. Get High-res Image Gene #71: 'Del Peak 41(18q12.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(18q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.73e-14 (Fisher's exact test), Q value = 4.5e-11

Table S28. Gene #71: 'Del Peak 41(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 41(18Q12.2) MUTATED	219	10	113	9
DEL PEAK 41(18Q12.2) WILD-TYPE	137	44	29	4

Figure S28. Get High-res Image Gene #71: 'Del Peak 41(18q12.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 42(18q21.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.62e-07 (Fisher's exact test), Q value = 0.00035

Table S29. Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
DEL PEAK 42(18Q21.2) MUTATED	243	128
DEL PEAK 42(18Q21.2) WILD-TYPE	169	30

Figure S29. Get High-res Image Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 42(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.42e-12 (Fisher's exact test), Q value = 5e-09

Table S30. Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 42(18Q21.2) MUTATED	228	14	115	11
DEL PEAK 42(18Q21.2) WILD-TYPE	128	40	27	2

Figure S30. Get High-res Image Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 42(18q21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 4.08e-06 (Fisher's exact test), Q value = 0.0031

Table S31. Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	327	140	103
DEL PEAK 42(18Q21.2) MUTATED	185	106	80
DEL PEAK 42(18Q21.2) WILD-TYPE	142	34	23

Figure S31. Get High-res Image Gene #72: 'Del Peak 42(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

'Del Peak 43(18q22.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.83e-06 (Fisher's exact test), Q value = 0.0075

Table S32. Gene #73: 'Del Peak 43(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients	COLON	RECTUM
ALL	412	158
DEL PEAK 43(18Q22.1) MUTATED	242	124
DEL PEAK 43(18Q22.1) WILD-TYPE	170	34

Figure S32. Get High-res Image Gene #73: 'Del Peak 43(18q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 43(18q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.25e-12 (Fisher's exact test), Q value = 9.7e-10

Table S33. Gene #73: 'Del Peak 43(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA	RECTAL ADENOCARCINOMA	RECTAL MUCINOUS ADENOCARCINOMA
ALL	356	54	142	13
DEL PEAK 43(18Q22.1) MUTATED	229	12	114	9
DEL PEAK 43(18Q22.1) WILD-TYPE	127	42	28	4

Figure S33. Get High-res Image Gene #73: 'Del Peak 43(18q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

'Del Peak 43(18q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.06e-05 (Fisher's exact test), Q value = 0.016

Table S34. Gene #73: 'Del Peak 43(18q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	327	140	103
DEL PEAK 43(18Q22.1) MUTATED	184	103	79
DEL PEAK 43(18Q22.1) WILD-TYPE	143	37	24

Figure S34. Get High-res Image Gene #73: 'Del Peak 43(18q22.1) 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.clin.merged.picked.txt
Number of patients = 574
Number of copy number variation regions = 78
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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