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

Ovarian Serous Cystadenocarcinoma (Primary solid tumor)

22 February 2013 | analyses__2013_02_22

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1FX77NG

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 70 different clustering approaches and 6 clinical features across 552 patients, 12 significant findings detected with Q value < 0.25.

2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p34.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 2(1q21.3) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q42.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 4(2p23.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 5(2q31.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 6(3q26.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 7(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 8(4q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 9(5p15.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 10(6p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 11(7q36.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 12(8p11.21) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 13(8q24.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 14(10p15.3) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 15(10q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 16(11q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 17(12p13.33) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 18(12p12.1) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 19(14q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 20(15q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 21(17q25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 22(18q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 23(19p13.12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 24(19q12) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 25(19q13.2) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 26(20p13) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 27(20q11.21) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 28(20q13.33) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 29(22q12.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 30(Xp11.23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 31(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(1q32.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 3(2p25.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 4(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 5(2q37.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 6(3p26.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 7(4q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 8(4q34.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 9(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 10(5q13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 11(6q27) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 12(7p22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 13(8p23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 14(8p21.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 15(9p24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 16(9q21.11) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 17(9q34.13) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 18(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 19(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 20(10q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 21(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 22(11q25) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 23(12q23.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 24(12q24.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 25(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 26(14q23.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 27(15q15.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 28(16p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 29(16q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 30(16q23.1) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 31(17p12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 32(17q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 33(18q23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 34(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 35(19q13.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 36(19q13.43) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 37(21q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 38(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 39(Xp21.1) 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 70 different clustering approaches and 6 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.


Clinical Features	Time to Death	AGE	PRIMARY SITE OF DISEASE	KARNOFSKY PERFORMANCE SCORE	TUMOR STAGE	RADIATIONS RADIATION REGIMENINDICATION
Statistical Tests	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test	Fisher's exact test
Amp Peak 1(1p34 3)	0.0333 (1.00)	0.00962 (1.00)	1 (1.00)	0.985 (1.00)	0.874 (1.00)	0.123 (1.00)
Amp Peak 2(1q21 3)	0.291 (1.00)	4.24e-06 (0.00176)	0.128 (1.00)	0.408 (1.00)	0.757 (1.00)	1 (1.00)
Amp Peak 3(1q42 2)	0.29 (1.00)	0.000643 (0.262)	0.252 (1.00)	0.736 (1.00)	0.173 (1.00)	0.597 (1.00)
Amp Peak 4(2p23 2)	0.915 (1.00)	0.0855 (1.00)	0.762 (1.00)	0.988 (1.00)	0.369 (1.00)	1 (1.00)
Amp Peak 5(2q31 2)	0.177 (1.00)	0.0132 (1.00)	0.756 (1.00)	0.693 (1.00)	0.00661 (1.00)	0.0847 (1.00)
Amp Peak 6(3q26 2)	0.955 (1.00)	0.000836 (0.34)	0.527 (1.00)	0.00131 (0.531)	0.0553 (1.00)	1 (1.00)
Amp Peak 7(4p16 3)	0.456 (1.00)	0.644 (1.00)	0.723 (1.00)	0.0728 (1.00)	0.831 (1.00)	1 (1.00)
Amp Peak 8(4q13 3)	0.204 (1.00)	0.208 (1.00)	0.571 (1.00)	0.42 (1.00)	0.407 (1.00)	1 (1.00)
Amp Peak 9(5p15 33)	0.0538 (1.00)	0.00274 (1.00)	0.751 (1.00)	0.798 (1.00)	0.292 (1.00)	0.604 (1.00)
Amp Peak 10(6p22 3)	0.132 (1.00)	0.00543 (1.00)	1 (1.00)	0.545 (1.00)	0.0489 (1.00)	0.618 (1.00)
Amp Peak 11(7q36 3)	0.291 (1.00)	0.858 (1.00)	1 (1.00)	0.1 (1.00)	0.741 (1.00)	0.599 (1.00)
Amp Peak 12(8p11 21)	0.335 (1.00)	0.000534 (0.219)	0.121 (1.00)	0.662 (1.00)	0.317 (1.00)	0.288 (1.00)
Amp Peak 13(8q24 21)	0.547 (1.00)	0.0995 (1.00)	1 (1.00)	0.628 (1.00)	0.188 (1.00)	0.518 (1.00)
Amp Peak 14(10p15 3)	0.13 (1.00)	0.000432 (0.178)	0.154 (1.00)	0.923 (1.00)	0.228 (1.00)	0.58 (1.00)
Amp Peak 15(10q22 3)	0.523 (1.00)	0.221 (1.00)	0.0934 (1.00)	0.989 (1.00)	0.751 (1.00)	1 (1.00)
Amp Peak 16(11q14 1)	0.298 (1.00)	0.335 (1.00)	0.256 (1.00)	0.474 (1.00)	0.0508 (1.00)	1 (1.00)
Amp Peak 17(12p13 33)	0.772 (1.00)	3.54e-07 (0.000148)	0.756 (1.00)	0.735 (1.00)	0.0955 (1.00)	1 (1.00)
Amp Peak 18(12p12 1)	0.0918 (1.00)	1.23e-08 (5.15e-06)	0.251 (1.00)	0.335 (1.00)	0.0316 (1.00)	0.603 (1.00)
Amp Peak 19(14q11 2)	0.752 (1.00)	0.0651 (1.00)	0.124 (1.00)	0.378 (1.00)	0.101 (1.00)	1 (1.00)
Amp Peak 20(15q26 3)	0.0716 (1.00)	0.284 (1.00)	0.728 (1.00)	0.42 (1.00)	0.147 (1.00)	0.564 (1.00)
Amp Peak 21(17q25 3)	0.0217 (1.00)	0.783 (1.00)	1 (1.00)	0.685 (1.00)	0.381 (1.00)	1 (1.00)
Amp Peak 22(18q11 2)	0.979 (1.00)	0.0441 (1.00)	0.114 (1.00)	0.18 (1.00)	0.843 (1.00)	0.567 (1.00)
Amp Peak 23(19p13 12)	0.199 (1.00)	0.072 (1.00)	0.461 (1.00)	0.597 (1.00)	0.119 (1.00)	0.596 (1.00)
Amp Peak 24(19q12)	0.602 (1.00)	1.19e-05 (0.00493)	0.162 (1.00)	0.51 (1.00)	0.104 (1.00)	1 (1.00)
Amp Peak 25(19q13 2)	0.0201 (1.00)	3.37e-06 (0.00141)	0.15 (1.00)	0.989 (1.00)	0.639 (1.00)	0.575 (1.00)
Amp Peak 26(20p13)	0.317 (1.00)	0.00756 (1.00)	0.753 (1.00)	0.11 (1.00)	0.0022 (0.889)	1 (1.00)
Amp Peak 27(20q11 21)	0.104 (1.00)	7.62e-08 (3.19e-05)	1 (1.00)	0.264 (1.00)	0.0856 (1.00)	1 (1.00)
Amp Peak 28(20q13 33)	0.331 (1.00)	9.1e-06 (0.00377)	1 (1.00)	0.752 (1.00)	0.546 (1.00)	1 (1.00)
Amp Peak 29(22q12 2)	0.545 (1.00)	0.0241 (1.00)	1 (1.00)	0.419 (1.00)	0.434 (1.00)	1 (1.00)
Amp Peak 30(Xp11 23)	0.144 (1.00)	0.0223 (1.00)	0.0781 (1.00)	0.275 (1.00)	0.364 (1.00)	0.559 (1.00)
Amp Peak 31(Xq28)	0.355 (1.00)	0.97 (1.00)	0.77 (1.00)	0.654 (1.00)	0.00163 (0.662)	0.0619 (1.00)
Del Peak 1(1p36 11)	0.169 (1.00)	0.187 (1.00)	0.751 (1.00)	0.427 (1.00)	0.496 (1.00)	1 (1.00)
Del Peak 2(1q32 3)	0.96 (1.00)	0.544 (1.00)	1 (1.00)	0.287 (1.00)	0.423 (1.00)	0.411 (1.00)
Del Peak 3(2p25 3)	0.922 (1.00)	0.425 (1.00)	0.615 (1.00)	0.875 (1.00)	0.0602 (1.00)	0.511 (1.00)
Del Peak 4(2q22 1)	0.25 (1.00)	0.385 (1.00)	0.656 (1.00)	0.595 (1.00)	0.356 (1.00)	1 (1.00)
Del Peak 5(2q37 3)	0.555 (1.00)	0.102 (1.00)	0.359 (1.00)	0.432 (1.00)	0.806 (1.00)	0.223 (1.00)
Del Peak 6(3p26 2)	0.792 (1.00)	0.00246 (0.99)	0.126 (1.00)	0.246 (1.00)	0.136 (1.00)	0.0493 (1.00)
Del Peak 7(4q22 1)	0.51 (1.00)	0.95 (1.00)	1 (1.00)	0.925 (1.00)	0.0436 (1.00)	1 (1.00)
Del Peak 8(4q34 3)	0.797 (1.00)	0.36 (1.00)	0.728 (1.00)	0.171 (1.00)	0.796 (1.00)	0.564 (1.00)
Del Peak 9(5q11 2)	0.737 (1.00)	0.628 (1.00)	0.767 (1.00)	0.325 (1.00)	0.243 (1.00)	0.568 (1.00)
Del Peak 10(5q13 2)	0.261 (1.00)	0.922 (1.00)	0.747 (1.00)	0.216 (1.00)	0.884 (1.00)	0.203 (1.00)
Del Peak 11(6q27)	0.301 (1.00)	0.000461 (0.189)	1 (1.00)	0.454 (1.00)	0.509 (1.00)	1 (1.00)
Del Peak 12(7p22 1)	0.09 (1.00)	0.0291 (1.00)	0.758 (1.00)	0.497 (1.00)	0.966 (1.00)	1 (1.00)
Del Peak 13(8p23 3)	0.271 (1.00)	0.0639 (1.00)	1 (1.00)	0.95 (1.00)	0.888 (1.00)	1 (1.00)
Del Peak 14(8p21 2)	0.672 (1.00)	0.0645 (1.00)	1 (1.00)	0.647 (1.00)	0.538 (1.00)	1 (1.00)
Del Peak 15(9p24 3)	0.943 (1.00)	0.025 (1.00)	0.45 (1.00)	0.928 (1.00)	0.397 (1.00)	0.587 (1.00)
Del Peak 16(9q21 11)	0.595 (1.00)	4.09e-06 (0.0017)	0.0533 (1.00)	0.634 (1.00)	0.00478 (1.00)	1 (1.00)
Del Peak 17(9q34 13)	0.786 (1.00)	0.0402 (1.00)	0.767 (1.00)	0.623 (1.00)	0.859 (1.00)	0.276 (1.00)
Del Peak 18(10p15 3)	0.336 (1.00)	0.83 (1.00)	0.608 (1.00)	0.72 (1.00)	0.392 (1.00)	0.505 (1.00)
Del Peak 19(10q23 31)	0.328 (1.00)	0.972 (1.00)	1 (1.00)	0.393 (1.00)	0.625 (1.00)	0.563 (1.00)
Del Peak 20(10q26 3)	0.0829 (1.00)	0.842 (1.00)	0.8 (1.00)	0.77 (1.00)	0.345 (1.00)	1 (1.00)
Del Peak 21(11p15 5)	0.0509 (1.00)	0.563 (1.00)	0.0267 (1.00)	0.267 (1.00)	0.675 (1.00)	1 (1.00)
Del Peak 22(11q25)	0.598 (1.00)	0.0797 (1.00)	0.225 (1.00)	0.631 (1.00)	0.0759 (1.00)	0.276 (1.00)
Del Peak 23(12q23 1)	0.271 (1.00)	0.0147 (1.00)	0.798 (1.00)	0.4 (1.00)	0.262 (1.00)	1 (1.00)
Del Peak 24(12q24 33)	0.655 (1.00)	0.112 (1.00)	0.13 (1.00)	0.652 (1.00)	0.539 (1.00)	0.296 (1.00)
Del Peak 25(13q14 2)	0.0714 (1.00)	0.561 (1.00)	0.777 (1.00)	0.592 (1.00)	0.747 (1.00)	0.561 (1.00)
Del Peak 26(14q23 2)	0.67 (1.00)	0.456 (1.00)	0.475 (1.00)	0.0423 (1.00)	0.313 (1.00)	0.106 (1.00)
Del Peak 27(15q15 1)	0.664 (1.00)	0.00579 (1.00)	0.411 (1.00)	0.253 (1.00)	0.0296 (1.00)	0.298 (1.00)
Del Peak 28(16p13 3)	0.886 (1.00)	0.883 (1.00)	0.751 (1.00)	0.578 (1.00)	0.217 (1.00)	0.603 (1.00)
Del Peak 29(16q22 1)	0.645 (1.00)	0.00497 (1.00)	0.193 (1.00)	0.275 (1.00)	0.547 (1.00)	1 (1.00)
Del Peak 30(16q23 1)	0.161 (1.00)	7.72e-05 (0.0318)	0.636 (1.00)	0.0778 (1.00)	0.128 (1.00)	1 (1.00)
Del Peak 31(17p12)	0.797 (1.00)	0.982 (1.00)	0.493 (1.00)	0.73 (1.00)	0.0127 (1.00)	1 (1.00)
Del Peak 32(17q11 2)	0.708 (1.00)	0.0331 (1.00)	0.0666 (1.00)	0.686 (1.00)	0.259 (1.00)	1 (1.00)
Del Peak 33(18q23)	0.669 (1.00)	0.795 (1.00)	0.229 (1.00)	0.544 (1.00)	0.693 (1.00)	1 (1.00)
Del Peak 34(19p13 3)	0.19 (1.00)	0.0164 (1.00)	1 (1.00)	0.00833 (1.00)	0.0647 (1.00)	1 (1.00)
Del Peak 35(19q13 33)	0.603 (1.00)	0.355 (1.00)	1 (1.00)	0.311 (1.00)	0.374 (1.00)	0.25 (1.00)
Del Peak 36(19q13 43)	0.456 (1.00)	0.0261 (1.00)	1 (1.00)	0.283 (1.00)	0.263 (1.00)	1 (1.00)
Del Peak 37(21q22 3)	0.584 (1.00)	0.35 (1.00)	0.774 (1.00)	0.665 (1.00)	0.124 (1.00)	1 (1.00)
Del Peak 38(22q13 32)	0.843 (1.00)	0.901 (1.00)	0.443 (1.00)	0.752 (1.00)	0.548 (1.00)	1 (1.00)
Del Peak 39(Xp21 1)	0.838 (1.00)	0.367 (1.00)	1 (1.00)	0.987 (1.00)	0.682 (1.00)	0.557 (1.00)

Clustering Approach #1: 'Amp Peak 1(1p34.3) mutation analysis'

Table S1. Description of clustering approach #1: 'Amp Peak 1(1p34.3) mutation analysis'

Cluster Labels	AMP PEAK 1(1P34.3) MUTATED	AMP PEAK 1(1P34.3) WILD-TYPE
Number of samples	275	277

Clustering Approach #2: 'Amp Peak 2(1q21.3) mutation analysis'

Table S2. Description of clustering approach #2: 'Amp Peak 2(1q21.3) mutation analysis'

Cluster Labels	AMP PEAK 2(1Q21.3) MUTATED	AMP PEAK 2(1Q21.3) WILD-TYPE
Number of samples	347	205

'Amp Peak 2(1q21.3) mutation analysis' versus 'AGE'

P value = 4.24e-06 (t-test), Q value = 0.0018

Table S3. Clustering Approach #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 2(1Q21.3) MUTATED	341	61.6 (11.0)
AMP PEAK 2(1Q21.3) WILD-TYPE	200	56.8 (12.0)

Figure S1. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1q21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #3: 'Amp Peak 3(1q42.2) mutation analysis'

Table S4. Description of clustering approach #3: 'Amp Peak 3(1q42.2) mutation analysis'

Cluster Labels	AMP PEAK 3(1Q42.2) MUTATED	AMP PEAK 3(1Q42.2) WILD-TYPE
Number of samples	298	254

Clustering Approach #4: 'Amp Peak 4(2p23.2) mutation analysis'

Table S5. Description of clustering approach #4: 'Amp Peak 4(2p23.2) mutation analysis'

Cluster Labels	AMP PEAK 4(2P23.2) MUTATED	AMP PEAK 4(2P23.2) WILD-TYPE
Number of samples	231	321

Clustering Approach #5: 'Amp Peak 5(2q31.2) mutation analysis'

Table S6. Description of clustering approach #5: 'Amp Peak 5(2q31.2) mutation analysis'

Cluster Labels	AMP PEAK 5(2Q31.2) MUTATED	AMP PEAK 5(2Q31.2) WILD-TYPE
Number of samples	243	309

Clustering Approach #6: 'Amp Peak 6(3q26.2) mutation analysis'

Table S7. Description of clustering approach #6: 'Amp Peak 6(3q26.2) mutation analysis'

Cluster Labels	AMP PEAK 6(3Q26.2) MUTATED	AMP PEAK 6(3Q26.2) WILD-TYPE
Number of samples	458	94

Clustering Approach #7: 'Amp Peak 7(4p16.3) mutation analysis'

Table S8. Description of clustering approach #7: 'Amp Peak 7(4p16.3) mutation analysis'

Cluster Labels	AMP PEAK 7(4P16.3) MUTATED	AMP PEAK 7(4P16.3) WILD-TYPE
Number of samples	151	401

Clustering Approach #8: 'Amp Peak 8(4q13.3) mutation analysis'

Table S9. Description of clustering approach #8: 'Amp Peak 8(4q13.3) mutation analysis'

Cluster Labels	AMP PEAK 8(4Q13.3) MUTATED	AMP PEAK 8(4Q13.3) WILD-TYPE
Number of samples	105	447

Clustering Approach #9: 'Amp Peak 9(5p15.33) mutation analysis'

Table S10. Description of clustering approach #9: 'Amp Peak 9(5p15.33) mutation analysis'

Cluster Labels	AMP PEAK 9(5P15.33) MUTATED	AMP PEAK 9(5P15.33) WILD-TYPE
Number of samples	292	260

Clustering Approach #10: 'Amp Peak 10(6p22.3) mutation analysis'

Table S11. Description of clustering approach #10: 'Amp Peak 10(6p22.3) mutation analysis'

Cluster Labels	AMP PEAK 10(6P22.3) MUTATED	AMP PEAK 10(6P22.3) WILD-TYPE
Number of samples	281	271

Clustering Approach #11: 'Amp Peak 11(7q36.3) mutation analysis'

Table S12. Description of clustering approach #11: 'Amp Peak 11(7q36.3) mutation analysis'

Cluster Labels	AMP PEAK 11(7Q36.3) MUTATED	AMP PEAK 11(7Q36.3) WILD-TYPE
Number of samples	296	256

Clustering Approach #12: 'Amp Peak 12(8p11.21) mutation analysis'

Table S13. Description of clustering approach #12: 'Amp Peak 12(8p11.21) mutation analysis'

Cluster Labels	AMP PEAK 12(8P11.21) MUTATED	AMP PEAK 12(8P11.21) WILD-TYPE
Number of samples	196	356

'Amp Peak 12(8p11.21) mutation analysis' versus 'AGE'

P value = 0.000534 (t-test), Q value = 0.22

Table S14. Clustering Approach #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 12(8P11.21) MUTATED	192	62.1 (10.8)
AMP PEAK 12(8P11.21) WILD-TYPE	349	58.6 (11.8)

Figure S2. Get High-res Image Clustering Approach #12: 'Amp Peak 12(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #13: 'Amp Peak 13(8q24.21) mutation analysis'

Table S15. Description of clustering approach #13: 'Amp Peak 13(8q24.21) mutation analysis'

Cluster Labels	AMP PEAK 13(8Q24.21) MUTATED	AMP PEAK 13(8Q24.21) WILD-TYPE
Number of samples	433	119

Clustering Approach #14: 'Amp Peak 14(10p15.3) mutation analysis'

Table S16. Description of clustering approach #14: 'Amp Peak 14(10p15.3) mutation analysis'

Cluster Labels	AMP PEAK 14(10P15.3) MUTATED	AMP PEAK 14(10P15.3) WILD-TYPE
Number of samples	237	315

'Amp Peak 14(10p15.3) mutation analysis' versus 'AGE'

P value = 0.000432 (t-test), Q value = 0.18

Table S17. Clustering Approach #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 14(10P15.3) MUTATED	233	61.8 (11.2)
AMP PEAK 14(10P15.3) WILD-TYPE	308	58.3 (11.7)

Figure S3. Get High-res Image Clustering Approach #14: 'Amp Peak 14(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #15: 'Amp Peak 15(10q22.3) mutation analysis'

Table S18. Description of clustering approach #15: 'Amp Peak 15(10q22.3) mutation analysis'

Cluster Labels	AMP PEAK 15(10Q22.3) MUTATED	AMP PEAK 15(10Q22.3) WILD-TYPE
Number of samples	173	379

Clustering Approach #16: 'Amp Peak 16(11q14.1) mutation analysis'

Table S19. Description of clustering approach #16: 'Amp Peak 16(11q14.1) mutation analysis'

Cluster Labels	AMP PEAK 16(11Q14.1) MUTATED	AMP PEAK 16(11Q14.1) WILD-TYPE
Number of samples	244	308

Clustering Approach #17: 'Amp Peak 17(12p13.33) mutation analysis'

Table S20. Description of clustering approach #17: 'Amp Peak 17(12p13.33) mutation analysis'

Cluster Labels	AMP PEAK 17(12P13.33) MUTATED	AMP PEAK 17(12P13.33) WILD-TYPE
Number of samples	308	244

'Amp Peak 17(12p13.33) mutation analysis' versus 'AGE'

P value = 3.54e-07 (t-test), Q value = 0.00015

Table S21. Clustering Approach #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 17(12P13.33) MUTATED	303	62.1 (10.8)
AMP PEAK 17(12P13.33) WILD-TYPE	238	56.9 (12.0)

Figure S4. Get High-res Image Clustering Approach #17: 'Amp Peak 17(12p13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #18: 'Amp Peak 18(12p12.1) mutation analysis'

Table S22. Description of clustering approach #18: 'Amp Peak 18(12p12.1) mutation analysis'

Cluster Labels	AMP PEAK 18(12P12.1) MUTATED	AMP PEAK 18(12P12.1) WILD-TYPE
Number of samples	293	259

'Amp Peak 18(12p12.1) mutation analysis' versus 'AGE'

P value = 1.23e-08 (t-test), Q value = 5.1e-06

Table S23. Clustering Approach #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 18(12P12.1) MUTATED	286	62.5 (11.2)
AMP PEAK 18(12P12.1) WILD-TYPE	255	56.8 (11.4)

Figure S5. Get High-res Image Clustering Approach #18: 'Amp Peak 18(12p12.1) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #19: 'Amp Peak 19(14q11.2) mutation analysis'

Table S24. Description of clustering approach #19: 'Amp Peak 19(14q11.2) mutation analysis'

Cluster Labels	AMP PEAK 19(14Q11.2) MUTATED	AMP PEAK 19(14Q11.2) WILD-TYPE
Number of samples	140	412

Clustering Approach #20: 'Amp Peak 20(15q26.3) mutation analysis'

Table S25. Description of clustering approach #20: 'Amp Peak 20(15q26.3) mutation analysis'

Cluster Labels	AMP PEAK 20(15Q26.3) MUTATED	AMP PEAK 20(15Q26.3) WILD-TYPE
Number of samples	153	399

Clustering Approach #21: 'Amp Peak 21(17q25.3) mutation analysis'

Table S26. Description of clustering approach #21: 'Amp Peak 21(17q25.3) mutation analysis'

Cluster Labels	AMP PEAK 21(17Q25.3) MUTATED	AMP PEAK 21(17Q25.3) WILD-TYPE
Number of samples	202	350

Clustering Approach #22: 'Amp Peak 22(18q11.2) mutation analysis'

Table S27. Description of clustering approach #22: 'Amp Peak 22(18q11.2) mutation analysis'

Cluster Labels	AMP PEAK 22(18Q11.2) MUTATED	AMP PEAK 22(18Q11.2) WILD-TYPE
Number of samples	134	418

Clustering Approach #23: 'Amp Peak 23(19p13.12) mutation analysis'

Table S28. Description of clustering approach #23: 'Amp Peak 23(19p13.12) mutation analysis'

Cluster Labels	AMP PEAK 23(19P13.12) MUTATED	AMP PEAK 23(19P13.12) WILD-TYPE
Number of samples	299	253

Clustering Approach #24: 'Amp Peak 24(19q12) mutation analysis'

Table S29. Description of clustering approach #24: 'Amp Peak 24(19q12) mutation analysis'

Cluster Labels	AMP PEAK 24(19Q12) MUTATED	AMP PEAK 24(19Q12) WILD-TYPE
Number of samples	305	247

'Amp Peak 24(19q12) mutation analysis' versus 'AGE'

P value = 1.19e-05 (t-test), Q value = 0.0049

Table S30. Clustering Approach #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 24(19Q12) MUTATED	300	61.8 (11.1)
AMP PEAK 24(19Q12) WILD-TYPE	241	57.4 (11.7)

Figure S6. Get High-res Image Clustering Approach #24: 'Amp Peak 24(19q12) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #25: 'Amp Peak 25(19q13.2) mutation analysis'

Table S31. Description of clustering approach #25: 'Amp Peak 25(19q13.2) mutation analysis'

Cluster Labels	AMP PEAK 25(19Q13.2) MUTATED	AMP PEAK 25(19Q13.2) WILD-TYPE
Number of samples	232	320

'Amp Peak 25(19q13.2) mutation analysis' versus 'AGE'

P value = 3.37e-06 (t-test), Q value = 0.0014

Table S32. Clustering Approach #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 25(19Q13.2) MUTATED	228	62.5 (11.2)
AMP PEAK 25(19Q13.2) WILD-TYPE	313	57.8 (11.5)

Figure S7. Get High-res Image Clustering Approach #25: 'Amp Peak 25(19q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #26: 'Amp Peak 26(20p13) mutation analysis'

Table S33. Description of clustering approach #26: 'Amp Peak 26(20p13) mutation analysis'

Cluster Labels	AMP PEAK 26(20P13) MUTATED	AMP PEAK 26(20P13) WILD-TYPE
Number of samples	299	253

Clustering Approach #27: 'Amp Peak 27(20q11.21) mutation analysis'

Table S34. Description of clustering approach #27: 'Amp Peak 27(20q11.21) mutation analysis'

Cluster Labels	AMP PEAK 27(20Q11.21) MUTATED	AMP PEAK 27(20Q11.21) WILD-TYPE
Number of samples	322	230

'Amp Peak 27(20q11.21) mutation analysis' versus 'AGE'

P value = 7.62e-08 (t-test), Q value = 3.2e-05

Table S35. Clustering Approach #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 27(20Q11.21) MUTATED	315	62.0 (11.5)
AMP PEAK 27(20Q11.21) WILD-TYPE	226	56.7 (11.0)

Figure S8. Get High-res Image Clustering Approach #27: 'Amp Peak 27(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #28: 'Amp Peak 28(20q13.33) mutation analysis'

Table S36. Description of clustering approach #28: 'Amp Peak 28(20q13.33) mutation analysis'

Cluster Labels	AMP PEAK 28(20Q13.33) MUTATED	AMP PEAK 28(20Q13.33) WILD-TYPE
Number of samples	384	168

'Amp Peak 28(20q13.33) mutation analysis' versus 'AGE'

P value = 9.1e-06 (t-test), Q value = 0.0038

Table S37. Clustering Approach #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
AMP PEAK 28(20Q13.33) MUTATED	376	61.2 (11.5)
AMP PEAK 28(20Q13.33) WILD-TYPE	165	56.5 (11.1)

Figure S9. Get High-res Image Clustering Approach #28: 'Amp Peak 28(20q13.33) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #29: 'Amp Peak 29(22q12.2) mutation analysis'

Table S38. Description of clustering approach #29: 'Amp Peak 29(22q12.2) mutation analysis'

Cluster Labels	AMP PEAK 29(22Q12.2) MUTATED	AMP PEAK 29(22Q12.2) WILD-TYPE
Number of samples	88	464

Clustering Approach #30: 'Amp Peak 30(Xp11.23) mutation analysis'

Table S39. Description of clustering approach #30: 'Amp Peak 30(Xp11.23) mutation analysis'

Cluster Labels	AMP PEAK 30(XP11.23) MUTATED	AMP PEAK 30(XP11.23) WILD-TYPE
Number of samples	162	390

Clustering Approach #31: 'Amp Peak 31(Xq28) mutation analysis'

Table S40. Description of clustering approach #31: 'Amp Peak 31(Xq28) mutation analysis'

Cluster Labels	AMP PEAK 31(XQ28) MUTATED	AMP PEAK 31(XQ28) WILD-TYPE
Number of samples	219	333

Clustering Approach #32: 'Del Peak 1(1p36.11) mutation analysis'

Table S41. Description of clustering approach #32: '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	260	292

Clustering Approach #33: 'Del Peak 2(1q32.3) mutation analysis'

Table S42. Description of clustering approach #33: 'Del Peak 2(1q32.3) mutation analysis'

Cluster Labels	DEL PEAK 2(1Q32.3) MUTATED	DEL PEAK 2(1Q32.3) WILD-TYPE
Number of samples	89	463

Clustering Approach #34: 'Del Peak 3(2p25.3) mutation analysis'

Table S43. Description of clustering approach #34: 'Del Peak 3(2p25.3) mutation analysis'

Cluster Labels	DEL PEAK 3(2P25.3) MUTATED	DEL PEAK 3(2P25.3) WILD-TYPE
Number of samples	117	435

Clustering Approach #35: 'Del Peak 4(2q22.1) mutation analysis'

Table S44. Description of clustering approach #35: 'Del Peak 4(2q22.1) mutation analysis'

Cluster Labels	DEL PEAK 4(2Q22.1) MUTATED	DEL PEAK 4(2Q22.1) WILD-TYPE
Number of samples	129	423

Clustering Approach #36: 'Del Peak 5(2q37.3) mutation analysis'

Table S45. Description of clustering approach #36: 'Del Peak 5(2q37.3) mutation analysis'

Cluster Labels	DEL PEAK 5(2Q37.3) MUTATED	DEL PEAK 5(2Q37.3) WILD-TYPE
Number of samples	169	383

Clustering Approach #37: 'Del Peak 6(3p26.2) mutation analysis'

Table S46. Description of clustering approach #37: 'Del Peak 6(3p26.2) mutation analysis'

Cluster Labels	DEL PEAK 6(3P26.2) MUTATED	DEL PEAK 6(3P26.2) WILD-TYPE
Number of samples	203	349

Clustering Approach #38: 'Del Peak 7(4q22.1) mutation analysis'

Table S47. Description of clustering approach #38: 'Del Peak 7(4q22.1) mutation analysis'

Cluster Labels	DEL PEAK 7(4Q22.1) MUTATED	DEL PEAK 7(4Q22.1) WILD-TYPE
Number of samples	369	183

Clustering Approach #39: 'Del Peak 8(4q34.3) mutation analysis'

Table S48. Description of clustering approach #39: 'Del Peak 8(4q34.3) mutation analysis'

Cluster Labels	DEL PEAK 8(4Q34.3) MUTATED	DEL PEAK 8(4Q34.3) WILD-TYPE
Number of samples	399	153

Clustering Approach #40: 'Del Peak 9(5q11.2) mutation analysis'

Table S49. Description of clustering approach #40: 'Del Peak 9(5q11.2) mutation analysis'

Cluster Labels	DEL PEAK 9(5Q11.2) MUTATED	DEL PEAK 9(5Q11.2) WILD-TYPE
Number of samples	329	223

Clustering Approach #41: 'Del Peak 10(5q13.2) mutation analysis'

Table S50. Description of clustering approach #41: 'Del Peak 10(5q13.2) mutation analysis'

Cluster Labels	DEL PEAK 10(5Q13.2) MUTATED	DEL PEAK 10(5Q13.2) WILD-TYPE
Number of samples	392	160

Clustering Approach #42: 'Del Peak 11(6q27) mutation analysis'

Table S51. Description of clustering approach #42: 'Del Peak 11(6q27) mutation analysis'

Cluster Labels	DEL PEAK 11(6Q27) MUTATED	DEL PEAK 11(6Q27) WILD-TYPE
Number of samples	356	196

'Del Peak 11(6q27) mutation analysis' versus 'AGE'

P value = 0.000461 (t-test), Q value = 0.19

Table S52. Clustering Approach #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
DEL PEAK 11(6Q27) MUTATED	350	58.5 (11.4)
DEL PEAK 11(6Q27) WILD-TYPE	191	62.2 (11.6)

Figure S10. Get High-res Image Clustering Approach #42: 'Del Peak 11(6q27) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #43: 'Del Peak 12(7p22.1) mutation analysis'

Table S53. Description of clustering approach #43: 'Del Peak 12(7p22.1) mutation analysis'

Cluster Labels	DEL PEAK 12(7P22.1) MUTATED	DEL PEAK 12(7P22.1) WILD-TYPE
Number of samples	240	312

Clustering Approach #44: 'Del Peak 13(8p23.3) mutation analysis'

Table S54. Description of clustering approach #44: 'Del Peak 13(8p23.3) mutation analysis'

Cluster Labels	DEL PEAK 13(8P23.3) MUTATED	DEL PEAK 13(8P23.3) WILD-TYPE
Number of samples	371	181

Clustering Approach #45: 'Del Peak 14(8p21.2) mutation analysis'

Table S55. Description of clustering approach #45: 'Del Peak 14(8p21.2) mutation analysis'

Cluster Labels	DEL PEAK 14(8P21.2) MUTATED	DEL PEAK 14(8P21.2) WILD-TYPE
Number of samples	386	166

Clustering Approach #46: 'Del Peak 15(9p24.3) mutation analysis'

Table S56. Description of clustering approach #46: 'Del Peak 15(9p24.3) mutation analysis'

Cluster Labels	DEL PEAK 15(9P24.3) MUTATED	DEL PEAK 15(9P24.3) WILD-TYPE
Number of samples	245	307

Clustering Approach #47: 'Del Peak 16(9q21.11) mutation analysis'

Table S57. Description of clustering approach #47: 'Del Peak 16(9q21.11) mutation analysis'

Cluster Labels	DEL PEAK 16(9Q21.11) MUTATED	DEL PEAK 16(9Q21.11) WILD-TYPE
Number of samples	266	286

'Del Peak 16(9q21.11) mutation analysis' versus 'AGE'

P value = 4.09e-06 (t-test), Q value = 0.0017

Table S58. Clustering Approach #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
DEL PEAK 16(9Q21.11) MUTATED	260	62.2 (11.5)
DEL PEAK 16(9Q21.11) WILD-TYPE	281	57.6 (11.3)

Figure S11. Get High-res Image Clustering Approach #47: 'Del Peak 16(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #48: 'Del Peak 17(9q34.13) mutation analysis'

Table S59. Description of clustering approach #48: 'Del Peak 17(9q34.13) mutation analysis'

Cluster Labels	DEL PEAK 17(9Q34.13) MUTATED	DEL PEAK 17(9Q34.13) WILD-TYPE
Number of samples	329	223

Clustering Approach #49: 'Del Peak 18(10p15.3) mutation analysis'

Table S60. Description of clustering approach #49: 'Del Peak 18(10p15.3) mutation analysis'

Cluster Labels	DEL PEAK 18(10P15.3) MUTATED	DEL PEAK 18(10P15.3) WILD-TYPE
Number of samples	115	437

Clustering Approach #50: 'Del Peak 19(10q23.31) mutation analysis'

Table S61. Description of clustering approach #50: 'Del Peak 19(10q23.31) mutation analysis'

Cluster Labels	DEL PEAK 19(10Q23.31) MUTATED	DEL PEAK 19(10Q23.31) WILD-TYPE
Number of samples	214	338

Clustering Approach #51: 'Del Peak 20(10q26.3) mutation analysis'

Table S62. Description of clustering approach #51: 'Del Peak 20(10q26.3) mutation analysis'

Cluster Labels	DEL PEAK 20(10Q26.3) MUTATED	DEL PEAK 20(10Q26.3) WILD-TYPE
Number of samples	186	366

Clustering Approach #52: 'Del Peak 21(11p15.5) mutation analysis'

Table S63. Description of clustering approach #52: 'Del Peak 21(11p15.5) mutation analysis'

Cluster Labels	DEL PEAK 21(11P15.5) MUTATED	DEL PEAK 21(11P15.5) WILD-TYPE
Number of samples	328	224

Clustering Approach #53: 'Del Peak 22(11q25) mutation analysis'

Table S64. Description of clustering approach #53: 'Del Peak 22(11q25) mutation analysis'

Cluster Labels	DEL PEAK 22(11Q25) MUTATED	DEL PEAK 22(11Q25) WILD-TYPE
Number of samples	191	361

Clustering Approach #54: 'Del Peak 23(12q23.1) mutation analysis'

Table S65. Description of clustering approach #54: 'Del Peak 23(12q23.1) mutation analysis'

Cluster Labels	DEL PEAK 23(12Q23.1) MUTATED	DEL PEAK 23(12Q23.1) WILD-TYPE
Number of samples	188	364

Clustering Approach #55: 'Del Peak 24(12q24.33) mutation analysis'

Table S66. Description of clustering approach #55: 'Del Peak 24(12q24.33) mutation analysis'

Cluster Labels	DEL PEAK 24(12Q24.33) MUTATED	DEL PEAK 24(12Q24.33) WILD-TYPE
Number of samples	207	345

Clustering Approach #56: 'Del Peak 25(13q14.2) mutation analysis'

Table S67. Description of clustering approach #56: 'Del Peak 25(13q14.2) mutation analysis'

Cluster Labels	DEL PEAK 25(13Q14.2) MUTATED	DEL PEAK 25(13Q14.2) WILD-TYPE
Number of samples	342	210

Clustering Approach #57: 'Del Peak 26(14q23.2) mutation analysis'

Table S68. Description of clustering approach #57: 'Del Peak 26(14q23.2) mutation analysis'

Cluster Labels	DEL PEAK 26(14Q23.2) MUTATED	DEL PEAK 26(14Q23.2) WILD-TYPE
Number of samples	290	262

Clustering Approach #58: 'Del Peak 27(15q15.1) mutation analysis'

Table S69. Description of clustering approach #58: 'Del Peak 27(15q15.1) mutation analysis'

Cluster Labels	DEL PEAK 27(15Q15.1) MUTATED	DEL PEAK 27(15Q15.1) WILD-TYPE
Number of samples	347	205

Clustering Approach #59: 'Del Peak 28(16p13.3) mutation analysis'

Table S70. Description of clustering approach #59: 'Del Peak 28(16p13.3) mutation analysis'

Cluster Labels	DEL PEAK 28(16P13.3) MUTATED	DEL PEAK 28(16P13.3) WILD-TYPE
Number of samples	293	259

Clustering Approach #60: 'Del Peak 29(16q22.1) mutation analysis'

Table S71. Description of clustering approach #60: 'Del Peak 29(16q22.1) mutation analysis'

Cluster Labels	DEL PEAK 29(16Q22.1) MUTATED	DEL PEAK 29(16Q22.1) WILD-TYPE
Number of samples	437	115

Clustering Approach #61: 'Del Peak 30(16q23.1) mutation analysis'

Table S72. Description of clustering approach #61: 'Del Peak 30(16q23.1) mutation analysis'

Cluster Labels	DEL PEAK 30(16Q23.1) MUTATED	DEL PEAK 30(16Q23.1) WILD-TYPE
Number of samples	429	123

'Del Peak 30(16q23.1) mutation analysis' versus 'AGE'

P value = 7.72e-05 (t-test), Q value = 0.032

Table S73. Clustering Approach #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	541	59.8 (11.6)
DEL PEAK 30(16Q23.1) MUTATED	423	60.8 (11.5)
DEL PEAK 30(16Q23.1) WILD-TYPE	118	56.1 (11.2)

Figure S12. Get High-res Image Clustering Approach #61: 'Del Peak 30(16q23.1) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #62: 'Del Peak 31(17p12) mutation analysis'

Table S74. Description of clustering approach #62: 'Del Peak 31(17p12) mutation analysis'

Cluster Labels	DEL PEAK 31(17P12) MUTATED	DEL PEAK 31(17P12) WILD-TYPE
Number of samples	466	86

Clustering Approach #63: 'Del Peak 32(17q11.2) mutation analysis'

Table S75. Description of clustering approach #63: 'Del Peak 32(17q11.2) mutation analysis'

Cluster Labels	DEL PEAK 32(17Q11.2) MUTATED	DEL PEAK 32(17Q11.2) WILD-TYPE
Number of samples	450	102

Clustering Approach #64: 'Del Peak 33(18q23) mutation analysis'

Table S76. Description of clustering approach #64: 'Del Peak 33(18q23) mutation analysis'

Cluster Labels	DEL PEAK 33(18Q23) MUTATED	DEL PEAK 33(18Q23) WILD-TYPE
Number of samples	359	193

Clustering Approach #65: 'Del Peak 34(19p13.3) mutation analysis'

Table S77. Description of clustering approach #65: 'Del Peak 34(19p13.3) mutation analysis'

Cluster Labels	DEL PEAK 34(19P13.3) MUTATED	DEL PEAK 34(19P13.3) WILD-TYPE
Number of samples	485	67

Clustering Approach #66: 'Del Peak 35(19q13.33) mutation analysis'

Table S78. Description of clustering approach #66: 'Del Peak 35(19q13.33) mutation analysis'

Cluster Labels	DEL PEAK 35(19Q13.33) MUTATED	DEL PEAK 35(19Q13.33) WILD-TYPE
Number of samples	286	266

Clustering Approach #67: 'Del Peak 36(19q13.43) mutation analysis'

Table S79. Description of clustering approach #67: 'Del Peak 36(19q13.43) mutation analysis'

Cluster Labels	DEL PEAK 36(19Q13.43) MUTATED	DEL PEAK 36(19Q13.43) WILD-TYPE
Number of samples	273	279

Clustering Approach #68: 'Del Peak 37(21q22.3) mutation analysis'

Table S80. Description of clustering approach #68: 'Del Peak 37(21q22.3) mutation analysis'

Cluster Labels	DEL PEAK 37(21Q22.3) MUTATED	DEL PEAK 37(21Q22.3) WILD-TYPE
Number of samples	214	338

Clustering Approach #69: 'Del Peak 38(22q13.32) mutation analysis'

Table S81. Description of clustering approach #69: 'Del Peak 38(22q13.32) mutation analysis'

Cluster Labels	DEL PEAK 38(22Q13.32) MUTATED	DEL PEAK 38(22Q13.32) WILD-TYPE
Number of samples	477	75

Clustering Approach #70: 'Del Peak 39(Xp21.1) mutation analysis'

Table S82. Description of clustering approach #70: 'Del Peak 39(Xp21.1) mutation analysis'

Cluster Labels	DEL PEAK 39(XP21.1) MUTATED	DEL PEAK 39(XP21.1) WILD-TYPE
Number of samples	352	200

Methods & Data

Input

Cluster data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = OV-TP.clin.merged.picked.txt
Number of patients = 552
Number of clustering approaches = 70
Number of selected clinical features = 6
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

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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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