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 68 peak regions and 10 clinical features across 413 patients, 34 significant findings detected with Q value < 0.25.

Amp Peak 11(13q12.13) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 12(13q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
Amp Peak 13(16p11.2) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Amp Peak 14(16q12.1) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Amp Peak 22(20q11.21) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 23(20q12) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Amp Peak 24(20q13.32) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 1(1p36.11) cnvs correlated to 'PATHOLOGICSPREAD(M)'.
Del Peak 9(4p16.2) cnvs correlated to 'Time to Death', 'PATHOLOGY.N', and 'PATHOLOGICSPREAD(M)'.
Del Peak 13(5q21.3) cnvs correlated to 'PATHOLOGY.N'.
Del Peak 18(8p23.3) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Del Peak 19(8p22) cnvs correlated to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
Del Peak 21(8p11.21) cnvs correlated to 'PATHOLOGY.N'.
Del Peak 28(13q14.13) cnvs correlated to 'PATHOLOGICSPREAD(M)'.
Del Peak 35(17p12) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 37(18p11.31) cnvs correlated to 'HISTOLOGICAL.TYPE'.
Del Peak 38(18q12.2) cnvs correlated to 'HISTOLOGICAL.TYPE' and 'TUMOR.STAGE'.
Del Peak 39(18q21.2) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 40(18q22.1) cnvs correlated to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
Del Peak 41(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 68 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	GENDER	HISTOLOGICAL TYPE	PATHOLOGY T	PATHOLOGY N	PATHOLOGICSPREAD(M)	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION	NEOADJUVANT THERAPY
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 9(4p16 2)	121 (29%)	292	0.00024 (0.157)	0.609 (1.00)	0.59 (1.00)	0.036 (1.00)	0.671 (1.00)	0.000257 (0.168)	0.000266 (0.173)	0.000571 (0.365)	0.0247 (1.00)	0.877 (1.00)
Del Peak 35(17p12)	229 (55%)	184	0.334 (1.00)	0.0108 (1.00)	0.43 (1.00)	3.38e-06 (0.00227)	0.868 (1.00)	2.62e-05 (0.0174)	0.0165 (1.00)	1.15e-06 (0.000772)	0.257 (1.00)	0.2 (1.00)
Del Peak 39(18q21 2)	260 (63%)	153	0.4 (1.00)	0.0992 (1.00)	0.127 (1.00)	3.87e-09 (2.62e-06)	0.813 (1.00)	0.000105 (0.0694)	0.00624 (1.00)	8.87e-06 (0.00592)	0.299 (1.00)	0.558 (1.00)
Del Peak 40(18q22 1)	260 (63%)	153	0.263 (1.00)	0.176 (1.00)	0.127 (1.00)	4.48e-10 (3.04e-07)	0.813 (1.00)	0.000105 (0.0694)	0.00624 (1.00)	1.94e-05 (0.0129)	0.299 (1.00)	0.77 (1.00)
Amp Peak 12(13q22 1)	254 (62%)	159	0.0716 (1.00)	0.565 (1.00)	0.363 (1.00)	8.13e-06 (0.00543)	1 (1.00)	0.00146 (0.912)	0.00698 (1.00)	0.000308 (0.2)	0.288 (1.00)	0.562 (1.00)
Amp Peak 13(16p11 2)	116 (28%)	297	0.426 (1.00)	0.0688 (1.00)	0.584 (1.00)	0.00867 (1.00)	0.479 (1.00)	0.000133 (0.0872)	0.323 (1.00)	0.000155 (0.102)	1 (1.00)	0.156 (1.00)
Amp Peak 14(16q12 1)	102 (25%)	311	0.356 (1.00)	0.0166 (1.00)	0.493 (1.00)	0.0112 (1.00)	0.951 (1.00)	0.000188 (0.123)	0.18 (1.00)	2.82e-05 (0.0188)	0.574 (1.00)	0.0713 (1.00)
Del Peak 18(8p23 3)	171 (41%)	242	0.566 (1.00)	0.251 (1.00)	0.193 (1.00)	0.0746 (1.00)	0.165 (1.00)	0.000318 (0.206)	0.0225 (1.00)	9.03e-05 (0.0596)	0.572 (1.00)	0.154 (1.00)
Del Peak 19(8p22)	185 (45%)	228	0.433 (1.00)	0.104 (1.00)	0.321 (1.00)	0.0185 (1.00)	0.223 (1.00)	8.04e-06 (0.00538)	0.00136 (0.855)	2.07e-07 (0.00014)	0.589 (1.00)	0.0898 (1.00)
Del Peak 38(18q12 2)	247 (60%)	166	0.983 (1.00)	0.0542 (1.00)	0.421 (1.00)	3.02e-10 (2.05e-07)	0.84 (1.00)	0.00201 (1.00)	0.0125 (1.00)	0.000369 (0.239)	0.277 (1.00)	0.773 (1.00)
Amp Peak 11(13q12 13)	250 (61%)	163	0.29 (1.00)	0.522 (1.00)	0.92 (1.00)	8.87e-07 (0.000598)	0.972 (1.00)	0.00316 (1.00)	0.00471 (1.00)	0.000458 (0.295)	0.282 (1.00)	0.47 (1.00)
Amp Peak 22(20q11 21)	296 (72%)	117	0.433 (1.00)	0.474 (1.00)	0.382 (1.00)	7.66e-06 (0.00513)	0.541 (1.00)	0.0241 (1.00)	0.0102 (1.00)	0.000849 (0.54)	0.562 (1.00)	1 (1.00)
Amp Peak 23(20q12)	297 (72%)	116	0.365 (1.00)	0.51 (1.00)	0.324 (1.00)	1.38e-06 (0.000926)	0.676 (1.00)	0.0286 (1.00)	0.00474 (1.00)	0.00057 (0.365)	0.563 (1.00)	0.754 (1.00)
Amp Peak 24(20q13 32)	300 (73%)	113	0.371 (1.00)	0.537 (1.00)	0.377 (1.00)	4.8e-06 (0.00322)	0.641 (1.00)	0.0179 (1.00)	0.00667 (1.00)	0.000552 (0.354)	0.565 (1.00)	0.874 (1.00)
Del Peak 1(1p36 11)	150 (36%)	263	0.0209 (1.00)	0.144 (1.00)	0.54 (1.00)	0.00362 (1.00)	0.66 (1.00)	0.00492 (1.00)	0.000122 (0.08)	0.000869 (0.551)	1 (1.00)	0.243 (1.00)
Del Peak 13(5q21 3)	117 (28%)	296	0.0728 (1.00)	0.0679 (1.00)	0.743 (1.00)	0.196 (1.00)	0.983 (1.00)	5.21e-05 (0.0345)	0.0201 (1.00)	0.000559 (0.358)	0.0223 (1.00)	0.0855 (1.00)
Del Peak 21(8p11 21)	43 (10%)	370	0.826 (1.00)	0.377 (1.00)	1 (1.00)	0.633 (1.00)	0.155 (1.00)	0.000288 (0.187)	0.00793 (1.00)	0.000868 (0.551)	0.282 (1.00)	0.644 (1.00)
Del Peak 28(13q14 13)	18 (4%)	395	0.312 (1.00)	0.279 (1.00)	1 (1.00)	1 (1.00)	0.719 (1.00)	0.0646 (1.00)	4.33e-05 (0.0287)	0.851 (1.00)	1 (1.00)	0.489 (1.00)
Del Peak 37(18p11 31)	220 (53%)	193	0.869 (1.00)	0.0199 (1.00)	1 (1.00)	8.39e-11 (5.71e-08)	0.822 (1.00)	0.0483 (1.00)	0.00385 (1.00)	0.00179 (1.00)	0.251 (1.00)	0.778 (1.00)
Del Peak 41(19p13 3)	57 (14%)	356	0.367 (1.00)	0.148 (1.00)	0.67 (1.00)	0.202 (1.00)	0.956 (1.00)	5.5e-05 (0.0363)	0.0321 (1.00)	0.00155 (0.968)	0.36 (1.00)	0.838 (1.00)
Amp Peak 1(2q33 1)	79 (19%)	334	0.0421 (1.00)	0.358 (1.00)	0.259 (1.00)	0.267 (1.00)	0.844 (1.00)	0.0211 (1.00)	0.639 (1.00)	0.0496 (1.00)	0.472 (1.00)	0.206 (1.00)
Amp Peak 2(5p13 2)	81 (20%)	332	0.344 (1.00)	0.234 (1.00)	0.322 (1.00)	0.856 (1.00)	0.525 (1.00)	0.0355 (1.00)	0.729 (1.00)	0.782 (1.00)	1 (1.00)	0.723 (1.00)
Amp Peak 3(5q22 3)	40 (10%)	373	0.975 (1.00)	0.768 (1.00)	0.74 (1.00)	0.332 (1.00)	0.787 (1.00)	0.204 (1.00)	0.00941 (1.00)	0.0708 (1.00)	0.264 (1.00)	0.812 (1.00)
Amp Peak 4(6p21 1)	89 (22%)	324	0.855 (1.00)	0.829 (1.00)	0.283 (1.00)	0.0505 (1.00)	0.575 (1.00)	0.00141 (0.882)	0.609 (1.00)	0.0104 (1.00)	0.00974 (1.00)	0.392 (1.00)
Amp Peak 5(8p11 23)	144 (35%)	269	0.875 (1.00)	0.293 (1.00)	0.757 (1.00)	0.168 (1.00)	0.795 (1.00)	0.744 (1.00)	0.569 (1.00)	0.931 (1.00)	0.279 (1.00)	0.656 (1.00)
Amp Peak 6(8p11 21)	173 (42%)	240	0.419 (1.00)	0.449 (1.00)	0.272 (1.00)	0.184 (1.00)	0.762 (1.00)	0.562 (1.00)	0.466 (1.00)	0.962 (1.00)	0.574 (1.00)	0.668 (1.00)
Amp Peak 7(8q12 1)	215 (52%)	198	0.858 (1.00)	0.113 (1.00)	0.844 (1.00)	0.0189 (1.00)	0.421 (1.00)	0.363 (1.00)	0.158 (1.00)	0.395 (1.00)	0.249 (1.00)	0.202 (1.00)
Amp Peak 8(8q24 21)	239 (58%)	174	0.637 (1.00)	0.074 (1.00)	0.485 (1.00)	0.0753 (1.00)	0.2 (1.00)	0.287 (1.00)	0.0847 (1.00)	0.249 (1.00)	0.267 (1.00)	0.39 (1.00)
Amp Peak 9(11p15 5)	86 (21%)	327	0.603 (1.00)	0.0407 (1.00)	0.544 (1.00)	0.00194 (1.00)	0.151 (1.00)	0.279 (1.00)	0.254 (1.00)	0.154 (1.00)	0.111 (1.00)	1 (1.00)
Amp Peak 10(12p13 33)	104 (25%)	309	0.2 (1.00)	0.139 (1.00)	0.734 (1.00)	0.501 (1.00)	0.159 (1.00)	0.14 (1.00)	0.2 (1.00)	0.113 (1.00)	0.575 (1.00)	0.145 (1.00)
Amp Peak 15(17q12)	101 (24%)	312	0.479 (1.00)	0.45 (1.00)	0.252 (1.00)	0.313 (1.00)	0.247 (1.00)	0.113 (1.00)	0.0126 (1.00)	0.0169 (1.00)	0.57 (1.00)	0.00513 (1.00)
Amp Peak 16(17q24 1)	92 (22%)	321	0.076 (1.00)	0.414 (1.00)	0.638 (1.00)	0.112 (1.00)	0.409 (1.00)	0.342 (1.00)	0.0351 (1.00)	0.209 (1.00)	0.531 (1.00)	0.000501 (0.322)
Amp Peak 17(19p13 2)	65 (16%)	348	0.63 (1.00)	0.618 (1.00)	0.0575 (1.00)	0.228 (1.00)	0.669 (1.00)	0.0189 (1.00)	0.00672 (1.00)	0.228 (1.00)	0.403 (1.00)	0.00146 (0.912)
Amp Peak 18(19q13 11)	83 (20%)	330	0.201 (1.00)	0.68 (1.00)	0.0648 (1.00)	0.364 (1.00)	0.945 (1.00)	0.13 (1.00)	0.0224 (1.00)	0.489 (1.00)	0.491 (1.00)	0.0758 (1.00)
Amp Peak 19(20p12 3)	184 (45%)	229	0.0533 (1.00)	0.491 (1.00)	0.197 (1.00)	0.0554 (1.00)	0.97 (1.00)	0.0801 (1.00)	0.00371 (1.00)	0.00696 (1.00)	0.0876 (1.00)	0.395 (1.00)
Amp Peak 20(20p11 23)	205 (50%)	208	0.234 (1.00)	0.974 (1.00)	0.2 (1.00)	0.0127 (1.00)	0.952 (1.00)	0.061 (1.00)	0.00206 (1.00)	0.00871 (1.00)	0.121 (1.00)	0.259 (1.00)
Amp Peak 21(20p11 21)	230 (56%)	183	0.453 (1.00)	0.466 (1.00)	0.165 (1.00)	0.00494 (1.00)	0.905 (1.00)	0.276 (1.00)	0.00305 (1.00)	0.013 (1.00)	0.258 (1.00)	0.478 (1.00)
Del Peak 2(1p33)	107 (26%)	306	0.00122 (0.766)	0.89 (1.00)	0.91 (1.00)	0.132 (1.00)	0.512 (1.00)	0.00453 (1.00)	0.00786 (1.00)	0.0143 (1.00)	0.572 (1.00)	0.419 (1.00)
Del Peak 3(1p13 1)	103 (25%)	310	0.0503 (1.00)	0.891 (1.00)	0.496 (1.00)	0.133 (1.00)	0.545 (1.00)	0.00101 (0.634)	0.000797 (0.508)	0.00853 (1.00)	1 (1.00)	0.513 (1.00)
Del Peak 4(1q43)	44 (11%)	369	0.488 (1.00)	0.525 (1.00)	0.875 (1.00)	0.818 (1.00)	0.286 (1.00)	0.181 (1.00)	0.077 (1.00)	0.156 (1.00)	0.287 (1.00)	0.818 (1.00)
Del Peak 5(2q37 2)	21 (5%)	392	0.368 (1.00)	0.447 (1.00)	0.374 (1.00)	0.748 (1.00)	0.447 (1.00)	0.86 (1.00)	0.361 (1.00)	0.462 (1.00)	1 (1.00)	0.056 (1.00)
Del Peak 6(3p26 1)	60 (15%)	353	0.000411 (0.266)	0.346 (1.00)	1 (1.00)	0.146 (1.00)	0.0576 (1.00)	0.0189 (1.00)	0.000457 (0.295)	0.000506 (0.325)	1 (1.00)	0.547 (1.00)
Del Peak 7(3p14 2)	75 (18%)	338	0.426 (1.00)	0.608 (1.00)	0.371 (1.00)	0.186 (1.00)	0.186 (1.00)	0.0474 (1.00)	0.0569 (1.00)	0.0517 (1.00)	1 (1.00)	0.584 (1.00)
Del Peak 8(3q26 31)	39 (9%)	374	0.452 (1.00)	0.85 (1.00)	1 (1.00)	0.14 (1.00)	0.0927 (1.00)	0.593 (1.00)	0.619 (1.00)	0.165 (1.00)	1 (1.00)	0.63 (1.00)
Del Peak 10(4q22 1)	126 (31%)	287	0.009 (1.00)	0.967 (1.00)	0.593 (1.00)	0.0174 (1.00)	0.341 (1.00)	0.00174 (1.00)	0.118 (1.00)	0.0167 (1.00)	0.0279 (1.00)	0.539 (1.00)
Del Peak 11(4q35 1)	137 (33%)	276	0.0437 (1.00)	0.255 (1.00)	0.249 (1.00)	0.0871 (1.00)	0.721 (1.00)	0.00591 (1.00)	0.221 (1.00)	0.042 (1.00)	0.036 (1.00)	0.176 (1.00)
Del Peak 12(5q11 2)	91 (22%)	322	0.0477 (1.00)	0.0453 (1.00)	0.408 (1.00)	0.112 (1.00)	0.901 (1.00)	0.00305 (1.00)	0.0574 (1.00)	0.00873 (1.00)	0.124 (1.00)	0.0873 (1.00)
Del Peak 14(5q23 1)	107 (26%)	306	0.129 (1.00)	0.285 (1.00)	0.311 (1.00)	0.0983 (1.00)	0.958 (1.00)	0.00587 (1.00)	0.0116 (1.00)	0.0362 (1.00)	0.017 (1.00)	0.521 (1.00)
Del Peak 15(6p25 3)	54 (13%)	359	0.704 (1.00)	0.0948 (1.00)	0.0794 (1.00)	0.516 (1.00)	0.122 (1.00)	0.937 (1.00)	0.18 (1.00)	0.838 (1.00)	1 (1.00)	0.4 (1.00)
Del Peak 16(6q26)	60 (15%)	353	0.0205 (1.00)	0.928 (1.00)	0.782 (1.00)	1 (1.00)	0.197 (1.00)	0.0241 (1.00)	0.0212 (1.00)	0.111 (1.00)	1 (1.00)	0.69 (1.00)
Del Peak 17(7q31 1)	11 (3%)	402	0.978 (1.00)	0.589 (1.00)	0.36 (1.00)	1 (1.00)	0.571 (1.00)	1 (1.00)	0.498 (1.00)	0.493 (1.00)	1 (1.00)	0.191 (1.00)
Del Peak 20(8p11 22)	80 (19%)	333	0.412 (1.00)	0.236 (1.00)	0.803 (1.00)	0.461 (1.00)	0.344 (1.00)	0.000878 (0.556)	0.0887 (1.00)	0.00256 (1.00)	0.0973 (1.00)	0.209 (1.00)
Del Peak 22(9p21 3)	56 (14%)	357	0.0248 (1.00)	0.0603 (1.00)	0.251 (1.00)	0.202 (1.00)	0.3 (1.00)	0.147 (1.00)	0.106 (1.00)	0.404 (1.00)	1 (1.00)	1 (1.00)
Del Peak 23(10p15 3)	68 (16%)	345	0.847 (1.00)	0.434 (1.00)	0.791 (1.00)	0.557 (1.00)	0.852 (1.00)	0.00165 (1.00)	0.00231 (1.00)	0.00103 (0.65)	0.0717 (1.00)	0.343 (1.00)
Del Peak 24(10q21 1)	82 (20%)	331	0.959 (1.00)	0.0528 (1.00)	0.388 (1.00)	0.0995 (1.00)	0.955 (1.00)	0.00841 (1.00)	0.0976 (1.00)	0.0193 (1.00)	0.102 (1.00)	0.378 (1.00)
Del Peak 25(10q23 31)	94 (23%)	319	0.834 (1.00)	0.0124 (1.00)	0.483 (1.00)	0.164 (1.00)	0.505 (1.00)	0.00542 (1.00)	0.00814 (1.00)	0.0217 (1.00)	0.131 (1.00)	0.0625 (1.00)
Del Peak 26(10q25 2)	93 (23%)	320	0.313 (1.00)	0.164 (1.00)	0.907 (1.00)	0.164 (1.00)	0.222 (1.00)	0.00362 (1.00)	0.0681 (1.00)	0.0166 (1.00)	0.129 (1.00)	0.501 (1.00)
Del Peak 27(12p13 2)	44 (11%)	369	0.384 (1.00)	0.633 (1.00)	0.338 (1.00)	0.00188 (1.00)	0.899 (1.00)	0.0827 (1.00)	0.166 (1.00)	0.0936 (1.00)	1 (1.00)	0.818 (1.00)
Del Peak 29(14q32 11)	133 (32%)	280	0.353 (1.00)	0.506 (1.00)	0.674 (1.00)	0.000917 (0.579)	0.634 (1.00)	0.0616 (1.00)	0.0367 (1.00)	0.00428 (1.00)	0.554 (1.00)	0.652 (1.00)
Del Peak 30(15q11 2)	160 (39%)	253	0.93 (1.00)	0.852 (1.00)	1 (1.00)	0.0238 (1.00)	0.916 (1.00)	0.0112 (1.00)	0.0635 (1.00)	0.00316 (1.00)	0.0575 (1.00)	0.471 (1.00)
Del Peak 31(15q21 1)	151 (37%)	262	0.0937 (1.00)	0.658 (1.00)	0.919 (1.00)	0.0488 (1.00)	0.97 (1.00)	0.0832 (1.00)	0.0887 (1.00)	0.0555 (1.00)	0.0483 (1.00)	0.463 (1.00)
Del Peak 32(15q22 33)	145 (35%)	268	0.255 (1.00)	0.426 (1.00)	0.918 (1.00)	0.00592 (1.00)	0.583 (1.00)	0.0426 (1.00)	0.0478 (1.00)	0.0216 (1.00)	0.0427 (1.00)	0.657 (1.00)
Del Peak 33(16p13 3)	45 (11%)	368	0.00179 (1.00)	0.426 (1.00)	0.755 (1.00)	1 (1.00)	0.0342 (1.00)	0.0628 (1.00)	0.357 (1.00)	0.162 (1.00)	1 (1.00)	0.82 (1.00)
Del Peak 34(16q23 1)	49 (12%)	364	0.00129 (0.808)	0.288 (1.00)	0.129 (1.00)	0.261 (1.00)	0.63 (1.00)	0.389 (1.00)	0.979 (1.00)	0.905 (1.00)	1 (1.00)	1 (1.00)
Del Peak 36(17q24 3)	59 (14%)	354	0.729 (1.00)	0.51 (1.00)	0.328 (1.00)	1 (1.00)	0.682 (1.00)	0.00818 (1.00)	0.253 (1.00)	0.0319 (1.00)	1 (1.00)	0.227 (1.00)
Del Peak 42(20p12 1)	79 (19%)	334	0.803 (1.00)	0.439 (1.00)	0.618 (1.00)	0.137 (1.00)	0.697 (1.00)	0.569 (1.00)	0.983 (1.00)	0.417 (1.00)	1 (1.00)	0.721 (1.00)
Del Peak 43(21q11 2)	125 (30%)	288	0.468 (1.00)	0.722 (1.00)	1 (1.00)	0.0101 (1.00)	0.269 (1.00)	0.0408 (1.00)	0.344 (1.00)	0.187 (1.00)	0.219 (1.00)	0.538 (1.00)
Del Peak 44(22q13 32)	138 (33%)	275	0.208 (1.00)	0.701 (1.00)	0.603 (1.00)	0.00499 (1.00)	0.734 (1.00)	0.00263 (1.00)	0.0348 (1.00)	0.0137 (1.00)	1 (1.00)	0.765 (1.00)

'Amp Peak 11(13q12.13) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.87e-07 (Fisher's exact test), Q value = 6e-04

Table S1. Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
AMP PEAK 11(13Q12.13) MUTATED	233	16
AMP PEAK 11(13Q12.13) WILD-TYPE	123	38

Figure S1. Get High-res Image Gene #11: 'Amp Peak 11(13q12.13) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(13q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.13e-06 (Fisher's exact test), Q value = 0.0054

Table S2. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
AMP PEAK 12(13Q22.1) MUTATED	235	18
AMP PEAK 12(13Q22.1) WILD-TYPE	121	36

Figure S2. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(13q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000308 (Fisher's exact test), Q value = 0.2

Table S3. Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
AMP PEAK 12(13Q22.1) MUTATED	40	79	78	45
AMP PEAK 12(13Q22.1) WILD-TYPE	27	78	38	11

Figure S3. Get High-res Image Gene #12: 'Amp Peak 12(13q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 13(16p11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000133 (Fisher's exact test), Q value = 0.087

Table S4. Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
AMP PEAK 13(16P11.2) MUTATED	50	35	30
AMP PEAK 13(16P11.2) WILD-TYPE	195	60	41

Figure S4. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Amp Peak 13(16p11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000155 (Fisher's exact test), Q value = 0.1

Table S5. Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
AMP PEAK 13(16P11.2) MUTATED	12	30	48	18
AMP PEAK 13(16P11.2) WILD-TYPE	55	127	68	38

Figure S5. Get High-res Image Gene #13: 'Amp Peak 13(16p11.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 14(16q12.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000188 (Fisher's exact test), Q value = 0.12

Table S6. Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
AMP PEAK 14(16Q12.1) MUTATED	43	33	26
AMP PEAK 14(16Q12.1) WILD-TYPE	202	62	45

Figure S6. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Amp Peak 14(16q12.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.82e-05 (Fisher's exact test), Q value = 0.019

Table S7. Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
AMP PEAK 14(16Q12.1) MUTATED	12	23	46	14
AMP PEAK 14(16Q12.1) WILD-TYPE	55	134	70	42

Figure S7. Get High-res Image Gene #14: 'Amp Peak 14(16q12.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Amp Peak 22(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.66e-06 (Fisher's exact test), Q value = 0.0051

Table S8. Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
AMP PEAK 22(20Q11.21) MUTATED	269	24
AMP PEAK 22(20Q11.21) WILD-TYPE	87	30

Figure S8. Get High-res Image Gene #22: 'Amp Peak 22(20q11.21) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(20q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.38e-06 (Fisher's exact test), Q value = 0.00093

Table S9. Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
AMP PEAK 23(20Q12) MUTATED	271	23
AMP PEAK 23(20Q12) WILD-TYPE	85	31

Figure S9. Get High-res Image Gene #23: 'Amp Peak 23(20q12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(20q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.8e-06 (Fisher's exact test), Q value = 0.0032

Table S10. Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
AMP PEAK 24(20Q13.32) MUTATED	273	24
AMP PEAK 24(20Q13.32) WILD-TYPE	83	30

Figure S10. Get High-res Image Gene #24: 'Amp Peak 24(20q13.32) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 1(1p36.11) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000122 (Chi-square test), Q value = 0.08

Table S11. Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
DEL PEAK 1(1P36.11) MUTATED	101	33	2	0	13
DEL PEAK 1(1P36.11) WILD-TYPE	211	16	5	1	23

Figure S11. Get High-res Image Gene #25: 'Del Peak 1(1p36.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 9(4p16.2) mutation analysis' versus 'Time to Death'

P value = 0.00024 (logrank test), Q value = 0.16

Table S12. Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	319	49	0.1 - 135.5 (7.7)
DEL PEAK 9(4P16.2) MUTATED	89	20	0.2 - 87.8 (7.6)
DEL PEAK 9(4P16.2) WILD-TYPE	230	29	0.1 - 135.5 (8.0)

Figure S12. Get High-res Image Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 9(4p16.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000257 (Fisher's exact test), Q value = 0.17

Table S13. Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 9(4P16.2) MUTATED	54	34	32
DEL PEAK 9(4P16.2) WILD-TYPE	191	61	39

Figure S13. Get High-res Image Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 9(4p16.2) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000266 (Chi-square test), Q value = 0.17

Table S14. Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
DEL PEAK 9(4P16.2) MUTATED	75	27	3	0	12
DEL PEAK 9(4P16.2) WILD-TYPE	237	22	4	1	24

Figure S14. Get High-res Image Gene #33: 'Del Peak 9(4p16.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 13(5q21.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.21e-05 (Fisher's exact test), Q value = 0.034

Table S15. Gene #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 13(5Q21.3) MUTATED	50	34	32
DEL PEAK 13(5Q21.3) WILD-TYPE	195	61	39

Figure S15. Get High-res Image Gene #37: 'Del Peak 13(5q21.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 18(8p23.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000318 (Fisher's exact test), Q value = 0.21

Table S16. Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 18(8P23.3) MUTATED	82	46	41
DEL PEAK 18(8P23.3) WILD-TYPE	163	49	30

Figure S16. Get High-res Image Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 18(8p23.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 9.03e-05 (Fisher's exact test), Q value = 0.06

Table S17. Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 18(8P23.3) MUTATED	24	48	59	34
DEL PEAK 18(8P23.3) WILD-TYPE	43	109	57	22

Figure S17. Get High-res Image Gene #42: 'Del Peak 18(8p23.3) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

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

P value = 8.04e-06 (Fisher's exact test), Q value = 0.0054

Table S18. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 19(8P22) MUTATED	87	49	47
DEL PEAK 19(8P22) WILD-TYPE	158	46	24

Figure S18. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

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

P value = 2.07e-07 (Fisher's exact test), Q value = 0.00014

Table S19. Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 19(8P22) MUTATED	24	50	66	39
DEL PEAK 19(8P22) WILD-TYPE	43	107	50	17

Figure S19. Get High-res Image Gene #43: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 21(8p11.21) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000288 (Fisher's exact test), Q value = 0.19

Table S20. Gene #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 21(8P11.21) MUTATED	14	14	15
DEL PEAK 21(8P11.21) WILD-TYPE	231	81	56

Figure S20. Get High-res Image Gene #45: 'Del Peak 21(8p11.21) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 28(13q14.13) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 4.33e-05 (Chi-square test), Q value = 0.029

Table S21. Gene #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

nPatients	M0	M1	M1A	M1B	MX
ALL	312	49	7	1	36
DEL PEAK 28(13Q14.13) MUTATED	12	1	0	1	2
DEL PEAK 28(13Q14.13) WILD-TYPE	300	48	7	0	34

Figure S21. Get High-res Image Gene #52: 'Del Peak 28(13q14.13) mutation analysis' versus Clinical Feature #7: 'PATHOLOGICSPREAD(M)'

'Del Peak 35(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.38e-06 (Fisher's exact test), Q value = 0.0023

Table S22. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
DEL PEAK 35(17P12) MUTATED	213	14
DEL PEAK 35(17P12) WILD-TYPE	143	40

Figure S22. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 35(17p12) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.62e-05 (Fisher's exact test), Q value = 0.017

Table S23. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 35(17P12) MUTATED	113	63	51
DEL PEAK 35(17P12) WILD-TYPE	132	32	20

Figure S23. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 35(17p12) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00077

Table S24. Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 35(17P12) MUTATED	34	64	80	41
DEL PEAK 35(17P12) WILD-TYPE	33	93	36	15

Figure S24. Get High-res Image Gene #59: 'Del Peak 35(17p12) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 37(18p11.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.39e-11 (Fisher's exact test), Q value = 5.7e-08

Table S25. Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
DEL PEAK 37(18P11.31) MUTATED	211	7
DEL PEAK 37(18P11.31) WILD-TYPE	145	47

Figure S25. Get High-res Image Gene #61: 'Del Peak 37(18p11.31) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 38(18q12.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.02e-10 (Fisher's exact test), Q value = 2e-07

Table S26. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
DEL PEAK 38(18Q12.2) MUTATED	235	11
DEL PEAK 38(18Q12.2) WILD-TYPE	121	43

Figure S26. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 38(18q12.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000369 (Fisher's exact test), Q value = 0.24

Table S27. Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 38(18Q12.2) MUTATED	34	78	78	43
DEL PEAK 38(18Q12.2) WILD-TYPE	33	79	38	13

Figure S27. Get High-res Image Gene #62: 'Del Peak 38(18q12.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 39(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.87e-09 (Fisher's exact test), Q value = 2.6e-06

Table S28. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
DEL PEAK 39(18Q21.2) MUTATED	245	14
DEL PEAK 39(18Q21.2) WILD-TYPE	111	40

Figure S28. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 39(18q21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000105 (Fisher's exact test), Q value = 0.069

Table S29. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 39(18Q21.2) MUTATED	134	68	56
DEL PEAK 39(18Q21.2) WILD-TYPE	111	27	15

Figure S29. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 39(18q21.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 8.87e-06 (Fisher's exact test), Q value = 0.0059

Table S30. Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 39(18Q21.2) MUTATED	36	81	83	47
DEL PEAK 39(18Q21.2) WILD-TYPE	31	76	33	9

Figure S30. Get High-res Image Gene #63: 'Del Peak 39(18q21.2) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 40(18q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.48e-10 (Fisher's exact test), Q value = 3e-07

Table S31. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

nPatients	COLON ADENOCARCINOMA	COLON MUCINOUS ADENOCARCINOMA
ALL	356	54
DEL PEAK 40(18Q22.1) MUTATED	246	13
DEL PEAK 40(18Q22.1) WILD-TYPE	110	41

Figure S31. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #4: 'HISTOLOGICAL.TYPE'

'Del Peak 40(18q22.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.000105 (Fisher's exact test), Q value = 0.069

Table S32. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 40(18Q22.1) MUTATED	134	68	56
DEL PEAK 40(18Q22.1) WILD-TYPE	111	27	15

Figure S32. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

'Del Peak 40(18q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.94e-05 (Fisher's exact test), Q value = 0.013

Table S33. Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

nPatients	I	II	III	IV
ALL	67	157	116	56
DEL PEAK 40(18Q22.1) MUTATED	36	82	82	47
DEL PEAK 40(18Q22.1) WILD-TYPE	31	75	34	9

Figure S33. Get High-res Image Gene #64: 'Del Peak 40(18q22.1) mutation analysis' versus Clinical Feature #8: 'TUMOR.STAGE'

'Del Peak 41(19p13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.5e-05 (Fisher's exact test), Q value = 0.036

Table S34. Gene #65: 'Del Peak 41(19p13.3) mutation analysis' versus Clinical Feature #6: 'PATHOLOGY.N'

nPatients	N0	N1	N2
ALL	245	95	71
DEL PEAK 41(19P13.3) MUTATED	22	13	22
DEL PEAK 41(19P13.3) WILD-TYPE	223	82	49

Figure S34. Get High-res Image Gene #65: 'Del Peak 41(19p13.3) mutation analysis' versus Clinical Feature #6: '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 = COAD.clin.merged.picked.txt
Number of patients = 413
Number of copy number variation regions = 68
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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