Correlation between copy number variation genes (focal) and selected clinical features

Overview

Introduction

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

Summary

Testing the association between subtypes identified by 75 different clustering approaches and 10 clinical features across 575 patients, 53 significant findings detected with Q value < 0.25.

2 subtypes identified in current cancer cohort by 'Amp Peak 1(1q31.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 2(2q33.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 3(5p12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 4(5q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 5(6p21.1) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 6(7p21.3) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 7(8p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 8(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 9(8q12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 10(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 11(10q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 12(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 13(12p13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 14(13q12.13) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 15(13q12.2) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 16(13q22.1) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE' and 'PATHOLOGY.N'.
2 subtypes identified in current cancer cohort by 'Amp Peak 17(15q26.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 18(16p11.2) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N' and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 19(17q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 20(17q24.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 21(19p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 22(19q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 23(20p11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 24(20p11.21) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 25(20q11.21) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 26(20q12) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 27(20q13.32) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 28(Xq28) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.11) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 2(1p33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 3(1p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 4(2p12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 5(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 6(2q37.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 7(3p26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 8(3p14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 9(3q26.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 10(4p16.1) mutation analysis'. These subtypes correlate to 'RADIATIONS.RADIATION.REGIMENINDICATION'.
2 subtypes identified in current cancer cohort by 'Del Peak 11(4q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 12(4q35.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 13(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 14(5q22.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 15(6p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 16(6q26) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 17(7q31.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 18(8p23.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 19(8p22) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 20(8p11.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 21(8q11.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 22(9p24.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 23(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 24(10q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 25(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 26(10q25.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 27(11q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 28(12p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 29(12q21.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 30(14q22.1) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE'.
2 subtypes identified in current cancer cohort by 'Del Peak 31(15q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 32(15q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 33(15q22.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 34(16p13.3) mutation analysis'. These subtypes correlate to 'Time to Death'.
2 subtypes identified in current cancer cohort by 'Del Peak 35(16q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 36(17p12) mutation analysis'. These subtypes correlate to 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 37(17q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 38(18p11.31) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.
2 subtypes identified in current cancer cohort by 'Del Peak 39(18q12.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 40(18q21.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 41(18q22.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', and 'TUMOR.STAGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 42(19p13.3) mutation analysis'. These subtypes correlate to 'PATHOLOGY.N'.
2 subtypes identified in current cancer cohort by 'Del Peak 43(19q13.43) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 44(20p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 45(20p12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 46(21q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 47(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 75 different clustering approaches 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
Statistical Tests	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
Amp Peak 1(1q31 1)	0.466 (1.00)	0.292 (1.00)	0.0268 (1.00)	0.236 (1.00)	0.0946 (1.00)	0.381 (1.00)	0.0539 (1.00)	0.175 (1.00)	0.0343 (1.00)	0.0357 (1.00)
Amp Peak 2(2q33 1)	0.135 (1.00)	0.385 (1.00)	0.031 (1.00)	1 (1.00)	0.00379 (1.00)	0.686 (1.00)	0.00128 (0.868)	0.541 (1.00)	0.0227 (1.00)	0.103 (1.00)
Amp Peak 3(5p12)	0.0162 (1.00)	0.372 (1.00)	0.151 (1.00)	0.748 (1.00)	0.0568 (1.00)	0.396 (1.00)	0.0431 (1.00)	0.354 (1.00)	0.191 (1.00)	0.379 (1.00)
Amp Peak 4(5q22 3)	0.75 (1.00)	0.865 (1.00)	0.445 (1.00)	0.891 (1.00)	0.316 (1.00)	0.907 (1.00)	0.176 (1.00)	0.032 (1.00)	0.12 (1.00)	1 (1.00)
Amp Peak 5(6p21 1)	0.489 (1.00)	0.682 (1.00)	0.0314 (1.00)	0.15 (1.00)	0.00236 (1.00)	0.215 (1.00)	3.17e-05 (0.0228)	0.109 (1.00)	0.000331 (0.231)	0.00136 (0.912)
Amp Peak 6(7p21 3)	0.304 (1.00)	0.103 (1.00)	0.0292 (1.00)	0.734 (1.00)	0.000225 (0.157)	0.889 (1.00)	1.23e-05 (0.00888)	0.0274 (1.00)	4.42e-06 (0.00322)	0.0882 (1.00)
Amp Peak 7(8p11 23)	0.472 (1.00)	0.752 (1.00)	0.625 (1.00)	0.482 (1.00)	0.232 (1.00)	0.409 (1.00)	0.503 (1.00)	0.413 (1.00)	0.88 (1.00)	0.498 (1.00)
Amp Peak 8(8p11 21)	0.633 (1.00)	0.597 (1.00)	0.636 (1.00)	0.204 (1.00)	0.12 (1.00)	0.5 (1.00)	0.333 (1.00)	0.305 (1.00)	0.475 (1.00)	0.742 (1.00)
Amp Peak 9(8q12 1)	0.907 (1.00)	0.19 (1.00)	0.303 (1.00)	0.615 (1.00)	0.0093 (1.00)	0.128 (1.00)	0.0853 (1.00)	0.0256 (1.00)	0.0726 (1.00)	0.0423 (1.00)
Amp Peak 10(8q24 21)	0.545 (1.00)	0.236 (1.00)	0.0863 (1.00)	0.394 (1.00)	0.0113 (1.00)	0.143 (1.00)	0.171 (1.00)	0.0551 (1.00)	0.233 (1.00)	0.0931 (1.00)
Amp Peak 11(10q22 3)	0.819 (1.00)	0.303 (1.00)	1 (1.00)	0.487 (1.00)	0.932 (1.00)	0.141 (1.00)	0.00814 (1.00)	0.912 (1.00)	0.116 (1.00)	0.434 (1.00)
Amp Peak 12(11p15 5)	0.709 (1.00)	0.0608 (1.00)	0.145 (1.00)	0.549 (1.00)	0.00144 (0.964)	0.293 (1.00)	0.712 (1.00)	0.385 (1.00)	0.808 (1.00)	0.12 (1.00)
Amp Peak 13(12p13 32)	0.26 (1.00)	0.0696 (1.00)	0.829 (1.00)	0.5 (1.00)	0.351 (1.00)	0.387 (1.00)	0.0536 (1.00)	0.0859 (1.00)	0.0625 (1.00)	0.698 (1.00)
Amp Peak 14(13q12 13)	0.126 (1.00)	0.314 (1.00)	0.00246 (1.00)	0.727 (1.00)	1.18e-09 (8.74e-07)	0.561 (1.00)	3.88e-05 (0.0278)	0.0101 (1.00)	7.49e-05 (0.0532)	1 (1.00)
Amp Peak 15(13q12 2)	0.101 (1.00)	0.239 (1.00)	0.00188 (1.00)	0.543 (1.00)	2.61e-09 (1.93e-06)	0.533 (1.00)	9.03e-05 (0.0639)	0.023 (1.00)	0.000184 (0.129)	1 (1.00)
Amp Peak 16(13q22 1)	0.0454 (1.00)	0.444 (1.00)	0.0249 (1.00)	0.221 (1.00)	3.13e-08 (2.31e-05)	0.736 (1.00)	0.000127 (0.0895)	0.024 (1.00)	0.0006 (0.416)	0.503 (1.00)
Amp Peak 17(15q26 1)	0.0824 (1.00)	0.753 (1.00)	0.291 (1.00)	0.0582 (1.00)	0.433 (1.00)	0.287 (1.00)	0.00409 (1.00)	0.649 (1.00)	0.198 (1.00)	0.141 (1.00)
Amp Peak 18(16p11 2)	0.838 (1.00)	0.26 (1.00)	0.918 (1.00)	0.71 (1.00)	0.0024 (1.00)	0.721 (1.00)	5.82e-05 (0.0415)	0.111 (1.00)	8.54e-05 (0.0605)	0.715 (1.00)
Amp Peak 19(17q12)	0.489 (1.00)	0.363 (1.00)	0.591 (1.00)	0.101 (1.00)	0.457 (1.00)	0.417 (1.00)	0.152 (1.00)	0.0117 (1.00)	0.0158 (1.00)	0.462 (1.00)
Amp Peak 20(17q24 1)	0.0431 (1.00)	0.245 (1.00)	0.911 (1.00)	0.617 (1.00)	0.0878 (1.00)	0.771 (1.00)	0.886 (1.00)	0.0549 (1.00)	0.219 (1.00)	0.691 (1.00)
Amp Peak 21(19p13 2)	0.144 (1.00)	0.493 (1.00)	0.216 (1.00)	0.182 (1.00)	0.0516 (1.00)	0.409 (1.00)	0.0339 (1.00)	0.233 (1.00)	0.126 (1.00)	1 (1.00)
Amp Peak 22(19q12)	0.628 (1.00)	0.941 (1.00)	0.256 (1.00)	0.185 (1.00)	0.0293 (1.00)	0.654 (1.00)	0.0943 (1.00)	0.139 (1.00)	0.226 (1.00)	0.692 (1.00)
Amp Peak 23(20p11 23)	0.699 (1.00)	0.921 (1.00)	0.0194 (1.00)	0.0364 (1.00)	0.00072 (0.495)	0.873 (1.00)	0.0368 (1.00)	0.00134 (0.901)	0.011 (1.00)	0.181 (1.00)
Amp Peak 24(20p11 21)	0.808 (1.00)	0.709 (1.00)	0.00784 (1.00)	0.0413 (1.00)	1.12e-05 (0.00815)	0.885 (1.00)	0.382 (1.00)	0.00312 (1.00)	0.0516 (1.00)	0.32 (1.00)
Amp Peak 25(20q11 21)	0.317 (1.00)	0.823 (1.00)	9.13e-06 (0.00664)	0.376 (1.00)	7.88e-12 (5.87e-09)	0.506 (1.00)	0.00141 (0.945)	0.00533 (1.00)	0.000107 (0.0757)	0.693 (1.00)
Amp Peak 26(20q12)	0.274 (1.00)	0.726 (1.00)	4.74e-06 (0.00345)	0.374 (1.00)	5.38e-13 (4.01e-10)	0.611 (1.00)	0.00101 (0.692)	0.00129 (0.869)	4.17e-05 (0.0298)	0.692 (1.00)
Amp Peak 27(20q13 32)	0.369 (1.00)	0.658 (1.00)	2.18e-05 (0.0158)	0.551 (1.00)	8.76e-12 (6.52e-09)	0.588 (1.00)	0.00158 (1.00)	0.00424 (1.00)	0.000131 (0.0922)	0.692 (1.00)
Amp Peak 28(Xq28)	0.245 (1.00)	0.209 (1.00)	0.421 (1.00)	0.838 (1.00)	0.0249 (1.00)	0.521 (1.00)	0.017 (1.00)	0.219 (1.00)	0.0635 (1.00)	0.693 (1.00)
Del Peak 1(1p36 11)	0.051 (1.00)	0.105 (1.00)	0.126 (1.00)	0.392 (1.00)	0.00644 (1.00)	0.238 (1.00)	0.000887 (0.607)	0.000615 (0.425)	0.000734 (0.503)	0.739 (1.00)
Del Peak 2(1p33)	0.0178 (1.00)	0.836 (1.00)	0.401 (1.00)	0.851 (1.00)	0.0797 (1.00)	0.226 (1.00)	0.00507 (1.00)	0.0106 (1.00)	0.0159 (1.00)	0.709 (1.00)
Del Peak 3(1p13 2)	0.0696 (1.00)	0.841 (1.00)	0.248 (1.00)	0.639 (1.00)	0.135 (1.00)	0.15 (1.00)	0.00213 (1.00)	0.00127 (0.86)	0.0162 (1.00)	0.265 (1.00)
Del Peak 4(2p12)	0.796 (1.00)	0.179 (1.00)	0.00346 (1.00)	0.821 (1.00)	0.0208 (1.00)	1 (1.00)	0.351 (1.00)	0.56 (1.00)	0.329 (1.00)	0.275 (1.00)
Del Peak 5(2q22 1)	0.85 (1.00)	0.564 (1.00)	0.842 (1.00)	0.474 (1.00)	0.927 (1.00)	0.669 (1.00)	0.609 (1.00)	0.689 (1.00)	0.174 (1.00)	1 (1.00)
Del Peak 6(2q37 2)	0.842 (1.00)	0.139 (1.00)	0.835 (1.00)	0.458 (1.00)	0.945 (1.00)	0.344 (1.00)	0.208 (1.00)	0.133 (1.00)	0.0449 (1.00)	1 (1.00)
Del Peak 7(3p26 3)	0.000643 (0.444)	0.855 (1.00)	0.691 (1.00)	0.723 (1.00)	0.19 (1.00)	0.0373 (1.00)	0.0192 (1.00)	0.00105 (0.712)	0.000684 (0.47)	0.131 (1.00)
Del Peak 8(3p14 2)	0.216 (1.00)	0.578 (1.00)	0.808 (1.00)	0.664 (1.00)	0.416 (1.00)	0.136 (1.00)	0.181 (1.00)	0.0317 (1.00)	0.0461 (1.00)	0.669 (1.00)
Del Peak 9(3q26 31)	0.714 (1.00)	0.996 (1.00)	0.874 (1.00)	0.0931 (1.00)	0.0423 (1.00)	0.0139 (1.00)	0.371 (1.00)	0.327 (1.00)	0.00215 (1.00)	0.216 (1.00)
Del Peak 10(4p16 1)	0.0406 (1.00)	0.954 (1.00)	0.0561 (1.00)	0.128 (1.00)	0.0277 (1.00)	0.985 (1.00)	0.00057 (0.396)	0.0131 (1.00)	0.00164 (1.00)	2.78e-05 (0.02)
Del Peak 11(4q22 1)	0.193 (1.00)	0.42 (1.00)	0.00417 (1.00)	0.187 (1.00)	0.00142 (0.95)	0.134 (1.00)	0.0018 (1.00)	0.369 (1.00)	0.0375 (1.00)	0.00114 (0.771)
Del Peak 12(4q35 1)	0.277 (1.00)	0.303 (1.00)	0.0325 (1.00)	0.863 (1.00)	0.021 (1.00)	0.702 (1.00)	0.00325 (1.00)	0.645 (1.00)	0.118 (1.00)	0.00185 (1.00)
Del Peak 13(5q11 2)	0.164 (1.00)	0.0866 (1.00)	0.0389 (1.00)	1 (1.00)	0.0275 (1.00)	0.976 (1.00)	0.0078 (1.00)	0.0232 (1.00)	0.0344 (1.00)	0.00103 (0.701)
Del Peak 14(5q22 2)	0.0866 (1.00)	0.359 (1.00)	0.155 (1.00)	0.648 (1.00)	0.0624 (1.00)	0.773 (1.00)	0.0168 (1.00)	0.0311 (1.00)	0.0332 (1.00)	0.000382 (0.266)
Del Peak 15(6p25 3)	0.611 (1.00)	0.0683 (1.00)	1 (1.00)	0.0876 (1.00)	0.544 (1.00)	0.261 (1.00)	0.534 (1.00)	0.326 (1.00)	0.223 (1.00)	0.351 (1.00)
Del Peak 16(6q26)	0.029 (1.00)	0.9 (1.00)	0.368 (1.00)	0.301 (1.00)	0.0485 (1.00)	0.0584 (1.00)	0.0136 (1.00)	0.0389 (1.00)	0.594 (1.00)	0.637 (1.00)
Del Peak 17(7q31 1)	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)	0.342 (1.00)	1 (1.00)
Del Peak 18(8p23 2)	0.619 (1.00)	0.205 (1.00)	2.4e-05 (0.0173)	0.18 (1.00)	2.9e-05 (0.0208)	0.081 (1.00)	2.78e-05 (0.02)	0.00989 (1.00)	3.4e-05 (0.0243)	0.0155 (1.00)
Del Peak 19(8p22)	0.597 (1.00)	0.317 (1.00)	0.000379 (0.265)	0.403 (1.00)	0.000256 (0.179)	0.0753 (1.00)	1.97e-06 (0.00144)	0.00381 (1.00)	1.24e-06 (0.000912)	0.0196 (1.00)
Del Peak 20(8p11 21)	0.598 (1.00)	0.329 (1.00)	0.031 (1.00)	0.542 (1.00)	0.167 (1.00)	0.535 (1.00)	0.00723 (1.00)	0.0823 (1.00)	0.027 (1.00)	0.414 (1.00)
Del Peak 21(8q11 1)	0.889 (1.00)	0.382 (1.00)	0.16 (1.00)	0.208 (1.00)	0.418 (1.00)	0.714 (1.00)	0.0274 (1.00)	0.00202 (1.00)	0.0962 (1.00)	0.514 (1.00)
Del Peak 22(9p24 2)	0.00207 (1.00)	0.12 (1.00)	0.496 (1.00)	0.0507 (1.00)	0.452 (1.00)	0.497 (1.00)	0.136 (1.00)	0.0231 (1.00)	0.291 (1.00)	0.351 (1.00)
Del Peak 23(10p15 3)	0.577 (1.00)	0.0282 (1.00)	0.271 (1.00)	0.913 (1.00)	0.364 (1.00)	0.721 (1.00)	0.00713 (1.00)	0.181 (1.00)	0.00847 (1.00)	0.00145 (0.967)
Del Peak 24(10q21 1)	0.869 (1.00)	0.0152 (1.00)	0.421 (1.00)	0.535 (1.00)	0.118 (1.00)	0.723 (1.00)	0.164 (1.00)	0.682 (1.00)	0.368 (1.00)	0.00326 (1.00)
Del Peak 25(10q23 31)	0.566 (1.00)	0.00668 (1.00)	0.0408 (1.00)	0.923 (1.00)	0.0208 (1.00)	0.206 (1.00)	0.0139 (1.00)	0.0621 (1.00)	0.0977 (1.00)	0.0013 (0.874)
Del Peak 26(10q25 2)	0.756 (1.00)	0.0715 (1.00)	0.128 (1.00)	0.846 (1.00)	0.0324 (1.00)	0.218 (1.00)	0.0134 (1.00)	0.43 (1.00)	0.116 (1.00)	0.00103 (0.701)
Del Peak 27(11q22 3)	0.473 (1.00)	0.396 (1.00)	0.086 (1.00)	0.588 (1.00)	0.0532 (1.00)	0.39 (1.00)	0.0514 (1.00)	0.633 (1.00)	0.0927 (1.00)	0.061 (1.00)
Del Peak 28(12p13 1)	0.466 (1.00)	0.472 (1.00)	0.0256 (1.00)	0.327 (1.00)	0.000677 (0.467)	0.501 (1.00)	0.0319 (1.00)	0.1 (1.00)	0.208 (1.00)	0.344 (1.00)
Del Peak 29(12q21 2)	0.636 (1.00)	0.709 (1.00)	0.0779 (1.00)	0.717 (1.00)	0.00837 (1.00)	0.675 (1.00)	0.0185 (1.00)	0.0916 (1.00)	0.239 (1.00)	0.117 (1.00)
Del Peak 30(14q22 1)	0.208 (1.00)	0.233 (1.00)	0.0212 (1.00)	0.421 (1.00)	1.15e-06 (0.000842)	0.78 (1.00)	0.00362 (1.00)	0.145 (1.00)	0.175 (1.00)	0.725 (1.00)
Del Peak 31(15q11 2)	0.771 (1.00)	0.618 (1.00)	0.216 (1.00)	0.496 (1.00)	0.0549 (1.00)	0.804 (1.00)	0.0148 (1.00)	0.264 (1.00)	0.0414 (1.00)	0.035 (1.00)
Del Peak 32(15q21 1)	0.434 (1.00)	0.603 (1.00)	0.0355 (1.00)	0.305 (1.00)	0.0247 (1.00)	0.846 (1.00)	0.0271 (1.00)	0.228 (1.00)	0.125 (1.00)	0.0327 (1.00)
Del Peak 33(15q22 33)	0.555 (1.00)	0.327 (1.00)	0.012 (1.00)	0.667 (1.00)	0.00595 (1.00)	0.0968 (1.00)	0.00679 (1.00)	0.211 (1.00)	0.0235 (1.00)	0.00229 (1.00)
Del Peak 34(16p13 3)	4.34e-05 (0.031)	0.254 (1.00)	0.359 (1.00)	0.89 (1.00)	0.418 (1.00)	0.0689 (1.00)	0.132 (1.00)	0.381 (1.00)	0.101 (1.00)	0.609 (1.00)
Del Peak 35(16q23 1)	0.0014 (0.937)	0.264 (1.00)	0.402 (1.00)	0.167 (1.00)	0.515 (1.00)	0.252 (1.00)	0.775 (1.00)	0.951 (1.00)	0.465 (1.00)	1 (1.00)
Del Peak 36(17p12)	0.656 (1.00)	0.0983 (1.00)	0.00169 (1.00)	0.609 (1.00)	6.48e-08 (4.78e-05)	0.419 (1.00)	0.000121 (0.0856)	0.041 (1.00)	3.15e-05 (0.0226)	0.325 (1.00)
Del Peak 37(17q24 3)	0.731 (1.00)	0.305 (1.00)	0.793 (1.00)	0.0994 (1.00)	0.99 (1.00)	0.243 (1.00)	0.0075 (1.00)	0.352 (1.00)	0.0357 (1.00)	0.626 (1.00)
Del Peak 38(18p11 31)	0.98 (1.00)	0.059 (1.00)	1.82e-06 (0.00134)	1 (1.00)	1.53e-16 (1.14e-13)	0.882 (1.00)	0.0106 (1.00)	0.000584 (0.406)	0.000895 (0.611)	0.322 (1.00)
Del Peak 39(18q12 2)	0.942 (1.00)	0.0817 (1.00)	1.57e-09 (1.16e-06)	0.477 (1.00)	8.59e-18 (6.44e-15)	0.421 (1.00)	0.000131 (0.0922)	0.00447 (1.00)	6.82e-05 (0.0485)	0.034 (1.00)
Del Peak 40(18q21 2)	0.481 (1.00)	0.0823 (1.00)	1.07e-09 (7.95e-07)	0.145 (1.00)	3.7e-16 (2.77e-13)	0.315 (1.00)	1.95e-06 (0.00142)	0.00162 (1.00)	4.1e-07 (0.000302)	0.0637 (1.00)
Del Peak 41(18q22 1)	0.332 (1.00)	0.221 (1.00)	1.94e-07 (0.000143)	0.239 (1.00)	2.07e-15 (1.55e-12)	0.444 (1.00)	1.14e-05 (0.00828)	0.00238 (1.00)	4.68e-06 (0.00341)	0.0632 (1.00)
Del Peak 42(19p13 3)	0.406 (1.00)	0.183 (1.00)	0.0305 (1.00)	0.733 (1.00)	0.0678 (1.00)	0.407 (1.00)	7.64e-05 (0.0542)	0.0275 (1.00)	0.00312 (1.00)	0.641 (1.00)
Del Peak 43(19q13 43)	0.509 (1.00)	0.816 (1.00)	0.146 (1.00)	0.3 (1.00)	0.417 (1.00)	0.44 (1.00)	0.0156 (1.00)	0.0712 (1.00)	0.17 (1.00)	0.289 (1.00)
Del Peak 44(20p12 1)	0.108 (1.00)	0.631 (1.00)	0.0445 (1.00)	0.321 (1.00)	0.144 (1.00)	0.468 (1.00)	0.319 (1.00)	0.827 (1.00)	0.191 (1.00)	0.0632 (1.00)
Del Peak 45(20p12 1)	0.108 (1.00)	0.631 (1.00)	0.0445 (1.00)	0.321 (1.00)	0.144 (1.00)	0.468 (1.00)	0.319 (1.00)	0.827 (1.00)	0.191 (1.00)	0.0632 (1.00)
Del Peak 46(21q11 2)	0.515 (1.00)	0.721 (1.00)	0.00555 (1.00)	0.66 (1.00)	0.000632 (0.436)	0.824 (1.00)	0.0458 (1.00)	0.614 (1.00)	0.325 (1.00)	0.175 (1.00)
Del Peak 47(22q13 32)	0.04 (1.00)	0.672 (1.00)	0.173 (1.00)	0.93 (1.00)	0.00961 (1.00)	0.45 (1.00)	0.000791 (0.542)	0.0275 (1.00)	0.00938 (1.00)	0.727 (1.00)

Clustering Approach #1: 'Amp Peak 1(1q31.1) mutation analysis'

Table S1. Description of clustering approach #1: 'Amp Peak 1(1q31.1) mutation analysis'

Cluster Labels	AMP PEAK 1(1Q31.1) MUTATED	AMP PEAK 1(1Q31.1) WILD-TYPE
Number of samples	134	441

Clustering Approach #2: 'Amp Peak 2(2q33.1) mutation analysis'

Table S2. Description of clustering approach #2: 'Amp Peak 2(2q33.1) mutation analysis'

Cluster Labels	AMP PEAK 2(2Q33.1) MUTATED	AMP PEAK 2(2Q33.1) WILD-TYPE
Number of samples	123	452

Clustering Approach #3: 'Amp Peak 3(5p12) mutation analysis'

Table S3. Description of clustering approach #3: 'Amp Peak 3(5p12) mutation analysis'

Cluster Labels	AMP PEAK 3(5P12) MUTATED	AMP PEAK 3(5P12) WILD-TYPE
Number of samples	107	468

Clustering Approach #4: 'Amp Peak 4(5q22.3) mutation analysis'

Table S4. Description of clustering approach #4: 'Amp Peak 4(5q22.3) mutation analysis'

Cluster Labels	AMP PEAK 4(5Q22.3) MUTATED	AMP PEAK 4(5Q22.3) WILD-TYPE
Number of samples	59	516

Clustering Approach #5: 'Amp Peak 5(6p21.1) mutation analysis'

Table S5. Description of clustering approach #5: 'Amp Peak 5(6p21.1) mutation analysis'

Cluster Labels	AMP PEAK 5(6P21.1) MUTATED	AMP PEAK 5(6P21.1) WILD-TYPE
Number of samples	146	429

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

P value = 3.17e-05 (Fisher's exact test), Q value = 0.023

Table S6. Clustering Approach #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 Clustering Approach #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 = 0.000331 (Fisher's exact test), Q value = 0.23

Table S7. Clustering Approach #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 Clustering Approach #5: 'Amp Peak 5(6p21.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #6: 'Amp Peak 6(7p21.3) mutation analysis'

Table S8. Description of clustering approach #6: 'Amp Peak 6(7p21.3) mutation analysis'

Cluster Labels	AMP PEAK 6(7P21.3) MUTATED	AMP PEAK 6(7P21.3) WILD-TYPE
Number of samples	337	238

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

P value = 0.000225 (Fisher's exact test), Q value = 0.16

Table S9. Clustering Approach #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 Clustering Approach #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 = 1.23e-05 (Fisher's exact test), Q value = 0.0089

Table S10. Clustering Approach #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 Clustering Approach #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 = 4.42e-06 (Fisher's exact test), Q value = 0.0032

Table S11. Clustering Approach #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 Clustering Approach #6: 'Amp Peak 6(7p21.3) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #7: 'Amp Peak 7(8p11.23) mutation analysis'

Table S12. Description of clustering approach #7: 'Amp Peak 7(8p11.23) mutation analysis'

Cluster Labels	AMP PEAK 7(8P11.23) MUTATED	AMP PEAK 7(8P11.23) WILD-TYPE
Number of samples	196	379

Clustering Approach #8: 'Amp Peak 8(8p11.21) mutation analysis'

Table S13. Description of clustering approach #8: 'Amp Peak 8(8p11.21) mutation analysis'

Cluster Labels	AMP PEAK 8(8P11.21) MUTATED	AMP PEAK 8(8P11.21) WILD-TYPE
Number of samples	238	337

Clustering Approach #9: 'Amp Peak 9(8q12.1) mutation analysis'

Table S14. Description of clustering approach #9: 'Amp Peak 9(8q12.1) mutation analysis'

Cluster Labels	AMP PEAK 9(8Q12.1) MUTATED	AMP PEAK 9(8Q12.1) WILD-TYPE
Number of samples	309	266

Clustering Approach #10: 'Amp Peak 10(8q24.21) mutation analysis'

Table S15. Description of clustering approach #10: 'Amp Peak 10(8q24.21) mutation analysis'

Cluster Labels	AMP PEAK 10(8Q24.21) MUTATED	AMP PEAK 10(8Q24.21) WILD-TYPE
Number of samples	345	230

Clustering Approach #11: 'Amp Peak 11(10q22.3) mutation analysis'

Table S16. Description of clustering approach #11: 'Amp Peak 11(10q22.3) mutation analysis'

Cluster Labels	AMP PEAK 11(10Q22.3) MUTATED	AMP PEAK 11(10Q22.3) WILD-TYPE
Number of samples	35	540

Clustering Approach #12: 'Amp Peak 12(11p15.5) mutation analysis'

Table S17. Description of clustering approach #12: 'Amp Peak 12(11p15.5) mutation analysis'

Cluster Labels	AMP PEAK 12(11P15.5) MUTATED	AMP PEAK 12(11P15.5) WILD-TYPE
Number of samples	129	446

Clustering Approach #13: 'Amp Peak 13(12p13.32) mutation analysis'

Table S18. Description of clustering approach #13: 'Amp Peak 13(12p13.32) mutation analysis'

Cluster Labels	AMP PEAK 13(12P13.32) MUTATED	AMP PEAK 13(12P13.32) WILD-TYPE
Number of samples	144	431

Clustering Approach #14: 'Amp Peak 14(13q12.13) mutation analysis'

Table S19. Description of clustering approach #14: 'Amp Peak 14(13q12.13) mutation analysis'

Cluster Labels	AMP PEAK 14(13Q12.13) MUTATED	AMP PEAK 14(13Q12.13) WILD-TYPE
Number of samples	371	204

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

P value = 1.18e-09 (Fisher's exact test), Q value = 8.7e-07

Table S20. Clustering Approach #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 Clustering Approach #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 = 3.88e-05 (Fisher's exact test), Q value = 0.028

Table S21. Clustering Approach #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 Clustering Approach #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 = 7.49e-05 (Fisher's exact test), Q value = 0.053

Table S22. Clustering Approach #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 Clustering Approach #14: 'Amp Peak 14(13q12.13) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #15: 'Amp Peak 15(13q12.2) mutation analysis'

Table S23. Description of clustering approach #15: 'Amp Peak 15(13q12.2) mutation analysis'

Cluster Labels	AMP PEAK 15(13Q12.2) MUTATED	AMP PEAK 15(13Q12.2) WILD-TYPE
Number of samples	366	209

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

P value = 2.61e-09 (Fisher's exact test), Q value = 1.9e-06

Table S24. Clustering Approach #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 Clustering Approach #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 = 9.03e-05 (Fisher's exact test), Q value = 0.064

Table S25. Clustering Approach #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 Clustering Approach #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 = 0.000184 (Fisher's exact test), Q value = 0.13

Table S26. Clustering Approach #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 Clustering Approach #15: 'Amp Peak 15(13q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #16: 'Amp Peak 16(13q22.1) mutation analysis'

Table S27. Description of clustering approach #16: 'Amp Peak 16(13q22.1) mutation analysis'

Cluster Labels	AMP PEAK 16(13Q22.1) MUTATED	AMP PEAK 16(13Q22.1) WILD-TYPE
Number of samples	371	204

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

P value = 3.13e-08 (Fisher's exact test), Q value = 2.3e-05

Table S28. Clustering Approach #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 Clustering Approach #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 = 0.000127 (Fisher's exact test), Q value = 0.089

Table S29. Clustering Approach #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 Clustering Approach #16: 'Amp Peak 16(13q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

Clustering Approach #17: 'Amp Peak 17(15q26.1) mutation analysis'

Table S30. Description of clustering approach #17: 'Amp Peak 17(15q26.1) mutation analysis'

Cluster Labels	AMP PEAK 17(15Q26.1) MUTATED	AMP PEAK 17(15Q26.1) WILD-TYPE
Number of samples	43	532

Clustering Approach #18: 'Amp Peak 18(16p11.2) mutation analysis'

Table S31. Description of clustering approach #18: 'Amp Peak 18(16p11.2) mutation analysis'

Cluster Labels	AMP PEAK 18(16P11.2) MUTATED	AMP PEAK 18(16P11.2) WILD-TYPE
Number of samples	161	414

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

P value = 5.82e-05 (Fisher's exact test), Q value = 0.041

Table S32. Clustering Approach #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 Clustering Approach #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 = 8.54e-05 (Fisher's exact test), Q value = 0.06

Table S33. Clustering Approach #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 Clustering Approach #18: 'Amp Peak 18(16p11.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #19: 'Amp Peak 19(17q12) mutation analysis'

Table S34. Description of clustering approach #19: 'Amp Peak 19(17q12) mutation analysis'

Cluster Labels	AMP PEAK 19(17Q12) MUTATED	AMP PEAK 19(17Q12) WILD-TYPE
Number of samples	144	431

Clustering Approach #20: 'Amp Peak 20(17q24.1) mutation analysis'

Table S35. Description of clustering approach #20: 'Amp Peak 20(17q24.1) mutation analysis'

Cluster Labels	AMP PEAK 20(17Q24.1) MUTATED	AMP PEAK 20(17Q24.1) WILD-TYPE
Number of samples	128	447

Clustering Approach #21: 'Amp Peak 21(19p13.2) mutation analysis'

Table S36. Description of clustering approach #21: 'Amp Peak 21(19p13.2) mutation analysis'

Cluster Labels	AMP PEAK 21(19P13.2) MUTATED	AMP PEAK 21(19P13.2) WILD-TYPE
Number of samples	97	478

Clustering Approach #22: 'Amp Peak 22(19q12) mutation analysis'

Table S37. Description of clustering approach #22: 'Amp Peak 22(19q12) mutation analysis'

Cluster Labels	AMP PEAK 22(19Q12) MUTATED	AMP PEAK 22(19Q12) WILD-TYPE
Number of samples	122	453

Clustering Approach #23: 'Amp Peak 23(20p11.23) mutation analysis'

Table S38. Description of clustering approach #23: 'Amp Peak 23(20p11.23) mutation analysis'

Cluster Labels	AMP PEAK 23(20P11.23) MUTATED	AMP PEAK 23(20P11.23) WILD-TYPE
Number of samples	301	274

Clustering Approach #24: 'Amp Peak 24(20p11.21) mutation analysis'

Table S39. Description of clustering approach #24: 'Amp Peak 24(20p11.21) mutation analysis'

Cluster Labels	AMP PEAK 24(20P11.21) MUTATED	AMP PEAK 24(20P11.21) WILD-TYPE
Number of samples	339	236

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

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0082

Table S40. Clustering Approach #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 Clustering Approach #24: 'Amp Peak 24(20p11.21) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Clustering Approach #25: 'Amp Peak 25(20q11.21) mutation analysis'

Table S41. Description of clustering approach #25: 'Amp Peak 25(20q11.21) mutation analysis'

Cluster Labels	AMP PEAK 25(20Q11.21) MUTATED	AMP PEAK 25(20Q11.21) WILD-TYPE
Number of samples	439	136

'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 S42. Clustering Approach #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 Clustering Approach #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 = 7.88e-12 (Fisher's exact test), Q value = 5.9e-09

Table S43. Clustering Approach #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 Clustering Approach #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 = 0.000107 (Fisher's exact test), Q value = 0.076

Table S44. Clustering Approach #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 Clustering Approach #25: 'Amp Peak 25(20q11.21) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #26: 'Amp Peak 26(20q12) mutation analysis'

Table S45. Description of clustering approach #26: 'Amp Peak 26(20q12) mutation analysis'

Cluster Labels	AMP PEAK 26(20Q12) MUTATED	AMP PEAK 26(20Q12) WILD-TYPE
Number of samples	441	134

'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 S46. Clustering Approach #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 Clustering Approach #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 = 5.38e-13 (Fisher's exact test), Q value = 4e-10

Table S47. Clustering Approach #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 Clustering Approach #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 4.17e-05 (Fisher's exact test), Q value = 0.03

Table S48. Clustering Approach #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 Clustering Approach #26: 'Amp Peak 26(20q12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #27: 'Amp Peak 27(20q13.32) mutation analysis'

Table S49. Description of clustering approach #27: 'Amp Peak 27(20q13.32) mutation analysis'

Cluster Labels	AMP PEAK 27(20Q13.32) MUTATED	AMP PEAK 27(20Q13.32) WILD-TYPE
Number of samples	444	131

'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 S50. Clustering Approach #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 Clustering Approach #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 = 8.76e-12 (Fisher's exact test), Q value = 6.5e-09

Table S51. Clustering Approach #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 Clustering Approach #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 = 0.000131 (Fisher's exact test), Q value = 0.092

Table S52. Clustering Approach #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 Clustering Approach #27: 'Amp Peak 27(20q13.32) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #28: 'Amp Peak 28(Xq28) mutation analysis'

Table S53. Description of clustering approach #28: 'Amp Peak 28(Xq28) mutation analysis'

Cluster Labels	AMP PEAK 28(XQ28) MUTATED	AMP PEAK 28(XQ28) WILD-TYPE
Number of samples	121	454

Clustering Approach #29: 'Del Peak 1(1p36.11) mutation analysis'

Table S54. Description of clustering approach #29: 'Del Peak 1(1p36.11) mutation analysis'

Cluster Labels	DEL PEAK 1(1P36.11) MUTATED	DEL PEAK 1(1P36.11) WILD-TYPE
Number of samples	222	353

Clustering Approach #30: 'Del Peak 2(1p33) mutation analysis'

Table S55. Description of clustering approach #30: 'Del Peak 2(1p33) mutation analysis'

Cluster Labels	DEL PEAK 2(1P33) MUTATED	DEL PEAK 2(1P33) WILD-TYPE
Number of samples	156	419

Clustering Approach #31: 'Del Peak 3(1p13.2) mutation analysis'

Table S56. Description of clustering approach #31: 'Del Peak 3(1p13.2) mutation analysis'

Cluster Labels	DEL PEAK 3(1P13.2) MUTATED	DEL PEAK 3(1P13.2) WILD-TYPE
Number of samples	157	418

Clustering Approach #32: 'Del Peak 4(2p12) mutation analysis'

Table S57. Description of clustering approach #32: 'Del Peak 4(2p12) mutation analysis'

Cluster Labels	DEL PEAK 4(2P12) MUTATED	DEL PEAK 4(2P12) WILD-TYPE
Number of samples	20	555

Clustering Approach #33: 'Del Peak 5(2q22.1) mutation analysis'

Table S58. Description of clustering approach #33: 'Del Peak 5(2q22.1) mutation analysis'

Cluster Labels	DEL PEAK 5(2Q22.1) MUTATED	DEL PEAK 5(2Q22.1) WILD-TYPE
Number of samples	33	542

Clustering Approach #34: 'Del Peak 6(2q37.2) mutation analysis'

Table S59. Description of clustering approach #34: 'Del Peak 6(2q37.2) mutation analysis'

Cluster Labels	DEL PEAK 6(2Q37.2) MUTATED	DEL PEAK 6(2Q37.2) WILD-TYPE
Number of samples	30	545

Clustering Approach #35: 'Del Peak 7(3p26.3) mutation analysis'

Table S60. Description of clustering approach #35: 'Del Peak 7(3p26.3) mutation analysis'

Cluster Labels	DEL PEAK 7(3P26.3) MUTATED	DEL PEAK 7(3P26.3) WILD-TYPE
Number of samples	84	491

Clustering Approach #36: 'Del Peak 8(3p14.2) mutation analysis'

Table S61. Description of clustering approach #36: 'Del Peak 8(3p14.2) mutation analysis'

Cluster Labels	DEL PEAK 8(3P14.2) MUTATED	DEL PEAK 8(3P14.2) WILD-TYPE
Number of samples	104	471

Clustering Approach #37: 'Del Peak 9(3q26.31) mutation analysis'

Table S62. Description of clustering approach #37: 'Del Peak 9(3q26.31) mutation analysis'

Cluster Labels	DEL PEAK 9(3Q26.31) MUTATED	DEL PEAK 9(3Q26.31) WILD-TYPE
Number of samples	56	519

Clustering Approach #38: 'Del Peak 10(4p16.1) mutation analysis'

Table S63. Description of clustering approach #38: 'Del Peak 10(4p16.1) mutation analysis'

Cluster Labels	DEL PEAK 10(4P16.1) MUTATED	DEL PEAK 10(4P16.1) WILD-TYPE
Number of samples	182	393

'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 S64. Clustering Approach #38: 'Del Peak 10(4p16.1) mutation analysis' versus Clinical Feature #10: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

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

Clustering Approach #39: 'Del Peak 11(4q22.1) mutation analysis'

Table S65. Description of clustering approach #39: 'Del Peak 11(4q22.1) mutation analysis'

Cluster Labels	DEL PEAK 11(4Q22.1) MUTATED	DEL PEAK 11(4Q22.1) WILD-TYPE
Number of samples	198	377

Clustering Approach #40: 'Del Peak 12(4q35.1) mutation analysis'

Table S66. Description of clustering approach #40: 'Del Peak 12(4q35.1) mutation analysis'

Cluster Labels	DEL PEAK 12(4Q35.1) MUTATED	DEL PEAK 12(4Q35.1) WILD-TYPE
Number of samples	211	364

Clustering Approach #41: 'Del Peak 13(5q11.2) mutation analysis'

Table S67. Description of clustering approach #41: 'Del Peak 13(5q11.2) mutation analysis'

Cluster Labels	DEL PEAK 13(5Q11.2) MUTATED	DEL PEAK 13(5Q11.2) WILD-TYPE
Number of samples	140	435

Clustering Approach #42: 'Del Peak 14(5q22.2) mutation analysis'

Table S68. Description of clustering approach #42: 'Del Peak 14(5q22.2) mutation analysis'

Cluster Labels	DEL PEAK 14(5Q22.2) MUTATED	DEL PEAK 14(5Q22.2) WILD-TYPE
Number of samples	172	403

Clustering Approach #43: 'Del Peak 15(6p25.3) mutation analysis'

Table S69. Description of clustering approach #43: 'Del Peak 15(6p25.3) mutation analysis'

Cluster Labels	DEL PEAK 15(6P25.3) MUTATED	DEL PEAK 15(6P25.3) WILD-TYPE
Number of samples	78	497

Clustering Approach #44: 'Del Peak 16(6q26) mutation analysis'

Table S70. Description of clustering approach #44: 'Del Peak 16(6q26) mutation analysis'

Cluster Labels	DEL PEAK 16(6Q26) MUTATED	DEL PEAK 16(6Q26) WILD-TYPE
Number of samples	90	485

Clustering Approach #45: 'Del Peak 17(7q31.1) mutation analysis'

Table S71. Description of clustering approach #45: 'Del Peak 17(7q31.1) mutation analysis'

Cluster Labels	DEL PEAK 17(7Q31.1) MUTATED	DEL PEAK 17(7Q31.1) WILD-TYPE
Number of samples	15	560

Clustering Approach #46: 'Del Peak 18(8p23.2) mutation analysis'

Table S72. Description of clustering approach #46: 'Del Peak 18(8p23.2) mutation analysis'

Cluster Labels	DEL PEAK 18(8P23.2) MUTATED	DEL PEAK 18(8P23.2) WILD-TYPE
Number of samples	272	303

'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 S73. Clustering Approach #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 Clustering Approach #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 = 2.9e-05 (Fisher's exact test), Q value = 0.021

Table S74. Clustering Approach #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 Clustering Approach #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 = 2.78e-05 (Fisher's exact test), Q value = 0.02

Table S75. Clustering Approach #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 Clustering Approach #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 = 3.4e-05 (Fisher's exact test), Q value = 0.024

Table S76. Clustering Approach #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 Clustering Approach #46: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #47: 'Del Peak 19(8p22) mutation analysis'

Table S77. Description of clustering approach #47: 'Del Peak 19(8p22) mutation analysis'

Cluster Labels	DEL PEAK 19(8P22) MUTATED	DEL PEAK 19(8P22) WILD-TYPE
Number of samples	285	290

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

P value = 0.000256 (Fisher's exact test), Q value = 0.18

Table S78. Clustering Approach #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 Clustering Approach #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 1.97e-06 (Fisher's exact test), Q value = 0.0014

Table S79. Clustering Approach #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 Clustering Approach #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

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

P value = 1.24e-06 (Fisher's exact test), Q value = 0.00091

Table S80. Clustering Approach #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 Clustering Approach #47: 'Del Peak 19(8p22) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #48: 'Del Peak 20(8p11.21) mutation analysis'

Table S81. Description of clustering approach #48: 'Del Peak 20(8p11.21) mutation analysis'

Cluster Labels	DEL PEAK 20(8P11.21) MUTATED	DEL PEAK 20(8P11.21) WILD-TYPE
Number of samples	124	451

Clustering Approach #49: 'Del Peak 21(8q11.1) mutation analysis'

Table S82. Description of clustering approach #49: 'Del Peak 21(8q11.1) mutation analysis'

Cluster Labels	DEL PEAK 21(8Q11.1) MUTATED	DEL PEAK 21(8Q11.1) WILD-TYPE
Number of samples	44	531

Clustering Approach #50: 'Del Peak 22(9p24.2) mutation analysis'

Table S83. Description of clustering approach #50: 'Del Peak 22(9p24.2) mutation analysis'

Cluster Labels	DEL PEAK 22(9P24.2) MUTATED	DEL PEAK 22(9P24.2) WILD-TYPE
Number of samples	78	497

Clustering Approach #51: 'Del Peak 23(10p15.3) mutation analysis'

Table S84. Description of clustering approach #51: 'Del Peak 23(10p15.3) mutation analysis'

Cluster Labels	DEL PEAK 23(10P15.3) MUTATED	DEL PEAK 23(10P15.3) WILD-TYPE
Number of samples	102	473

Clustering Approach #52: 'Del Peak 24(10q21.1) mutation analysis'

Table S85. Description of clustering approach #52: 'Del Peak 24(10q21.1) mutation analysis'

Cluster Labels	DEL PEAK 24(10Q21.1) MUTATED	DEL PEAK 24(10Q21.1) WILD-TYPE
Number of samples	118	457

Clustering Approach #53: 'Del Peak 25(10q23.31) mutation analysis'

Table S86. Description of clustering approach #53: 'Del Peak 25(10q23.31) mutation analysis'

Cluster Labels	DEL PEAK 25(10Q23.31) MUTATED	DEL PEAK 25(10Q23.31) WILD-TYPE
Number of samples	145	430

Clustering Approach #54: 'Del Peak 26(10q25.2) mutation analysis'

Table S87. Description of clustering approach #54: 'Del Peak 26(10q25.2) mutation analysis'

Cluster Labels	DEL PEAK 26(10Q25.2) MUTATED	DEL PEAK 26(10Q25.2) WILD-TYPE
Number of samples	140	435

Clustering Approach #55: 'Del Peak 27(11q22.3) mutation analysis'

Table S88. Description of clustering approach #55: 'Del Peak 27(11q22.3) mutation analysis'

Cluster Labels	DEL PEAK 27(11Q22.3) MUTATED	DEL PEAK 27(11Q22.3) WILD-TYPE
Number of samples	104	471

Clustering Approach #56: 'Del Peak 28(12p13.1) mutation analysis'

Table S89. Description of clustering approach #56: 'Del Peak 28(12p13.1) mutation analysis'

Cluster Labels	DEL PEAK 28(12P13.1) MUTATED	DEL PEAK 28(12P13.1) WILD-TYPE
Number of samples	77	498

Clustering Approach #57: 'Del Peak 29(12q21.2) mutation analysis'

Table S90. Description of clustering approach #57: 'Del Peak 29(12q21.2) mutation analysis'

Cluster Labels	DEL PEAK 29(12Q21.2) MUTATED	DEL PEAK 29(12Q21.2) WILD-TYPE
Number of samples	80	495

Clustering Approach #58: 'Del Peak 30(14q22.1) mutation analysis'

Table S91. Description of clustering approach #58: 'Del Peak 30(14q22.1) mutation analysis'

Cluster Labels	DEL PEAK 30(14Q22.1) MUTATED	DEL PEAK 30(14Q22.1) WILD-TYPE
Number of samples	185	390

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

P value = 1.15e-06 (Fisher's exact test), Q value = 0.00084

Table S92. Clustering Approach #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 Clustering Approach #58: 'Del Peak 30(14q22.1) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Clustering Approach #59: 'Del Peak 31(15q11.2) mutation analysis'

Table S93. Description of clustering approach #59: 'Del Peak 31(15q11.2) mutation analysis'

Cluster Labels	DEL PEAK 31(15Q11.2) MUTATED	DEL PEAK 31(15Q11.2) WILD-TYPE
Number of samples	233	342

Clustering Approach #60: 'Del Peak 32(15q21.1) mutation analysis'

Table S94. Description of clustering approach #60: 'Del Peak 32(15q21.1) mutation analysis'

Cluster Labels	DEL PEAK 32(15Q21.1) MUTATED	DEL PEAK 32(15Q21.1) WILD-TYPE
Number of samples	227	348

Clustering Approach #61: 'Del Peak 33(15q22.33) mutation analysis'

Table S95. Description of clustering approach #61: 'Del Peak 33(15q22.33) mutation analysis'

Cluster Labels	DEL PEAK 33(15Q22.33) MUTATED	DEL PEAK 33(15Q22.33) WILD-TYPE
Number of samples	217	358

Clustering Approach #62: 'Del Peak 34(16p13.3) mutation analysis'

Table S96. Description of clustering approach #62: 'Del Peak 34(16p13.3) mutation analysis'

Cluster Labels	DEL PEAK 34(16P13.3) MUTATED	DEL PEAK 34(16P13.3) WILD-TYPE
Number of samples	58	517

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

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

Table S97. Clustering Approach #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 Clustering Approach #62: 'Del Peak 34(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

Clustering Approach #63: 'Del Peak 35(16q23.1) mutation analysis'

Table S98. Description of clustering approach #63: 'Del Peak 35(16q23.1) mutation analysis'

Cluster Labels	DEL PEAK 35(16Q23.1) MUTATED	DEL PEAK 35(16Q23.1) WILD-TYPE
Number of samples	72	503

Clustering Approach #64: 'Del Peak 36(17p12) mutation analysis'

Table S99. Description of clustering approach #64: 'Del Peak 36(17p12) mutation analysis'

Cluster Labels	DEL PEAK 36(17P12) MUTATED	DEL PEAK 36(17P12) WILD-TYPE
Number of samples	343	232

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

P value = 6.48e-08 (Fisher's exact test), Q value = 4.8e-05

Table S100. Clustering Approach #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 Clustering Approach #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

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

P value = 0.000121 (Fisher's exact test), Q value = 0.086

Table S101. Clustering Approach #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 Clustering Approach #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

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

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

Table S102. Clustering Approach #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 Clustering Approach #64: 'Del Peak 36(17p12) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #65: 'Del Peak 37(17q24.3) mutation analysis'

Table S103. Description of clustering approach #65: 'Del Peak 37(17q24.3) mutation analysis'

Cluster Labels	DEL PEAK 37(17Q24.3) MUTATED	DEL PEAK 37(17Q24.3) WILD-TYPE
Number of samples	84	491

Clustering Approach #66: 'Del Peak 38(18p11.31) mutation analysis'

Table S104. Description of clustering approach #66: 'Del Peak 38(18p11.31) mutation analysis'

Cluster Labels	DEL PEAK 38(18P11.31) MUTATED	DEL PEAK 38(18P11.31) WILD-TYPE
Number of samples	341	234

'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 S105. Clustering Approach #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 Clustering Approach #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 = 1.53e-16 (Fisher's exact test), Q value = 1.1e-13

Table S106. Clustering Approach #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 Clustering Approach #66: 'Del Peak 38(18p11.31) mutation analysis' versus Clinical Feature #5: 'HISTOLOGICAL.TYPE'

Clustering Approach #67: 'Del Peak 39(18q12.2) mutation analysis'

Table S107. Description of clustering approach #67: 'Del Peak 39(18q12.2) mutation analysis'

Cluster Labels	DEL PEAK 39(18Q12.2) MUTATED	DEL PEAK 39(18Q12.2) WILD-TYPE
Number of samples	386	189

'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 S108. Clustering Approach #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 Clustering Approach #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 = 8.59e-18 (Fisher's exact test), Q value = 6.4e-15

Table S109. Clustering Approach #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 Clustering Approach #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 S110. Clustering Approach #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 Clustering Approach #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 = 6.82e-05 (Fisher's exact test), Q value = 0.049

Table S111. Clustering Approach #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 Clustering Approach #67: 'Del Peak 39(18q12.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #68: 'Del Peak 40(18q21.2) mutation analysis'

Table S112. Description of clustering approach #68: 'Del Peak 40(18q21.2) mutation analysis'

Cluster Labels	DEL PEAK 40(18Q21.2) MUTATED	DEL PEAK 40(18Q21.2) WILD-TYPE
Number of samples	403	172

'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 S113. Clustering Approach #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 Clustering Approach #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 = 3.7e-16 (Fisher's exact test), Q value = 2.8e-13

Table S114. Clustering Approach #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 Clustering Approach #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 = 1.95e-06 (Fisher's exact test), Q value = 0.0014

Table S115. Clustering Approach #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 Clustering Approach #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 = 4.1e-07 (Fisher's exact test), Q value = 3e-04

Table S116. Clustering Approach #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 Clustering Approach #68: 'Del Peak 40(18q21.2) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #69: 'Del Peak 41(18q22.1) mutation analysis'

Table S117. Description of clustering approach #69: 'Del Peak 41(18q22.1) mutation analysis'

Cluster Labels	DEL PEAK 41(18Q22.1) MUTATED	DEL PEAK 41(18Q22.1) WILD-TYPE
Number of samples	398	177

'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 S118. Clustering Approach #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 Clustering Approach #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 = 2.07e-15 (Fisher's exact test), Q value = 1.5e-12

Table S119. Clustering Approach #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 Clustering Approach #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 = 1.14e-05 (Fisher's exact test), Q value = 0.0083

Table S120. Clustering Approach #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 Clustering Approach #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 = 4.68e-06 (Fisher's exact test), Q value = 0.0034

Table S121. Clustering Approach #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 Clustering Approach #69: 'Del Peak 41(18q22.1) mutation analysis' versus Clinical Feature #9: 'TUMOR.STAGE'

Clustering Approach #70: 'Del Peak 42(19p13.3) mutation analysis'

Table S122. Description of clustering approach #70: 'Del Peak 42(19p13.3) mutation analysis'

Cluster Labels	DEL PEAK 42(19P13.3) MUTATED	DEL PEAK 42(19P13.3) WILD-TYPE
Number of samples	92	483

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

P value = 7.64e-05 (Fisher's exact test), Q value = 0.054

Table S123. Clustering Approach #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 Clustering Approach #70: 'Del Peak 42(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.N'

Clustering Approach #71: 'Del Peak 43(19q13.43) mutation analysis'

Table S124. Description of clustering approach #71: 'Del Peak 43(19q13.43) mutation analysis'

Cluster Labels	DEL PEAK 43(19Q13.43) MUTATED	DEL PEAK 43(19Q13.43) WILD-TYPE
Number of samples	68	507

Clustering Approach #72: 'Del Peak 44(20p12.1) mutation analysis'

Table S125. Description of clustering approach #72: 'Del Peak 44(20p12.1) mutation analysis'

Cluster Labels	DEL PEAK 44(20P12.1) MUTATED	DEL PEAK 44(20P12.1) WILD-TYPE
Number of samples	179	396

Clustering Approach #73: 'Del Peak 45(20p12.1) mutation analysis'

Table S126. Description of clustering approach #73: 'Del Peak 45(20p12.1) mutation analysis'

Cluster Labels	DEL PEAK 45(20P12.1) MUTATED	DEL PEAK 45(20P12.1) WILD-TYPE
Number of samples	179	396

Clustering Approach #74: 'Del Peak 46(21q11.2) mutation analysis'

Table S127. Description of clustering approach #74: 'Del Peak 46(21q11.2) mutation analysis'

Cluster Labels	DEL PEAK 46(21Q11.2) MUTATED	DEL PEAK 46(21Q11.2) WILD-TYPE
Number of samples	195	380

Clustering Approach #75: 'Del Peak 47(22q13.32) mutation analysis'

Table S128. Description of clustering approach #75: 'Del Peak 47(22q13.32) mutation analysis'

Cluster Labels	DEL PEAK 47(22Q13.32) MUTATED	DEL PEAK 47(22Q13.32) WILD-TYPE
Number of samples	204	371

Methods & Data

Input

Cluster data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = COADREAD-TP.clin.merged.picked.txt
Number of patients = 575
Number of clustering approaches = 75
Number of selected clinical features = 10
Exclude small clusters that include fewer than K patients, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.test' function in R

Fisher's exact test

For binary clinical features, 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)

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