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

Skin Cutaneous Melanoma (Metastatic)

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/C19K48GT

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 51 different clustering approaches and 7 clinical features across 149 patients, no significant finding detected with Q value < 0.25.

2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p12) 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 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(3p13) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 5(4q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 6(5p15.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 7(5q35.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 8(6p25.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 9(6q12) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 10(7p22.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 11(7q34) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 12(8q11.21) 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(9p24.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 15(11q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 16(11q13.4) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 17(12q14.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 18(12q15) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 19(15q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 20(17q25.3) 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(20q13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Amp Peak 23(22q13.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 2(1p22.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 3(2q37.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 4(3q23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 5(4q34.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 6(5q11.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 7(5q31.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 8(6q26) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 9(7q31.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 10(8p23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 11(9p23) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 12(9p21.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 13(10p15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 14(10q23.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 15(10q26.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 16(11q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 17(12p13.31) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 18(12q23.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 19(12q24.33) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 20(13q34) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 21(14q32.2) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 22(15q13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 23(15q15.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 24(16p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 25(16q12.1) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 26(16q24.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 27(19p13.3) mutation analysis'. These subtypes do not correlate to any clinical features.
2 subtypes identified in current cancer cohort by 'Del Peak 28(22q13.31) 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 51 different clustering approaches and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.


Clinical Features	Time to Death	AGE	GENDER	DISTANT METASTASIS	LYMPH NODE METASTASIS	TUMOR STAGECODE	NEOPLASM DISEASESTAGE
Statistical Tests	logrank test	t-test	Fisher's exact test	Chi-square test	Chi-square test	t-test	Chi-square test
Amp Peak 1(1p12)	0.0289 (1.00)	0.859 (1.00)	0.584 (1.00)	0.78 (1.00)	0.311 (1.00)		0.102 (1.00)
Amp Peak 2(1q21 3)	0.862 (1.00)	0.569 (1.00)	1 (1.00)	0.316 (1.00)	0.306 (1.00)		0.682 (1.00)
Amp Peak 3(1q44)	0.181 (1.00)	0.793 (1.00)	0.734 (1.00)	0.324 (1.00)	0.349 (1.00)		0.203 (1.00)
Amp Peak 4(3p13)	0.146 (1.00)	0.0333 (1.00)	0.411 (1.00)	0.611 (1.00)	0.976 (1.00)		0.248 (1.00)
Amp Peak 5(4q12)	0.328 (1.00)	0.213 (1.00)	0.669 (1.00)	0.657 (1.00)	0.886 (1.00)		0.737 (1.00)
Amp Peak 6(5p15 33)	0.065 (1.00)	0.496 (1.00)	1 (1.00)	0.21 (1.00)	0.568 (1.00)		0.313 (1.00)
Amp Peak 7(5q35 3)	0.528 (1.00)	0.257 (1.00)	0.218 (1.00)	0.0307 (1.00)	0.526 (1.00)		0.653 (1.00)
Amp Peak 8(6p25 1)	0.0189 (1.00)	0.0648 (1.00)	1 (1.00)	0.456 (1.00)	0.0513 (1.00)		0.599 (1.00)
Amp Peak 9(6q12)	0.631 (1.00)	0.916 (1.00)	0.837 (1.00)	0.77 (1.00)	0.251 (1.00)		0.349 (1.00)
Amp Peak 10(7p22 3)	0.71 (1.00)	0.763 (1.00)	0.493 (1.00)	0.215 (1.00)	0.542 (1.00)		0.225 (1.00)
Amp Peak 11(7q34)	0.98 (1.00)	0.32 (1.00)	0.494 (1.00)	0.244 (1.00)	0.486 (1.00)		0.0752 (1.00)
Amp Peak 12(8q11 21)	0.548 (1.00)	0.0929 (1.00)	0.303 (1.00)	0.175 (1.00)	0.905 (1.00)		0.836 (1.00)
Amp Peak 13(8q24 21)	0.394 (1.00)	0.171 (1.00)	0.396 (1.00)	0.295 (1.00)	0.976 (1.00)		0.933 (1.00)
Amp Peak 14(9p24 1)	0.601 (1.00)	0.649 (1.00)	0.36 (1.00)	0.0483 (1.00)	0.609 (1.00)		0.0937 (1.00)
Amp Peak 15(11q13 3)	0.65 (1.00)	0.585 (1.00)	0.0571 (1.00)	0.871 (1.00)	0.47 (1.00)		0.521 (1.00)
Amp Peak 16(11q13 4)	0.829 (1.00)	0.98 (1.00)	0.0571 (1.00)	0.552 (1.00)	0.304 (1.00)		0.708 (1.00)
Amp Peak 17(12q14 1)	0.932 (1.00)	0.769 (1.00)	0.641 (1.00)	0.595 (1.00)	0.259 (1.00)		0.0562 (1.00)
Amp Peak 18(12q15)	0.551 (1.00)	0.383 (1.00)	1 (1.00)	0.918 (1.00)	0.0628 (1.00)		0.0548 (1.00)
Amp Peak 19(15q24 3)	0.587 (1.00)	0.578 (1.00)	0.857 (1.00)	0.292 (1.00)	0.64 (1.00)		0.364 (1.00)
Amp Peak 20(17q25 3)	0.346 (1.00)	0.0135 (1.00)	0.164 (1.00)	0.559 (1.00)	0.819 (1.00)		0.852 (1.00)
Amp Peak 21(19p13 2)	0.715 (1.00)	0.915 (1.00)	0.526 (1.00)	0.00162 (0.496)	0.439 (1.00)		0.188 (1.00)
Amp Peak 22(20q13 2)	0.438 (1.00)	0.151 (1.00)	0.127 (1.00)	0.142 (1.00)	0.606 (1.00)		0.404 (1.00)
Amp Peak 23(22q13 2)	0.493 (1.00)	0.801 (1.00)	0.611 (1.00)	0.866 (1.00)	0.353 (1.00)		0.576 (1.00)
Del Peak 1(1p36 31)	0.548 (1.00)	0.446 (1.00)	0.695 (1.00)	0.0913 (1.00)	0.652 (1.00)		0.722 (1.00)
Del Peak 2(1p22 1)	0.0235 (1.00)	0.00861 (1.00)	0.702 (1.00)	0.104 (1.00)	0.496 (1.00)		0.463 (1.00)
Del Peak 3(2q37 3)	0.329 (1.00)	0.775 (1.00)	0.339 (1.00)	0.0222 (1.00)	0.655 (1.00)		0.536 (1.00)
Del Peak 4(3q23)	0.794 (1.00)	0.0898 (1.00)	0.231 (1.00)	0.00533 (1.00)	0.722 (1.00)		0.114 (1.00)
Del Peak 5(4q34 3)	0.419 (1.00)	0.154 (1.00)	0.0128 (1.00)	0.31 (1.00)	0.923 (1.00)		0.0784 (1.00)
Del Peak 6(5q11 2)	0.128 (1.00)	0.945 (1.00)	1 (1.00)	0.398 (1.00)	0.482 (1.00)		0.541 (1.00)
Del Peak 7(5q31 3)	0.107 (1.00)	0.508 (1.00)	1 (1.00)	0.553 (1.00)	0.656 (1.00)		0.904 (1.00)
Del Peak 8(6q26)	0.924 (1.00)	0.296 (1.00)	0.483 (1.00)	0.727 (1.00)	0.195 (1.00)		0.769 (1.00)
Del Peak 9(7q31 1)	0.462 (1.00)	0.818 (1.00)	0.768 (1.00)	0.381 (1.00)	0.892 (1.00)		0.514 (1.00)
Del Peak 10(8p23 3)	0.716 (1.00)	0.0363 (1.00)	0.236 (1.00)	0.217 (1.00)	0.429 (1.00)		0.267 (1.00)
Del Peak 11(9p23)	0.852 (1.00)	0.816 (1.00)	0.582 (1.00)	0.109 (1.00)	0.2 (1.00)		0.625 (1.00)
Del Peak 12(9p21 3)	0.267 (1.00)	0.543 (1.00)	0.404 (1.00)	0.675 (1.00)	0.211 (1.00)		0.833 (1.00)
Del Peak 13(10p15 3)	0.397 (1.00)	0.463 (1.00)	0.234 (1.00)	0.269 (1.00)	0.436 (1.00)		0.963 (1.00)
Del Peak 14(10q23 31)	0.442 (1.00)	0.184 (1.00)	0.0144 (1.00)	0.692 (1.00)	0.61 (1.00)		0.617 (1.00)
Del Peak 15(10q26 3)	0.22 (1.00)	0.0353 (1.00)	0.0144 (1.00)	0.284 (1.00)	0.728 (1.00)		0.823 (1.00)
Del Peak 16(11q23 3)	0.317 (1.00)	0.32 (1.00)	0.49 (1.00)	0.674 (1.00)	0.0115 (1.00)		0.197 (1.00)
Del Peak 17(12p13 31)	0.331 (1.00)	0.326 (1.00)	0.331 (1.00)	0.575 (1.00)	0.223 (1.00)		0.689 (1.00)
Del Peak 18(12q23 3)	0.331 (1.00)	0.433 (1.00)	1 (1.00)	0.154 (1.00)	0.0711 (1.00)		0.628 (1.00)
Del Peak 19(12q24 33)	0.525 (1.00)	0.896 (1.00)	0.541 (1.00)	0.591 (1.00)	0.0608 (1.00)		0.431 (1.00)
Del Peak 20(13q34)	0.239 (1.00)	0.845 (1.00)	1 (1.00)	0.0437 (1.00)	0.0504 (1.00)		0.177 (1.00)
Del Peak 21(14q32 2)	0.758 (1.00)	0.495 (1.00)	0.274 (1.00)	0.198 (1.00)	0.281 (1.00)		0.352 (1.00)
Del Peak 22(15q13 3)	0.379 (1.00)	0.944 (1.00)	0.695 (1.00)	0.274 (1.00)	0.628 (1.00)		0.827 (1.00)
Del Peak 23(15q15 3)	0.2 (1.00)	0.839 (1.00)	0.324 (1.00)	0.26 (1.00)	0.798 (1.00)		0.668 (1.00)
Del Peak 24(16p13 3)	0.992 (1.00)	0.324 (1.00)	0.0518 (1.00)	0.801 (1.00)	0.412 (1.00)		0.892 (1.00)
Del Peak 25(16q12 1)	0.129 (1.00)	0.753 (1.00)	0.286 (1.00)	0.373 (1.00)	0.846 (1.00)		0.657 (1.00)
Del Peak 26(16q24 3)	0.0425 (1.00)	0.575 (1.00)	0.287 (1.00)	0.378 (1.00)	0.192 (1.00)		0.449 (1.00)
Del Peak 27(19p13 3)	0.669 (1.00)	0.937 (1.00)	0.204 (1.00)	0.0909 (1.00)	0.721 (1.00)		0.26 (1.00)
Del Peak 28(22q13 31)	0.112 (1.00)	0.613 (1.00)	0.62 (1.00)	0.883 (1.00)	0.748 (1.00)		0.434 (1.00)

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

Table S1. Description of clustering approach #1: 'Amp Peak 1(1p12) mutation analysis'

Cluster Labels	AMP PEAK 1(1P12) MUTATED	AMP PEAK 1(1P12) WILD-TYPE
Number of samples	45	104

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	79	70

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	80	69

Clustering Approach #4: 'Amp Peak 4(3p13) mutation analysis'

Table S4. Description of clustering approach #4: 'Amp Peak 4(3p13) mutation analysis'

Cluster Labels	AMP PEAK 4(3P13) MUTATED	AMP PEAK 4(3P13) WILD-TYPE
Number of samples	32	117

Clustering Approach #5: 'Amp Peak 5(4q12) mutation analysis'

Table S5. Description of clustering approach #5: 'Amp Peak 5(4q12) mutation analysis'

Cluster Labels	AMP PEAK 5(4Q12) MUTATED	AMP PEAK 5(4Q12) WILD-TYPE
Number of samples	29	120

Clustering Approach #6: 'Amp Peak 6(5p15.33) mutation analysis'

Table S6. Description of clustering approach #6: 'Amp Peak 6(5p15.33) mutation analysis'

Cluster Labels	AMP PEAK 6(5P15.33) MUTATED	AMP PEAK 6(5P15.33) WILD-TYPE
Number of samples	41	108

Clustering Approach #7: 'Amp Peak 7(5q35.3) mutation analysis'

Table S7. Description of clustering approach #7: 'Amp Peak 7(5q35.3) mutation analysis'

Cluster Labels	AMP PEAK 7(5Q35.3) MUTATED	AMP PEAK 7(5Q35.3) WILD-TYPE
Number of samples	20	129

Clustering Approach #8: 'Amp Peak 8(6p25.1) mutation analysis'

Table S8. Description of clustering approach #8: 'Amp Peak 8(6p25.1) mutation analysis'

Cluster Labels	AMP PEAK 8(6P25.1) MUTATED	AMP PEAK 8(6P25.1) WILD-TYPE
Number of samples	89	60

Clustering Approach #9: 'Amp Peak 9(6q12) mutation analysis'

Table S9. Description of clustering approach #9: 'Amp Peak 9(6q12) mutation analysis'

Cluster Labels	AMP PEAK 9(6Q12) MUTATED	AMP PEAK 9(6Q12) WILD-TYPE
Number of samples	32	117

Clustering Approach #10: 'Amp Peak 10(7p22.3) mutation analysis'

Table S10. Description of clustering approach #10: 'Amp Peak 10(7p22.3) mutation analysis'

Cluster Labels	AMP PEAK 10(7P22.3) MUTATED	AMP PEAK 10(7P22.3) WILD-TYPE
Number of samples	85	64

Clustering Approach #11: 'Amp Peak 11(7q34) mutation analysis'

Table S11. Description of clustering approach #11: 'Amp Peak 11(7q34) mutation analysis'

Cluster Labels	AMP PEAK 11(7Q34) MUTATED	AMP PEAK 11(7Q34) WILD-TYPE
Number of samples	86	63

Clustering Approach #12: 'Amp Peak 12(8q11.21) mutation analysis'

Table S12. Description of clustering approach #12: 'Amp Peak 12(8q11.21) mutation analysis'

Cluster Labels	AMP PEAK 12(8Q11.21) MUTATED	AMP PEAK 12(8Q11.21) WILD-TYPE
Number of samples	60	89

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

Table S13. 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	70	79

Clustering Approach #14: 'Amp Peak 14(9p24.1) mutation analysis'

Table S14. Description of clustering approach #14: 'Amp Peak 14(9p24.1) mutation analysis'

Cluster Labels	AMP PEAK 14(9P24.1) MUTATED	AMP PEAK 14(9P24.1) WILD-TYPE
Number of samples	12	137

Clustering Approach #15: 'Amp Peak 15(11q13.3) mutation analysis'

Table S15. Description of clustering approach #15: 'Amp Peak 15(11q13.3) mutation analysis'

Cluster Labels	AMP PEAK 15(11Q13.3) MUTATED	AMP PEAK 15(11Q13.3) WILD-TYPE
Number of samples	22	127

Clustering Approach #16: 'Amp Peak 16(11q13.4) mutation analysis'

Table S16. Description of clustering approach #16: 'Amp Peak 16(11q13.4) mutation analysis'

Cluster Labels	AMP PEAK 16(11Q13.4) MUTATED	AMP PEAK 16(11Q13.4) WILD-TYPE
Number of samples	22	127

Clustering Approach #17: 'Amp Peak 17(12q14.1) mutation analysis'

Table S17. Description of clustering approach #17: 'Amp Peak 17(12q14.1) mutation analysis'

Cluster Labels	AMP PEAK 17(12Q14.1) MUTATED	AMP PEAK 17(12Q14.1) WILD-TYPE
Number of samples	22	127

Clustering Approach #18: 'Amp Peak 18(12q15) mutation analysis'

Table S18. Description of clustering approach #18: 'Amp Peak 18(12q15) mutation analysis'

Cluster Labels	AMP PEAK 18(12Q15) MUTATED	AMP PEAK 18(12Q15) WILD-TYPE
Number of samples	17	132

Clustering Approach #19: 'Amp Peak 19(15q24.3) mutation analysis'

Table S19. Description of clustering approach #19: 'Amp Peak 19(15q24.3) mutation analysis'

Cluster Labels	AMP PEAK 19(15Q24.3) MUTATED	AMP PEAK 19(15Q24.3) WILD-TYPE
Number of samples	48	101

Clustering Approach #20: 'Amp Peak 20(17q25.3) mutation analysis'

Table S20. Description of clustering approach #20: 'Amp Peak 20(17q25.3) mutation analysis'

Cluster Labels	AMP PEAK 20(17Q25.3) MUTATED	AMP PEAK 20(17Q25.3) WILD-TYPE
Number of samples	58	91

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

Table S21. 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	29	120

Clustering Approach #22: 'Amp Peak 22(20q13.2) mutation analysis'

Table S22. Description of clustering approach #22: 'Amp Peak 22(20q13.2) mutation analysis'

Cluster Labels	AMP PEAK 22(20Q13.2) MUTATED	AMP PEAK 22(20Q13.2) WILD-TYPE
Number of samples	78	71

Clustering Approach #23: 'Amp Peak 23(22q13.2) mutation analysis'

Table S23. Description of clustering approach #23: 'Amp Peak 23(22q13.2) mutation analysis'

Cluster Labels	AMP PEAK 23(22Q13.2) MUTATED	AMP PEAK 23(22Q13.2) WILD-TYPE
Number of samples	70	79

Clustering Approach #24: 'Del Peak 1(1p36.31) mutation analysis'

Table S24. Description of clustering approach #24: 'Del Peak 1(1p36.31) mutation analysis'

Cluster Labels	DEL PEAK 1(1P36.31) MUTATED	DEL PEAK 1(1P36.31) WILD-TYPE
Number of samples	37	112

Clustering Approach #25: 'Del Peak 2(1p22.1) mutation analysis'

Table S25. Description of clustering approach #25: 'Del Peak 2(1p22.1) mutation analysis'

Cluster Labels	DEL PEAK 2(1P22.1) MUTATED	DEL PEAK 2(1P22.1) WILD-TYPE
Number of samples	38	111

Clustering Approach #26: 'Del Peak 3(2q37.3) mutation analysis'

Table S26. Description of clustering approach #26: 'Del Peak 3(2q37.3) mutation analysis'

Cluster Labels	DEL PEAK 3(2Q37.3) MUTATED	DEL PEAK 3(2Q37.3) WILD-TYPE
Number of samples	39	110

Clustering Approach #27: 'Del Peak 4(3q23) mutation analysis'

Table S27. Description of clustering approach #27: 'Del Peak 4(3q23) mutation analysis'

Cluster Labels	DEL PEAK 4(3Q23) MUTATED	DEL PEAK 4(3Q23) WILD-TYPE
Number of samples	22	127

Clustering Approach #28: 'Del Peak 5(4q34.3) mutation analysis'

Table S28. Description of clustering approach #28: 'Del Peak 5(4q34.3) mutation analysis'

Cluster Labels	DEL PEAK 5(4Q34.3) MUTATED	DEL PEAK 5(4Q34.3) WILD-TYPE
Number of samples	39	110

Clustering Approach #29: 'Del Peak 6(5q11.2) mutation analysis'

Table S29. Description of clustering approach #29: 'Del Peak 6(5q11.2) mutation analysis'

Cluster Labels	DEL PEAK 6(5Q11.2) MUTATED	DEL PEAK 6(5Q11.2) WILD-TYPE
Number of samples	44	105

Clustering Approach #30: 'Del Peak 7(5q31.3) mutation analysis'

Table S30. Description of clustering approach #30: 'Del Peak 7(5q31.3) mutation analysis'

Cluster Labels	DEL PEAK 7(5Q31.3) MUTATED	DEL PEAK 7(5Q31.3) WILD-TYPE
Number of samples	58	91

Clustering Approach #31: 'Del Peak 8(6q26) mutation analysis'

Table S31. Description of clustering approach #31: 'Del Peak 8(6q26) mutation analysis'

Cluster Labels	DEL PEAK 8(6Q26) MUTATED	DEL PEAK 8(6Q26) WILD-TYPE
Number of samples	94	55

Clustering Approach #32: 'Del Peak 9(7q31.1) mutation analysis'

Table S32. Description of clustering approach #32: 'Del Peak 9(7q31.1) mutation analysis'

Cluster Labels	DEL PEAK 9(7Q31.1) MUTATED	DEL PEAK 9(7Q31.1) WILD-TYPE
Number of samples	13	136

Clustering Approach #33: 'Del Peak 10(8p23.3) mutation analysis'

Table S33. Description of clustering approach #33: 'Del Peak 10(8p23.3) mutation analysis'

Cluster Labels	DEL PEAK 10(8P23.3) MUTATED	DEL PEAK 10(8P23.3) WILD-TYPE
Number of samples	36	113

Clustering Approach #34: 'Del Peak 11(9p23) mutation analysis'

Table S34. Description of clustering approach #34: 'Del Peak 11(9p23) mutation analysis'

Cluster Labels	DEL PEAK 11(9P23) MUTATED	DEL PEAK 11(9P23) WILD-TYPE
Number of samples	103	46

Clustering Approach #35: 'Del Peak 12(9p21.3) mutation analysis'

Table S35. Description of clustering approach #35: 'Del Peak 12(9p21.3) mutation analysis'

Cluster Labels	DEL PEAK 12(9P21.3) MUTATED	DEL PEAK 12(9P21.3) WILD-TYPE
Number of samples	118	31

Clustering Approach #36: 'Del Peak 13(10p15.3) mutation analysis'

Table S36. Description of clustering approach #36: 'Del Peak 13(10p15.3) mutation analysis'

Cluster Labels	DEL PEAK 13(10P15.3) MUTATED	DEL PEAK 13(10P15.3) WILD-TYPE
Number of samples	79	70

Clustering Approach #37: 'Del Peak 14(10q23.31) mutation analysis'

Table S37. Description of clustering approach #37: 'Del Peak 14(10q23.31) mutation analysis'

Cluster Labels	DEL PEAK 14(10Q23.31) MUTATED	DEL PEAK 14(10Q23.31) WILD-TYPE
Number of samples	91	58

Clustering Approach #38: 'Del Peak 15(10q26.3) mutation analysis'

Table S38. Description of clustering approach #38: 'Del Peak 15(10q26.3) mutation analysis'

Cluster Labels	DEL PEAK 15(10Q26.3) MUTATED	DEL PEAK 15(10Q26.3) WILD-TYPE
Number of samples	91	58

Clustering Approach #39: 'Del Peak 16(11q23.3) mutation analysis'

Table S39. Description of clustering approach #39: 'Del Peak 16(11q23.3) mutation analysis'

Cluster Labels	DEL PEAK 16(11Q23.3) MUTATED	DEL PEAK 16(11Q23.3) WILD-TYPE
Number of samples	88	61

Clustering Approach #40: 'Del Peak 17(12p13.31) mutation analysis'

Table S40. Description of clustering approach #40: 'Del Peak 17(12p13.31) mutation analysis'

Cluster Labels	DEL PEAK 17(12P13.31) MUTATED	DEL PEAK 17(12P13.31) WILD-TYPE
Number of samples	21	128

Clustering Approach #41: 'Del Peak 18(12q23.3) mutation analysis'

Table S41. Description of clustering approach #41: 'Del Peak 18(12q23.3) mutation analysis'

Cluster Labels	DEL PEAK 18(12Q23.3) MUTATED	DEL PEAK 18(12Q23.3) WILD-TYPE
Number of samples	32	117

Clustering Approach #42: 'Del Peak 19(12q24.33) mutation analysis'

Table S42. Description of clustering approach #42: 'Del Peak 19(12q24.33) mutation analysis'

Cluster Labels	DEL PEAK 19(12Q24.33) MUTATED	DEL PEAK 19(12Q24.33) WILD-TYPE
Number of samples	33	116

Clustering Approach #43: 'Del Peak 20(13q34) mutation analysis'

Table S43. Description of clustering approach #43: 'Del Peak 20(13q34) mutation analysis'

Cluster Labels	DEL PEAK 20(13Q34) MUTATED	DEL PEAK 20(13Q34) WILD-TYPE
Number of samples	38	111

Clustering Approach #44: 'Del Peak 21(14q32.2) mutation analysis'

Table S44. Description of clustering approach #44: 'Del Peak 21(14q32.2) mutation analysis'

Cluster Labels	DEL PEAK 21(14Q32.2) MUTATED	DEL PEAK 21(14Q32.2) WILD-TYPE
Number of samples	47	102

Clustering Approach #45: 'Del Peak 22(15q13.3) mutation analysis'

Table S45. Description of clustering approach #45: 'Del Peak 22(15q13.3) mutation analysis'

Cluster Labels	DEL PEAK 22(15Q13.3) MUTATED	DEL PEAK 22(15Q13.3) WILD-TYPE
Number of samples	37	112

Clustering Approach #46: 'Del Peak 23(15q15.3) mutation analysis'

Table S46. Description of clustering approach #46: 'Del Peak 23(15q15.3) mutation analysis'

Cluster Labels	DEL PEAK 23(15Q15.3) MUTATED	DEL PEAK 23(15Q15.3) WILD-TYPE
Number of samples	36	113

Clustering Approach #47: 'Del Peak 24(16p13.3) mutation analysis'

Table S47. Description of clustering approach #47: 'Del Peak 24(16p13.3) mutation analysis'

Cluster Labels	DEL PEAK 24(16P13.3) MUTATED	DEL PEAK 24(16P13.3) WILD-TYPE
Number of samples	28	121

Clustering Approach #48: 'Del Peak 25(16q12.1) mutation analysis'

Table S48. Description of clustering approach #48: 'Del Peak 25(16q12.1) mutation analysis'

Cluster Labels	DEL PEAK 25(16Q12.1) MUTATED	DEL PEAK 25(16Q12.1) WILD-TYPE
Number of samples	51	98

Clustering Approach #49: 'Del Peak 26(16q24.3) mutation analysis'

Table S49. Description of clustering approach #49: 'Del Peak 26(16q24.3) mutation analysis'

Cluster Labels	DEL PEAK 26(16Q24.3) MUTATED	DEL PEAK 26(16Q24.3) WILD-TYPE
Number of samples	53	96

Clustering Approach #50: 'Del Peak 27(19p13.3) mutation analysis'

Table S50. Description of clustering approach #50: 'Del Peak 27(19p13.3) mutation analysis'

Cluster Labels	DEL PEAK 27(19P13.3) MUTATED	DEL PEAK 27(19P13.3) WILD-TYPE
Number of samples	47	102

Clustering Approach #51: 'Del Peak 28(22q13.31) mutation analysis'

Table S51. Description of clustering approach #51: 'Del Peak 28(22q13.31) mutation analysis'

Cluster Labels	DEL PEAK 28(22Q13.31) MUTATED	DEL PEAK 28(22Q13.31) WILD-TYPE
Number of samples	19	130

Methods & Data

Input

Cluster data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = SKCM-TM.clin.merged.picked.txt
Number of patients = 149
Number of clustering approaches = 51
Number of selected clinical features = 7
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.

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] 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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