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

Glioblastoma Multiforme (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/C16W9886

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 5 clinical features across 544 patients, 15 significant findings detected with Q value < 0.25.

2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p36.21) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 2(1q32.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q44) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 4(2p24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 5(3q26.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 6(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 7(4q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 8(7p11.2) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 9(7q11.21) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 10(7q21.2) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Amp Peak 11(7q31.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 12(7q36.1) mutation analysis'. These subtypes do not correlate to any clinical features.
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(11p13) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 15(12p13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 16(12q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 17(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 18(13q34) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 19(14q32.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 20(17p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 21(17q25.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 22(19p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 23(19q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 24(21q21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 2(1p36.23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 3(1p32.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 4(1p22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 5(1q42.11) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 6(1q44) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 7(2q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 8(2q37.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 9(3p21.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 10(3q13.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 11(3q22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 12(3q29) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 13(4p16.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 14(4q34.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 15(5q35.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 16(6q22.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 17(6q26) 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 do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 19(9p21.3) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 20(9q34.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 21(10p15.3) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 22(10p13) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 23(10p11.23) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 24(10q23.31) mutation analysis'. These subtypes correlate to 'Time to Death' and 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 25(10q26.3) mutation analysis'. These subtypes correlate to 'AGE'.
2 subtypes identified in current cancer cohort by 'Del Peak 26(11p15.5) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 27(11p11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 28(11q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 29(12p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 30(12q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 31(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 32(13q14.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 33(14q13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 34(14q24.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 35(14q31.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 36(15q14) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 37(16p12.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 38(16q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 39(17p13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 40(17p13.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 41(17q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 42(18q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 43(19q13.41) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 44(21q22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 45(22q13.32) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 46(Xp22.2) 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 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.


Clinical Features	Time to Death	AGE	GENDER	KARNOFSKY PERFORMANCE SCORE	RADIATIONS RADIATION REGIMENINDICATION
Statistical Tests	logrank test	t-test	Fisher's exact test	t-test	Fisher's exact test
Amp Peak 1(1p36 21)	0.0861 (1.00)	0.316 (1.00)	0.283 (1.00)	0.653 (1.00)	0.618 (1.00)
Amp Peak 2(1q32 1)	0.436 (1.00)	0.261 (1.00)	0.624 (1.00)	0.279 (1.00)	0.837 (1.00)
Amp Peak 3(1q44)	0.497 (1.00)	0.903 (1.00)	0.297 (1.00)	0.599 (1.00)	0.903 (1.00)
Amp Peak 4(2p24 3)	0.151 (1.00)	0.268 (1.00)	0.424 (1.00)	0.583 (1.00)	1 (1.00)
Amp Peak 5(3q26 33)	0.286 (1.00)	0.0296 (1.00)	0.824 (1.00)	0.688 (1.00)	0.353 (1.00)
Amp Peak 6(4p16 3)	0.554 (1.00)	0.539 (1.00)	0.526 (1.00)	0.429 (1.00)	0.0943 (1.00)
Amp Peak 7(4q12)	0.619 (1.00)	0.532 (1.00)	0.219 (1.00)	0.597 (1.00)	0.292 (1.00)
Amp Peak 8(7p11 2)	2.57e-06 (0.000885)	5.95e-09 (2.08e-06)	0.502 (1.00)	0.0351 (1.00)	0.0239 (1.00)
Amp Peak 9(7q11 21)	0.000152 (0.0513)	8.05e-08 (2.79e-05)	0.224 (1.00)	0.658 (1.00)	0.0268 (1.00)
Amp Peak 10(7q21 2)	0.000974 (0.326)	1.06e-05 (0.0036)	0.483 (1.00)	0.49 (1.00)	0.0851 (1.00)
Amp Peak 11(7q31 2)	0.0246 (1.00)	0.00146 (0.486)	0.362 (1.00)	0.513 (1.00)	0.0234 (1.00)
Amp Peak 12(7q36 1)	0.061 (1.00)	0.00223 (0.74)	0.485 (1.00)	0.732 (1.00)	0.18 (1.00)
Amp Peak 13(8q24 21)	0.381 (1.00)	0.14 (1.00)	0.275 (1.00)	0.804 (1.00)	0.667 (1.00)
Amp Peak 14(11p13)	0.911 (1.00)	0.237 (1.00)	0.528 (1.00)	0.316 (1.00)	0.269 (1.00)
Amp Peak 15(12p13 32)	0.839 (1.00)	0.145 (1.00)	0.901 (1.00)	0.695 (1.00)	0.795 (1.00)
Amp Peak 16(12q14 1)	0.125 (1.00)	0.87 (1.00)	0.468 (1.00)	0.808 (1.00)	0.665 (1.00)
Amp Peak 17(12q15)	0.945 (1.00)	0.697 (1.00)	0.339 (1.00)	0.911 (1.00)	0.135 (1.00)
Amp Peak 18(13q34)	0.828 (1.00)	0.847 (1.00)	0.338 (1.00)	0.838 (1.00)	1 (1.00)
Amp Peak 19(14q32 33)	0.0676 (1.00)	0.00493 (1.00)	0.453 (1.00)	0.254 (1.00)	1 (1.00)
Amp Peak 20(17p13 2)	0.847 (1.00)	0.749 (1.00)	0.255 (1.00)	0.109 (1.00)	0.497 (1.00)
Amp Peak 21(17q25 1)	0.0765 (1.00)	0.0404 (1.00)	0.202 (1.00)	0.837 (1.00)	0.593 (1.00)
Amp Peak 22(19p13 2)	0.143 (1.00)	0.658 (1.00)	0.859 (1.00)	0.441 (1.00)	0.853 (1.00)
Amp Peak 23(19q12)	0.333 (1.00)	0.397 (1.00)	0.649 (1.00)	0.996 (1.00)	0.849 (1.00)
Amp Peak 24(21q21 1)	0.582 (1.00)	0.0125 (1.00)	0.681 (1.00)	0.549 (1.00)	0.565 (1.00)
Del Peak 1(1p36 32)	0.403 (1.00)	0.817 (1.00)	0.0503 (1.00)	0.999 (1.00)	1 (1.00)
Del Peak 2(1p36 23)	0.996 (1.00)	0.02 (1.00)	0.0102 (1.00)	0.193 (1.00)	0.915 (1.00)
Del Peak 3(1p32 3)	0.761 (1.00)	0.06 (1.00)	0.159 (1.00)	0.687 (1.00)	0.0786 (1.00)
Del Peak 4(1p22 1)	0.272 (1.00)	0.321 (1.00)	1 (1.00)	0.585 (1.00)	1 (1.00)
Del Peak 5(1q42 11)	0.0871 (1.00)	0.0607 (1.00)	1 (1.00)	0.0102 (1.00)	0.137 (1.00)
Del Peak 6(1q44)	0.3 (1.00)	0.286 (1.00)	0.851 (1.00)	0.0669 (1.00)	0.695 (1.00)
Del Peak 7(2q22 1)	0.311 (1.00)	0.0941 (1.00)	0.198 (1.00)	0.686 (1.00)	0.174 (1.00)
Del Peak 8(2q37 1)	0.76 (1.00)	0.345 (1.00)	0.146 (1.00)	0.657 (1.00)	0.361 (1.00)
Del Peak 9(3p21 1)	0.0237 (1.00)	0.0119 (1.00)	0.883 (1.00)	0.698 (1.00)	0.086 (1.00)
Del Peak 10(3q13 31)	0.528 (1.00)	0.063 (1.00)	0.383 (1.00)	0.306 (1.00)	0.29 (1.00)
Del Peak 11(3q22 1)	0.656 (1.00)	0.136 (1.00)	1 (1.00)	0.49 (1.00)	0.29 (1.00)
Del Peak 12(3q29)	0.26 (1.00)	0.194 (1.00)	0.891 (1.00)	0.459 (1.00)	0.193 (1.00)
Del Peak 13(4p16 3)	0.313 (1.00)	0.0312 (1.00)	0.209 (1.00)	0.154 (1.00)	0.427 (1.00)
Del Peak 14(4q34 3)	0.165 (1.00)	0.0944 (1.00)	0.0581 (1.00)	0.66 (1.00)	0.174 (1.00)
Del Peak 15(5q35 3)	0.0182 (1.00)	0.181 (1.00)	1 (1.00)	0.564 (1.00)	0.438 (1.00)
Del Peak 16(6q22 31)	0.0438 (1.00)	0.31 (1.00)	0.0965 (1.00)	0.454 (1.00)	0.683 (1.00)
Del Peak 17(6q26)	0.215 (1.00)	0.665 (1.00)	0.186 (1.00)	0.702 (1.00)	0.767 (1.00)
Del Peak 18(8p23 2)	0.181 (1.00)	0.0441 (1.00)	0.589 (1.00)	0.634 (1.00)	0.48 (1.00)
Del Peak 19(9p21 3)	0.0223 (1.00)	0.000156 (0.0524)	0.552 (1.00)	0.0926 (1.00)	0.255 (1.00)
Del Peak 20(9q34 2)	0.441 (1.00)	0.806 (1.00)	1 (1.00)	0.498 (1.00)	0.784 (1.00)
Del Peak 21(10p15 3)	1.06e-05 (0.00361)	4.22e-08 (1.47e-05)	0.088 (1.00)	0.596 (1.00)	0.0427 (1.00)
Del Peak 22(10p13)	6.7e-06 (0.00229)	2.12e-07 (7.33e-05)	0.0297 (1.00)	0.884 (1.00)	0.151 (1.00)
Del Peak 23(10p11 23)	9.14e-07 (0.000315)	1.16e-08 (4.04e-06)	0.103 (1.00)	0.232 (1.00)	0.18 (1.00)
Del Peak 24(10q23 31)	2.27e-05 (0.0077)	2.71e-06 (0.000931)	0.572 (1.00)	0.0751 (1.00)	0.302 (1.00)
Del Peak 25(10q26 3)	0.00151 (0.501)	2.89e-05 (0.00976)	0.478 (1.00)	0.0613 (1.00)	0.551 (1.00)
Del Peak 26(11p15 5)	0.0325 (1.00)	0.00446 (1.00)	0.145 (1.00)	0.242 (1.00)	0.827 (1.00)
Del Peak 27(11p11 2)	0.0736 (1.00)	0.595 (1.00)	0.139 (1.00)	0.796 (1.00)	0.342 (1.00)
Del Peak 28(11q14 1)	0.747 (1.00)	0.865 (1.00)	0.245 (1.00)	0.538 (1.00)	0.0201 (1.00)
Del Peak 29(12p13 1)	0.338 (1.00)	0.795 (1.00)	0.442 (1.00)	0.846 (1.00)	1 (1.00)
Del Peak 30(12q12)	0.641 (1.00)	0.798 (1.00)	0.898 (1.00)	0.81 (1.00)	0.285 (1.00)
Del Peak 31(12q15)	0.516 (1.00)	0.952 (1.00)	0.371 (1.00)	0.186 (1.00)	0.285 (1.00)
Del Peak 32(13q14 2)	0.586 (1.00)	0.538 (1.00)	0.929 (1.00)	0.828 (1.00)	0.355 (1.00)
Del Peak 33(14q13 1)	0.756 (1.00)	0.529 (1.00)	0.222 (1.00)	0.262 (1.00)	0.694 (1.00)
Del Peak 34(14q24 2)	0.867 (1.00)	0.443 (1.00)	0.394 (1.00)	0.605 (1.00)	0.843 (1.00)
Del Peak 35(14q31 3)	0.924 (1.00)	0.721 (1.00)	0.628 (1.00)	0.647 (1.00)	0.685 (1.00)
Del Peak 36(15q14)	0.459 (1.00)	0.0774 (1.00)	0.622 (1.00)	0.808 (1.00)	0.149 (1.00)
Del Peak 37(16p12 2)	0.333 (1.00)	0.31 (1.00)	0.237 (1.00)	0.808 (1.00)	0.804 (1.00)
Del Peak 38(16q23 3)	0.219 (1.00)	0.956 (1.00)	0.485 (1.00)	0.266 (1.00)	0.0288 (1.00)
Del Peak 39(17p13 2)	0.601 (1.00)	0.554 (1.00)	0.221 (1.00)	0.189 (1.00)	0.609 (1.00)
Del Peak 40(17p13 1)	0.826 (1.00)	0.183 (1.00)	0.0613 (1.00)	0.797 (1.00)	0.11 (1.00)
Del Peak 41(17q11 2)	0.605 (1.00)	0.583 (1.00)	1 (1.00)	0.245 (1.00)	0.0498 (1.00)
Del Peak 42(18q22 3)	0.918 (1.00)	0.448 (1.00)	0.708 (1.00)	0.128 (1.00)	0.603 (1.00)
Del Peak 43(19q13 41)	0.066 (1.00)	0.449 (1.00)	1 (1.00)	0.264 (1.00)	0.406 (1.00)
Del Peak 44(21q22 3)	0.757 (1.00)	0.0758 (1.00)	0.258 (1.00)	0.198 (1.00)	0.883 (1.00)
Del Peak 45(22q13 32)	0.581 (1.00)	0.387 (1.00)	0.856 (1.00)	0.518 (1.00)	0.705 (1.00)
Del Peak 46(Xp22 2)	0.277 (1.00)	0.467 (1.00)	0.675 (1.00)	0.825 (1.00)	1 (1.00)

Clustering Approach #1: 'Amp Peak 1(1p36.21) mutation analysis'

Table S1. Description of clustering approach #1: 'Amp Peak 1(1p36.21) mutation analysis'

Cluster Labels	AMP PEAK 1(1P36.21) MUTATED	AMP PEAK 1(1P36.21) WILD-TYPE
Number of samples	87	457

Clustering Approach #2: 'Amp Peak 2(1q32.1) mutation analysis'

Table S2. Description of clustering approach #2: 'Amp Peak 2(1q32.1) mutation analysis'

Cluster Labels	AMP PEAK 2(1Q32.1) MUTATED	AMP PEAK 2(1Q32.1) WILD-TYPE
Number of samples	148	396

Clustering Approach #3: 'Amp Peak 3(1q44) mutation analysis'

Table S3. Description of clustering approach #3: 'Amp Peak 3(1q44) mutation analysis'

Cluster Labels	AMP PEAK 3(1Q44) MUTATED	AMP PEAK 3(1Q44) WILD-TYPE
Number of samples	94	450

Clustering Approach #4: 'Amp Peak 4(2p24.3) mutation analysis'

Table S4. Description of clustering approach #4: 'Amp Peak 4(2p24.3) mutation analysis'

Cluster Labels	AMP PEAK 4(2P24.3) MUTATED	AMP PEAK 4(2P24.3) WILD-TYPE
Number of samples	44	500

Clustering Approach #5: 'Amp Peak 5(3q26.33) mutation analysis'

Table S5. Description of clustering approach #5: 'Amp Peak 5(3q26.33) mutation analysis'

Cluster Labels	AMP PEAK 5(3Q26.33) MUTATED	AMP PEAK 5(3Q26.33) WILD-TYPE
Number of samples	105	439

Clustering Approach #6: 'Amp Peak 6(4p16.3) mutation analysis'

Table S6. Description of clustering approach #6: 'Amp Peak 6(4p16.3) mutation analysis'

Cluster Labels	AMP PEAK 6(4P16.3) MUTATED	AMP PEAK 6(4P16.3) WILD-TYPE
Number of samples	45	499

Clustering Approach #7: 'Amp Peak 7(4q12) mutation analysis'

Table S7. Description of clustering approach #7: 'Amp Peak 7(4q12) mutation analysis'

Cluster Labels	AMP PEAK 7(4Q12) MUTATED	AMP PEAK 7(4Q12) WILD-TYPE
Number of samples	103	441

Clustering Approach #8: 'Amp Peak 8(7p11.2) mutation analysis'

Table S8. Description of clustering approach #8: 'Amp Peak 8(7p11.2) mutation analysis'

Cluster Labels	AMP PEAK 8(7P11.2) MUTATED	AMP PEAK 8(7P11.2) WILD-TYPE
Number of samples	478	66

'Amp Peak 8(7p11.2) mutation analysis' versus 'Time to Death'

P value = 2.57e-06 (logrank test), Q value = 0.00088

Table S9. Clustering Approach #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
AMP PEAK 8(7P11.2) MUTATED	478	367	0.1 - 127.6 (9.2)
AMP PEAK 8(7P11.2) WILD-TYPE	66	44	0.2 - 108.8 (13.5)

Figure S1. Get High-res Image Clustering Approach #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 8(7p11.2) mutation analysis' versus 'AGE'

P value = 5.95e-09 (t-test), Q value = 2.1e-06

Table S10. Clustering Approach #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
AMP PEAK 8(7P11.2) MUTATED	478	59.7 (12.4)
AMP PEAK 8(7P11.2) WILD-TYPE	66	43.9 (19.0)

Figure S2. Get High-res Image Clustering Approach #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #9: 'Amp Peak 9(7q11.21) mutation analysis'

Table S11. Description of clustering approach #9: 'Amp Peak 9(7q11.21) mutation analysis'

Cluster Labels	AMP PEAK 9(7Q11.21) MUTATED	AMP PEAK 9(7Q11.21) WILD-TYPE
Number of samples	439	105

'Amp Peak 9(7q11.21) mutation analysis' versus 'Time to Death'

P value = 0.000152 (logrank test), Q value = 0.051

Table S12. Clustering Approach #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
AMP PEAK 9(7Q11.21) MUTATED	439	333	0.1 - 127.6 (9.2)
AMP PEAK 9(7Q11.21) WILD-TYPE	105	78	0.2 - 108.8 (12.4)

Figure S3. Get High-res Image Clustering Approach #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 9(7q11.21) mutation analysis' versus 'AGE'

P value = 8.05e-08 (t-test), Q value = 2.8e-05

Table S13. Clustering Approach #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
AMP PEAK 9(7Q11.21) MUTATED	439	59.9 (12.3)
AMP PEAK 9(7Q11.21) WILD-TYPE	105	49.2 (18.3)

Figure S4. Get High-res Image Clustering Approach #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #10: 'Amp Peak 10(7q21.2) mutation analysis'

Table S14. Description of clustering approach #10: 'Amp Peak 10(7q21.2) mutation analysis'

Cluster Labels	AMP PEAK 10(7Q21.2) MUTATED	AMP PEAK 10(7Q21.2) WILD-TYPE
Number of samples	453	91

'Amp Peak 10(7q21.2) mutation analysis' versus 'AGE'

P value = 1.06e-05 (t-test), Q value = 0.0036

Table S15. Clustering Approach #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
AMP PEAK 10(7Q21.2) MUTATED	453	59.5 (12.2)
AMP PEAK 10(7Q21.2) WILD-TYPE	91	49.5 (19.9)

Figure S5. Get High-res Image Clustering Approach #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #11: 'Amp Peak 11(7q31.2) mutation analysis'

Table S16. Description of clustering approach #11: 'Amp Peak 11(7q31.2) mutation analysis'

Cluster Labels	AMP PEAK 11(7Q31.2) MUTATED	AMP PEAK 11(7Q31.2) WILD-TYPE
Number of samples	446	98

Clustering Approach #12: 'Amp Peak 12(7q36.1) mutation analysis'

Table S17. Description of clustering approach #12: 'Amp Peak 12(7q36.1) mutation analysis'

Cluster Labels	AMP PEAK 12(7Q36.1) MUTATED	AMP PEAK 12(7Q36.1) WILD-TYPE
Number of samples	451	93

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

Table S18. 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	63	481

Clustering Approach #14: 'Amp Peak 14(11p13) mutation analysis'

Table S19. Description of clustering approach #14: 'Amp Peak 14(11p13) mutation analysis'

Cluster Labels	AMP PEAK 14(11P13) MUTATED	AMP PEAK 14(11P13) WILD-TYPE
Number of samples	24	520

Clustering Approach #15: 'Amp Peak 15(12p13.32) mutation analysis'

Table S20. Description of clustering approach #15: 'Amp Peak 15(12p13.32) mutation analysis'

Cluster Labels	AMP PEAK 15(12P13.32) MUTATED	AMP PEAK 15(12P13.32) WILD-TYPE
Number of samples	78	466

Clustering Approach #16: 'Amp Peak 16(12q14.1) mutation analysis'

Table S21. Description of clustering approach #16: 'Amp Peak 16(12q14.1) mutation analysis'

Cluster Labels	AMP PEAK 16(12Q14.1) MUTATED	AMP PEAK 16(12Q14.1) WILD-TYPE
Number of samples	127	417

Clustering Approach #17: 'Amp Peak 17(12q15) mutation analysis'

Table S22. Description of clustering approach #17: 'Amp Peak 17(12q15) mutation analysis'

Cluster Labels	AMP PEAK 17(12Q15) MUTATED	AMP PEAK 17(12Q15) WILD-TYPE
Number of samples	87	457

Clustering Approach #18: 'Amp Peak 18(13q34) mutation analysis'

Table S23. Description of clustering approach #18: 'Amp Peak 18(13q34) mutation analysis'

Cluster Labels	AMP PEAK 18(13Q34) MUTATED	AMP PEAK 18(13Q34) WILD-TYPE
Number of samples	30	514

Clustering Approach #19: 'Amp Peak 19(14q32.33) mutation analysis'

Table S24. Description of clustering approach #19: 'Amp Peak 19(14q32.33) mutation analysis'

Cluster Labels	AMP PEAK 19(14Q32.33) MUTATED	AMP PEAK 19(14Q32.33) WILD-TYPE
Number of samples	31	513

Clustering Approach #20: 'Amp Peak 20(17p13.2) mutation analysis'

Table S25. Description of clustering approach #20: 'Amp Peak 20(17p13.2) mutation analysis'

Cluster Labels	AMP PEAK 20(17P13.2) MUTATED	AMP PEAK 20(17P13.2) WILD-TYPE
Number of samples	43	501

Clustering Approach #21: 'Amp Peak 21(17q25.1) mutation analysis'

Table S26. Description of clustering approach #21: 'Amp Peak 21(17q25.1) mutation analysis'

Cluster Labels	AMP PEAK 21(17Q25.1) MUTATED	AMP PEAK 21(17Q25.1) WILD-TYPE
Number of samples	74	470

Clustering Approach #22: 'Amp Peak 22(19p13.2) mutation analysis'

Table S27. Description of clustering approach #22: 'Amp Peak 22(19p13.2) mutation analysis'

Cluster Labels	AMP PEAK 22(19P13.2) MUTATED	AMP PEAK 22(19P13.2) WILD-TYPE
Number of samples	231	313

Clustering Approach #23: 'Amp Peak 23(19q12) mutation analysis'

Table S28. Description of clustering approach #23: 'Amp Peak 23(19q12) mutation analysis'

Cluster Labels	AMP PEAK 23(19Q12) MUTATED	AMP PEAK 23(19Q12) WILD-TYPE
Number of samples	196	348

Clustering Approach #24: 'Amp Peak 24(21q21.1) mutation analysis'

Table S29. Description of clustering approach #24: 'Amp Peak 24(21q21.1) mutation analysis'

Cluster Labels	AMP PEAK 24(21Q21.1) MUTATED	AMP PEAK 24(21Q21.1) WILD-TYPE
Number of samples	62	482

Clustering Approach #25: 'Del Peak 1(1p36.32) mutation analysis'

Table S30. Description of clustering approach #25: 'Del Peak 1(1p36.32) mutation analysis'

Cluster Labels	DEL PEAK 1(1P36.32) MUTATED	DEL PEAK 1(1P36.32) WILD-TYPE
Number of samples	95	449

Clustering Approach #26: 'Del Peak 2(1p36.23) mutation analysis'

Table S31. Description of clustering approach #26: 'Del Peak 2(1p36.23) mutation analysis'

Cluster Labels	DEL PEAK 2(1P36.23) MUTATED	DEL PEAK 2(1P36.23) WILD-TYPE
Number of samples	131	413

Clustering Approach #27: 'Del Peak 3(1p32.3) mutation analysis'

Table S32. Description of clustering approach #27: 'Del Peak 3(1p32.3) mutation analysis'

Cluster Labels	DEL PEAK 3(1P32.3) MUTATED	DEL PEAK 3(1P32.3) WILD-TYPE
Number of samples	59	485

Clustering Approach #28: 'Del Peak 4(1p22.1) mutation analysis'

Table S33. Description of clustering approach #28: 'Del Peak 4(1p22.1) mutation analysis'

Cluster Labels	DEL PEAK 4(1P22.1) MUTATED	DEL PEAK 4(1P22.1) WILD-TYPE
Number of samples	46	498

Clustering Approach #29: 'Del Peak 5(1q42.11) mutation analysis'

Table S34. Description of clustering approach #29: 'Del Peak 5(1q42.11) mutation analysis'

Cluster Labels	DEL PEAK 5(1Q42.11) MUTATED	DEL PEAK 5(1Q42.11) WILD-TYPE
Number of samples	45	499

Clustering Approach #30: 'Del Peak 6(1q44) mutation analysis'

Table S35. Description of clustering approach #30: 'Del Peak 6(1q44) mutation analysis'

Cluster Labels	DEL PEAK 6(1Q44) MUTATED	DEL PEAK 6(1Q44) WILD-TYPE
Number of samples	31	513

Clustering Approach #31: 'Del Peak 7(2q22.1) mutation analysis'

Table S36. Description of clustering approach #31: 'Del Peak 7(2q22.1) mutation analysis'

Cluster Labels	DEL PEAK 7(2Q22.1) MUTATED	DEL PEAK 7(2Q22.1) WILD-TYPE
Number of samples	43	501

Clustering Approach #32: 'Del Peak 8(2q37.1) mutation analysis'

Table S37. Description of clustering approach #32: 'Del Peak 8(2q37.1) mutation analysis'

Cluster Labels	DEL PEAK 8(2Q37.1) MUTATED	DEL PEAK 8(2Q37.1) WILD-TYPE
Number of samples	55	489

Clustering Approach #33: 'Del Peak 9(3p21.1) mutation analysis'

Table S38. Description of clustering approach #33: 'Del Peak 9(3p21.1) mutation analysis'

Cluster Labels	DEL PEAK 9(3P21.1) MUTATED	DEL PEAK 9(3P21.1) WILD-TYPE
Number of samples	52	492

Clustering Approach #34: 'Del Peak 10(3q13.31) mutation analysis'

Table S39. Description of clustering approach #34: 'Del Peak 10(3q13.31) mutation analysis'

Cluster Labels	DEL PEAK 10(3Q13.31) MUTATED	DEL PEAK 10(3Q13.31) WILD-TYPE
Number of samples	55	489

Clustering Approach #35: 'Del Peak 11(3q22.1) mutation analysis'

Table S40. Description of clustering approach #35: 'Del Peak 11(3q22.1) mutation analysis'

Cluster Labels	DEL PEAK 11(3Q22.1) MUTATED	DEL PEAK 11(3Q22.1) WILD-TYPE
Number of samples	55	489

Clustering Approach #36: 'Del Peak 12(3q29) mutation analysis'

Table S41. Description of clustering approach #36: 'Del Peak 12(3q29) mutation analysis'

Cluster Labels	DEL PEAK 12(3Q29) MUTATED	DEL PEAK 12(3Q29) WILD-TYPE
Number of samples	62	482

Clustering Approach #37: 'Del Peak 13(4p16.3) mutation analysis'

Table S42. Description of clustering approach #37: 'Del Peak 13(4p16.3) mutation analysis'

Cluster Labels	DEL PEAK 13(4P16.3) MUTATED	DEL PEAK 13(4P16.3) WILD-TYPE
Number of samples	76	468

Clustering Approach #38: 'Del Peak 14(4q34.3) mutation analysis'

Table S43. Description of clustering approach #38: 'Del Peak 14(4q34.3) mutation analysis'

Cluster Labels	DEL PEAK 14(4Q34.3) MUTATED	DEL PEAK 14(4Q34.3) WILD-TYPE
Number of samples	89	455

Clustering Approach #39: 'Del Peak 15(5q35.3) mutation analysis'

Table S44. Description of clustering approach #39: 'Del Peak 15(5q35.3) mutation analysis'

Cluster Labels	DEL PEAK 15(5Q35.3) MUTATED	DEL PEAK 15(5Q35.3) WILD-TYPE
Number of samples	52	492

Clustering Approach #40: 'Del Peak 16(6q22.31) mutation analysis'

Table S45. Description of clustering approach #40: 'Del Peak 16(6q22.31) mutation analysis'

Cluster Labels	DEL PEAK 16(6Q22.31) MUTATED	DEL PEAK 16(6Q22.31) WILD-TYPE
Number of samples	152	392

Clustering Approach #41: 'Del Peak 17(6q26) mutation analysis'

Table S46. Description of clustering approach #41: 'Del Peak 17(6q26) mutation analysis'

Cluster Labels	DEL PEAK 17(6Q26) MUTATED	DEL PEAK 17(6Q26) WILD-TYPE
Number of samples	171	373

Clustering Approach #42: 'Del Peak 18(8p23.2) mutation analysis'

Table S47. Description of clustering approach #42: '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	65	479

Clustering Approach #43: 'Del Peak 19(9p21.3) mutation analysis'

Table S48. Description of clustering approach #43: 'Del Peak 19(9p21.3) mutation analysis'

Cluster Labels	DEL PEAK 19(9P21.3) MUTATED	DEL PEAK 19(9P21.3) WILD-TYPE
Number of samples	399	145

'Del Peak 19(9p21.3) mutation analysis' versus 'AGE'

P value = 0.000156 (t-test), Q value = 0.052

Table S49. Clustering Approach #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 19(9P21.3) MUTATED	399	59.3 (13.5)
DEL PEAK 19(9P21.3) WILD-TYPE	145	53.7 (15.7)

Figure S6. Get High-res Image Clustering Approach #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #44: 'Del Peak 20(9q34.2) mutation analysis'

Table S50. Description of clustering approach #44: 'Del Peak 20(9q34.2) mutation analysis'

Cluster Labels	DEL PEAK 20(9Q34.2) MUTATED	DEL PEAK 20(9Q34.2) WILD-TYPE
Number of samples	70	474

Clustering Approach #45: 'Del Peak 21(10p15.3) mutation analysis'

Table S51. Description of clustering approach #45: 'Del Peak 21(10p15.3) mutation analysis'

Cluster Labels	DEL PEAK 21(10P15.3) MUTATED	DEL PEAK 21(10P15.3) WILD-TYPE
Number of samples	445	99

'Del Peak 21(10p15.3) mutation analysis' versus 'Time to Death'

P value = 1.06e-05 (logrank test), Q value = 0.0036

Table S52. Clustering Approach #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
DEL PEAK 21(10P15.3) MUTATED	445	342	0.1 - 92.6 (9.4)
DEL PEAK 21(10P15.3) WILD-TYPE	99	69	0.1 - 127.6 (10.6)

Figure S7. Get High-res Image Clustering Approach #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 21(10p15.3) mutation analysis' versus 'AGE'

P value = 4.22e-08 (t-test), Q value = 1.5e-05

Table S53. Clustering Approach #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 21(10P15.3) MUTATED	445	59.9 (12.3)
DEL PEAK 21(10P15.3) WILD-TYPE	99	48.5 (18.4)

Figure S8. Get High-res Image Clustering Approach #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #46: 'Del Peak 22(10p13) mutation analysis'

Table S54. Description of clustering approach #46: 'Del Peak 22(10p13) mutation analysis'

Cluster Labels	DEL PEAK 22(10P13) MUTATED	DEL PEAK 22(10P13) WILD-TYPE
Number of samples	447	97

'Del Peak 22(10p13) mutation analysis' versus 'Time to Death'

P value = 6.7e-06 (logrank test), Q value = 0.0023

Table S55. Clustering Approach #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
DEL PEAK 22(10P13) MUTATED	447	343	0.1 - 92.6 (9.4)
DEL PEAK 22(10P13) WILD-TYPE	97	68	0.1 - 127.6 (9.8)

Figure S9. Get High-res Image Clustering Approach #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 22(10p13) mutation analysis' versus 'AGE'

P value = 2.12e-07 (t-test), Q value = 7.3e-05

Table S56. Clustering Approach #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 22(10P13) MUTATED	447	59.8 (12.2)
DEL PEAK 22(10P13) WILD-TYPE	97	48.7 (18.9)

Figure S10. Get High-res Image Clustering Approach #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #47: 'Del Peak 23(10p11.23) mutation analysis'

Table S57. Description of clustering approach #47: 'Del Peak 23(10p11.23) mutation analysis'

Cluster Labels	DEL PEAK 23(10P11.23) MUTATED	DEL PEAK 23(10P11.23) WILD-TYPE
Number of samples	451	93

'Del Peak 23(10p11.23) mutation analysis' versus 'Time to Death'

P value = 9.14e-07 (logrank test), Q value = 0.00032

Table S58. Clustering Approach #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
DEL PEAK 23(10P11.23) MUTATED	451	345	0.1 - 92.6 (9.4)
DEL PEAK 23(10P11.23) WILD-TYPE	93	66	0.1 - 127.6 (12.4)

Figure S11. Get High-res Image Clustering Approach #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 23(10p11.23) mutation analysis' versus 'AGE'

P value = 1.16e-08 (t-test), Q value = 4e-06

Table S59. Clustering Approach #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 23(10P11.23) MUTATED	451	60.0 (12.1)
DEL PEAK 23(10P11.23) WILD-TYPE	93	47.4 (18.8)

Figure S12. Get High-res Image Clustering Approach #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #48: 'Del Peak 24(10q23.31) mutation analysis'

Table S60. Description of clustering approach #48: 'Del Peak 24(10q23.31) mutation analysis'

Cluster Labels	DEL PEAK 24(10Q23.31) MUTATED	DEL PEAK 24(10Q23.31) WILD-TYPE
Number of samples	486	58

'Del Peak 24(10q23.31) mutation analysis' versus 'Time to Death'

P value = 2.27e-05 (logrank test), Q value = 0.0077

Table S61. Clustering Approach #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	544	411	0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) MUTATED	486	372	0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) WILD-TYPE	58	39	0.2 - 108.8 (10.9)

Figure S13. Get High-res Image Clustering Approach #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 24(10q23.31) mutation analysis' versus 'AGE'

P value = 2.71e-06 (t-test), Q value = 0.00093

Table S62. Clustering Approach #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 24(10Q23.31) MUTATED	486	59.2 (13.0)
DEL PEAK 24(10Q23.31) WILD-TYPE	58	46.2 (18.7)

Figure S14. Get High-res Image Clustering Approach #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #49: 'Del Peak 25(10q26.3) mutation analysis'

Table S63. Description of clustering approach #49: 'Del Peak 25(10q26.3) mutation analysis'

Cluster Labels	DEL PEAK 25(10Q26.3) MUTATED	DEL PEAK 25(10Q26.3) WILD-TYPE
Number of samples	487	57

'Del Peak 25(10q26.3) mutation analysis' versus 'AGE'

P value = 2.89e-05 (t-test), Q value = 0.0098

Table S64. Clustering Approach #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'

	nPatients	Mean (Std.Dev)
ALL	544	57.8 (14.3)
DEL PEAK 25(10Q26.3) MUTATED	487	59.0 (13.1)
DEL PEAK 25(10Q26.3) WILD-TYPE	57	47.4 (19.0)

Figure S15. Get High-res Image Clustering Approach #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Clustering Approach #50: 'Del Peak 26(11p15.5) mutation analysis'

Table S65. Description of clustering approach #50: 'Del Peak 26(11p15.5) mutation analysis'

Cluster Labels	DEL PEAK 26(11P15.5) MUTATED	DEL PEAK 26(11P15.5) WILD-TYPE
Number of samples	124	420

Clustering Approach #51: 'Del Peak 27(11p11.2) mutation analysis'

Table S66. Description of clustering approach #51: 'Del Peak 27(11p11.2) mutation analysis'

Cluster Labels	DEL PEAK 27(11P11.2) MUTATED	DEL PEAK 27(11P11.2) WILD-TYPE
Number of samples	99	445

Clustering Approach #52: 'Del Peak 28(11q14.1) mutation analysis'

Table S67. Description of clustering approach #52: 'Del Peak 28(11q14.1) mutation analysis'

Cluster Labels	DEL PEAK 28(11Q14.1) MUTATED	DEL PEAK 28(11Q14.1) WILD-TYPE
Number of samples	93	451

Clustering Approach #53: 'Del Peak 29(12p13.1) mutation analysis'

Table S68. Description of clustering approach #53: 'Del Peak 29(12p13.1) mutation analysis'

Cluster Labels	DEL PEAK 29(12P13.1) MUTATED	DEL PEAK 29(12P13.1) WILD-TYPE
Number of samples	73	471

Clustering Approach #54: 'Del Peak 30(12q12) mutation analysis'

Table S69. Description of clustering approach #54: 'Del Peak 30(12q12) mutation analysis'

Cluster Labels	DEL PEAK 30(12Q12) MUTATED	DEL PEAK 30(12Q12) WILD-TYPE
Number of samples	74	470

Clustering Approach #55: 'Del Peak 31(12q15) mutation analysis'

Table S70. Description of clustering approach #55: 'Del Peak 31(12q15) mutation analysis'

Cluster Labels	DEL PEAK 31(12Q15) MUTATED	DEL PEAK 31(12Q15) WILD-TYPE
Number of samples	74	470

Clustering Approach #56: 'Del Peak 32(13q14.2) mutation analysis'

Table S71. Description of clustering approach #56: 'Del Peak 32(13q14.2) mutation analysis'

Cluster Labels	DEL PEAK 32(13Q14.2) MUTATED	DEL PEAK 32(13Q14.2) WILD-TYPE
Number of samples	230	314

Clustering Approach #57: 'Del Peak 33(14q13.1) mutation analysis'

Table S72. Description of clustering approach #57: 'Del Peak 33(14q13.1) mutation analysis'

Cluster Labels	DEL PEAK 33(14Q13.1) MUTATED	DEL PEAK 33(14Q13.1) WILD-TYPE
Number of samples	173	371

Clustering Approach #58: 'Del Peak 34(14q24.2) mutation analysis'

Table S73. Description of clustering approach #58: 'Del Peak 34(14q24.2) mutation analysis'

Cluster Labels	DEL PEAK 34(14Q24.2) MUTATED	DEL PEAK 34(14Q24.2) WILD-TYPE
Number of samples	168	376

Clustering Approach #59: 'Del Peak 35(14q31.3) mutation analysis'

Table S74. Description of clustering approach #59: 'Del Peak 35(14q31.3) mutation analysis'

Cluster Labels	DEL PEAK 35(14Q31.3) MUTATED	DEL PEAK 35(14Q31.3) WILD-TYPE
Number of samples	155	389

Clustering Approach #60: 'Del Peak 36(15q14) mutation analysis'

Table S75. Description of clustering approach #60: 'Del Peak 36(15q14) mutation analysis'

Cluster Labels	DEL PEAK 36(15Q14) MUTATED	DEL PEAK 36(15Q14) WILD-TYPE
Number of samples	146	398

Clustering Approach #61: 'Del Peak 37(16p12.2) mutation analysis'

Table S76. Description of clustering approach #61: 'Del Peak 37(16p12.2) mutation analysis'

Cluster Labels	DEL PEAK 37(16P12.2) MUTATED	DEL PEAK 37(16P12.2) WILD-TYPE
Number of samples	89	455

Clustering Approach #62: 'Del Peak 38(16q23.3) mutation analysis'

Table S77. Description of clustering approach #62: 'Del Peak 38(16q23.3) mutation analysis'

Cluster Labels	DEL PEAK 38(16Q23.3) MUTATED	DEL PEAK 38(16Q23.3) WILD-TYPE
Number of samples	93	451

Clustering Approach #63: 'Del Peak 39(17p13.2) mutation analysis'

Table S78. Description of clustering approach #63: 'Del Peak 39(17p13.2) mutation analysis'

Cluster Labels	DEL PEAK 39(17P13.2) MUTATED	DEL PEAK 39(17P13.2) WILD-TYPE
Number of samples	81	463

Clustering Approach #64: 'Del Peak 40(17p13.1) mutation analysis'

Table S79. Description of clustering approach #64: 'Del Peak 40(17p13.1) mutation analysis'

Cluster Labels	DEL PEAK 40(17P13.1) MUTATED	DEL PEAK 40(17P13.1) WILD-TYPE
Number of samples	91	453

Clustering Approach #65: 'Del Peak 41(17q11.2) mutation analysis'

Table S80. Description of clustering approach #65: 'Del Peak 41(17q11.2) mutation analysis'

Cluster Labels	DEL PEAK 41(17Q11.2) MUTATED	DEL PEAK 41(17Q11.2) WILD-TYPE
Number of samples	67	477

Clustering Approach #66: 'Del Peak 42(18q22.3) mutation analysis'

Table S81. Description of clustering approach #66: 'Del Peak 42(18q22.3) mutation analysis'

Cluster Labels	DEL PEAK 42(18Q22.3) MUTATED	DEL PEAK 42(18Q22.3) WILD-TYPE
Number of samples	78	466

Clustering Approach #67: 'Del Peak 43(19q13.41) mutation analysis'

Table S82. Description of clustering approach #67: 'Del Peak 43(19q13.41) mutation analysis'

Cluster Labels	DEL PEAK 43(19Q13.41) MUTATED	DEL PEAK 43(19Q13.41) WILD-TYPE
Number of samples	98	446

Clustering Approach #68: 'Del Peak 44(21q22.3) mutation analysis'

Table S83. Description of clustering approach #68: 'Del Peak 44(21q22.3) mutation analysis'

Cluster Labels	DEL PEAK 44(21Q22.3) MUTATED	DEL PEAK 44(21Q22.3) WILD-TYPE
Number of samples	58	486

Clustering Approach #69: 'Del Peak 45(22q13.32) mutation analysis'

Table S84. Description of clustering approach #69: 'Del Peak 45(22q13.32) mutation analysis'

Cluster Labels	DEL PEAK 45(22Q13.32) MUTATED	DEL PEAK 45(22Q13.32) WILD-TYPE
Number of samples	204	340

Clustering Approach #70: 'Del Peak 46(Xp22.2) mutation analysis'

Table S85. Description of clustering approach #70: 'Del Peak 46(Xp22.2) mutation analysis'

Cluster Labels	DEL PEAK 46(XP22.2) MUTATED	DEL PEAK 46(XP22.2) WILD-TYPE
Number of samples	122	422

Methods & Data

Input

Cluster data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = GBM-TP.clin.merged.picked.txt
Number of patients = 544
Number of clustering approaches = 70
Number of selected clinical features = 5
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)

Made with Nozzle