Correlation between copy number variation genes and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv) genes and molecular subtypes.

Summary

Testing the association between copy number variation of 46 peak regions and 8 molecular subtypes across 147 patients, 25 significant findings detected with Q value < 0.25.

Amp Peak 2(1q31.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 3(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 7(6p25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 9(7p22.1) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(7q34) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(8q24.21) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(15q24.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 16(15q26.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(17q25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 19(22q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 7(4q25) cnvs correlated to 'CN_CNMF'.
Del Peak 10(5q31.3) cnvs correlated to 'METHLYATION_CNMF'.
Del Peak 11(6q25.3) cnvs correlated to 'CN_CNMF'.
Del Peak 12(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 13(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 14(9p21.3) cnvs correlated to 'CN_CNMF'.
Del Peak 15(10p15.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 16(10q23.31) cnvs correlated to 'CN_CNMF'.
Del Peak 17(10q26.3) cnvs correlated to 'CN_CNMF'.
Del Peak 18(11p11.12) cnvs correlated to 'CN_CNMF'.
Del Peak 19(11q23.3) cnvs correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 46 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 25 significant findings detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
Del Peak 2(1p22 1)	42 (29%)	105	0.00969 (1.00)	0.000686 (0.236)	0.905 (1.00)	0.252 (1.00)	2.93e-05 (0.0105)	0.000894 (0.305)	0.116 (1.00)	0.857 (1.00)
Del Peak 15(10p15 3)	79 (54%)	68	5.42e-06 (0.00196)	0.000839 (0.288)	0.867 (1.00)	0.509 (1.00)	0.00064 (0.222)	0.00412 (1.00)	0.727 (1.00)	0.281 (1.00)
Amp Peak 2(1q31 2)	74 (50%)	73	2.31e-06 (0.000838)	0.152 (1.00)	0.545 (1.00)	0.346 (1.00)	0.24 (1.00)	0.343 (1.00)	0.425 (1.00)	0.908 (1.00)
Amp Peak 3(1q44)	76 (52%)	71	7.33e-05 (0.026)	0.257 (1.00)	0.545 (1.00)	0.49 (1.00)	0.103 (1.00)	0.539 (1.00)	0.121 (1.00)	0.43 (1.00)
Amp Peak 5(5p15 33)	38 (26%)	109	0.000664 (0.229)	0.439 (1.00)	0.826 (1.00)	0.881 (1.00)	0.863 (1.00)	0.784 (1.00)	0.025 (1.00)	0.294 (1.00)
Amp Peak 7(6p25 3)	84 (57%)	63	4.76e-05 (0.017)	0.0358 (1.00)	0.066 (1.00)	0.519 (1.00)	0.756 (1.00)	0.407 (1.00)	0.197 (1.00)	0.0069 (1.00)
Amp Peak 9(7p22 1)	81 (55%)	66	0.000578 (0.201)	0.472 (1.00)	0.381 (1.00)	0.256 (1.00)	0.224 (1.00)	0.664 (1.00)	0.581 (1.00)	0.823 (1.00)
Amp Peak 10(7q34)	85 (58%)	62	1.19e-05 (0.00428)	0.512 (1.00)	0.895 (1.00)	0.327 (1.00)	0.379 (1.00)	0.309 (1.00)	0.199 (1.00)	0.437 (1.00)
Amp Peak 11(8q24 21)	70 (48%)	77	0.000276 (0.0967)	0.00337 (1.00)	0.652 (1.00)	0.456 (1.00)	0.00181 (0.613)	0.0581 (1.00)	0.0615 (1.00)	0.679 (1.00)
Amp Peak 15(15q24 3)	48 (33%)	99	2.17e-06 (0.000791)	0.539 (1.00)	0.402 (1.00)	0.163 (1.00)	0.791 (1.00)	0.011 (1.00)	0.258 (1.00)	0.519 (1.00)
Amp Peak 16(15q26 3)	53 (36%)	94	4.78e-05 (0.017)	0.332 (1.00)	0.295 (1.00)	0.175 (1.00)	0.8 (1.00)	0.011 (1.00)	0.0834 (1.00)	0.612 (1.00)
Amp Peak 17(17q25 3)	57 (39%)	90	0.000146 (0.0515)	0.00792 (1.00)	0.172 (1.00)	0.281 (1.00)	0.495 (1.00)	0.74 (1.00)	0.144 (1.00)	0.414 (1.00)
Amp Peak 19(22q13 2)	64 (44%)	83	5.19e-07 (0.00019)	0.134 (1.00)	0.578 (1.00)	0.842 (1.00)	0.687 (1.00)	0.256 (1.00)	0.353 (1.00)	0.85 (1.00)
Del Peak 7(4q25)	33 (22%)	114	0.000553 (0.193)	0.681 (1.00)	0.826 (1.00)	0.948 (1.00)	0.073 (1.00)	0.124 (1.00)	0.251 (1.00)	0.123 (1.00)
Del Peak 10(5q31 3)	59 (40%)	88	0.0602 (1.00)	0.000311 (0.109)	0.762 (1.00)	0.99 (1.00)	0.526 (1.00)	0.745 (1.00)	0.074 (1.00)	0.353 (1.00)
Del Peak 11(6q25 3)	89 (61%)	58	3.05e-08 (1.12e-05)	0.0143 (1.00)	0.247 (1.00)	0.541 (1.00)	0.00265 (0.884)	0.622 (1.00)	0.475 (1.00)	0.904 (1.00)
Del Peak 12(6q26)	84 (57%)	63	2.62e-07 (9.6e-05)	0.00495 (1.00)	0.642 (1.00)	0.626 (1.00)	0.00086 (0.294)	0.493 (1.00)	0.741 (1.00)	0.769 (1.00)
Del Peak 13(9p23)	103 (70%)	44	0.000349 (0.122)	0.0242 (1.00)	0.92 (1.00)	0.498 (1.00)	0.0192 (1.00)	0.0683 (1.00)	0.893 (1.00)	0.333 (1.00)
Del Peak 14(9p21 3)	115 (78%)	32	7.72e-07 (0.000282)	0.00201 (0.677)	0.847 (1.00)	0.361 (1.00)	0.00192 (0.648)	0.00722 (1.00)	0.783 (1.00)	0.232 (1.00)
Del Peak 16(10q23 31)	91 (62%)	56	6.33e-06 (0.00228)	0.101 (1.00)	0.964 (1.00)	0.861 (1.00)	0.00261 (0.876)	0.0973 (1.00)	0.0957 (1.00)	0.642 (1.00)
Del Peak 17(10q26 3)	92 (63%)	55	9.23e-05 (0.0327)	0.246 (1.00)	0.624 (1.00)	0.991 (1.00)	0.00141 (0.478)	0.0126 (1.00)	0.23 (1.00)	1 (1.00)
Del Peak 18(11p11 12)	54 (37%)	93	9.39e-05 (0.0331)	0.00631 (1.00)	0.766 (1.00)	0.963 (1.00)	0.0221 (1.00)	0.837 (1.00)	0.186 (1.00)	0.709 (1.00)
Del Peak 19(11q23 3)	79 (54%)	68	1.38e-05 (0.00494)	0.15 (1.00)	0.834 (1.00)	0.564 (1.00)	0.129 (1.00)	0.0969 (1.00)	0.0416 (1.00)	0.215 (1.00)
Amp Peak 1(1p12)	44 (30%)	103	0.00384 (1.00)	0.447 (1.00)	0.6 (1.00)	0.146 (1.00)	0.108 (1.00)	0.753 (1.00)	0.0689 (1.00)	0.291 (1.00)
Amp Peak 4(3p13)	34 (23%)	113	0.107 (1.00)	0.29 (1.00)	0.0496 (1.00)	0.0433 (1.00)	0.676 (1.00)	0.646 (1.00)	0.242 (1.00)	0.728 (1.00)
Amp Peak 6(5q35 3)	16 (11%)	131	0.111 (1.00)	0.0306 (1.00)	1 (1.00)	0.878 (1.00)	0.186 (1.00)	0.73 (1.00)	0.402 (1.00)	0.437 (1.00)
Amp Peak 8(6q12)	33 (22%)	114	0.525 (1.00)	0.659 (1.00)	0.674 (1.00)	0.898 (1.00)	0.108 (1.00)	0.0647 (1.00)	0.0566 (1.00)	0.33 (1.00)
Amp Peak 12(9p13 3)	16 (11%)	131	0.127 (1.00)	0.713 (1.00)	0.867 (1.00)	0.782 (1.00)	1 (1.00)	0.73 (1.00)	0.379 (1.00)	0.852 (1.00)
Amp Peak 13(11q13 3)	23 (16%)	124	0.176 (1.00)	0.265 (1.00)	1 (1.00)	0.962 (1.00)	0.616 (1.00)	0.955 (1.00)	1 (1.00)	0.618 (1.00)
Amp Peak 14(12q14 1)	27 (18%)	120	0.00151 (0.514)	0.0841 (1.00)	0.443 (1.00)	0.0565 (1.00)	0.379 (1.00)	0.411 (1.00)	0.853 (1.00)	0.624 (1.00)
Amp Peak 18(19p13 2)	28 (19%)	119	0.332 (1.00)	0.0503 (1.00)	0.279 (1.00)	0.322 (1.00)	0.0549 (1.00)	0.0135 (1.00)	0.462 (1.00)	0.307 (1.00)
Amp Peak 20(Xq28)	24 (16%)	123	0.277 (1.00)	0.0771 (1.00)	0.858 (1.00)	0.489 (1.00)	0.0984 (1.00)	0.23 (1.00)	0.805 (1.00)	0.669 (1.00)
Del Peak 1(1p36 31)	37 (25%)	110	0.318 (1.00)	0.0449 (1.00)	0.897 (1.00)	0.389 (1.00)	0.0744 (1.00)	0.00294 (0.979)	0.331 (1.00)	0.881 (1.00)
Del Peak 3(2q37 3)	36 (24%)	111	0.428 (1.00)	0.453 (1.00)	0.749 (1.00)	0.346 (1.00)	0.141 (1.00)	0.345 (1.00)	0.166 (1.00)	0.0732 (1.00)
Del Peak 4(3p24 3)	21 (14%)	126	0.165 (1.00)	0.438 (1.00)	0.811 (1.00)	0.187 (1.00)	0.236 (1.00)	0.276 (1.00)	0.448 (1.00)	0.765 (1.00)
Del Peak 5(3q23)	21 (14%)	126	0.468 (1.00)	0.0367 (1.00)	0.203 (1.00)	0.537 (1.00)	0.634 (1.00)	1 (1.00)	0.953 (1.00)	0.138 (1.00)
Del Peak 6(4p16 3)	31 (21%)	116	0.193 (1.00)	0.163 (1.00)	0.95 (1.00)	0.603 (1.00)	0.0438 (1.00)	0.0171 (1.00)	0.778 (1.00)	0.829 (1.00)
Del Peak 8(4q34 3)	35 (24%)	112	0.00597 (1.00)	0.831 (1.00)	0.953 (1.00)	0.937 (1.00)	0.195 (1.00)	0.294 (1.00)	0.906 (1.00)	0.0504 (1.00)
Del Peak 9(5q11 2)	44 (30%)	103	0.423 (1.00)	0.00852 (1.00)	0.39 (1.00)	0.471 (1.00)	0.185 (1.00)	0.522 (1.00)	0.172 (1.00)	0.353 (1.00)
Del Peak 20(12q24 33)	33 (22%)	114	0.208 (1.00)	0.0306 (1.00)	0.275 (1.00)	0.515 (1.00)	0.654 (1.00)	0.967 (1.00)	0.966 (1.00)	0.571 (1.00)
Del Peak 21(13q34)	40 (27%)	107	0.125 (1.00)	0.0846 (1.00)	0.959 (1.00)	0.857 (1.00)	0.751 (1.00)	1 (1.00)	0.362 (1.00)	0.13 (1.00)
Del Peak 22(14q32 2)	47 (32%)	100	0.0115 (1.00)	0.372 (1.00)	0.322 (1.00)	0.629 (1.00)	0.112 (1.00)	0.256 (1.00)	0.454 (1.00)	1 (1.00)
Del Peak 23(15q13 3)	35 (24%)	112	0.0678 (1.00)	0.184 (1.00)	0.447 (1.00)	0.467 (1.00)	0.0482 (1.00)	0.369 (1.00)	0.593 (1.00)	0.381 (1.00)
Del Peak 24(15q15 2)	37 (25%)	110	0.0829 (1.00)	0.434 (1.00)	0.538 (1.00)	0.866 (1.00)	0.35 (1.00)	0.642 (1.00)	0.424 (1.00)	0.0984 (1.00)
Del Peak 25(16p13 3)	26 (18%)	121	0.626 (1.00)	0.0169 (1.00)	0.948 (1.00)	0.781 (1.00)	0.0931 (1.00)	0.595 (1.00)	0.0834 (1.00)	0.947 (1.00)
Del Peak 26(16q24 2)	52 (35%)	95	0.0195 (1.00)	0.305 (1.00)	0.396 (1.00)	0.485 (1.00)	0.0169 (1.00)	0.485 (1.00)	0.0103 (1.00)	0.0854 (1.00)

'Amp Peak 2(1q31.2) mutation analysis' versus 'CN_CNMF'

P value = 2.31e-06 (Fisher's exact test), Q value = 0.00084

Table S1. Gene #2: 'Amp Peak 2(1q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 2(1Q31.2) MUTATED	23	13	14	24
AMP PEAK 2(1Q31.2) WILD-TYPE	1	13	27	32

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q31.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 3(1q44) mutation analysis' versus 'CN_CNMF'

P value = 7.33e-05 (Fisher's exact test), Q value = 0.026

Table S2. Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 3(1Q44) MUTATED	22	13	15	26
AMP PEAK 3(1Q44) WILD-TYPE	2	13	26	30

Figure S2. Get High-res Image Gene #3: 'Amp Peak 3(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 5(5p15.33) mutation analysis' versus 'CN_CNMF'

P value = 0.000664 (Fisher's exact test), Q value = 0.23

Table S3. Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 5(5P15.33) MUTATED	4	14	13	7
AMP PEAK 5(5P15.33) WILD-TYPE	20	12	28	49

Figure S3. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(6p25.3) mutation analysis' versus 'CN_CNMF'

P value = 4.76e-05 (Fisher's exact test), Q value = 0.017

Table S4. Gene #7: 'Amp Peak 7(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 7(6P25.3) MUTATED	19	12	32	21
AMP PEAK 7(6P25.3) WILD-TYPE	5	14	9	35

Figure S4. Get High-res Image Gene #7: 'Amp Peak 7(6p25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 9(7p22.1) mutation analysis' versus 'CN_CNMF'

P value = 0.000578 (Fisher's exact test), Q value = 0.2

Table S5. Gene #9: 'Amp Peak 9(7p22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 9(7P22.1) MUTATED	13	22	25	21
AMP PEAK 9(7P22.1) WILD-TYPE	11	4	16	35

Figure S5. Get High-res Image Gene #9: 'Amp Peak 9(7p22.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 10(7q34) mutation analysis' versus 'CN_CNMF'

P value = 1.19e-05 (Fisher's exact test), Q value = 0.0043

Table S6. Gene #10: 'Amp Peak 10(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 10(7Q34) MUTATED	10	24	28	23
AMP PEAK 10(7Q34) WILD-TYPE	14	2	13	33

Figure S6. Get High-res Image Gene #10: 'Amp Peak 10(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(8q24.21) mutation analysis' versus 'CN_CNMF'

P value = 0.000276 (Fisher's exact test), Q value = 0.097

Table S7. Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 11(8Q24.21) MUTATED	15	16	25	14
AMP PEAK 11(8Q24.21) WILD-TYPE	9	10	16	42

Figure S7. Get High-res Image Gene #11: 'Amp Peak 11(8q24.21) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 15(15q24.3) mutation analysis' versus 'CN_CNMF'

P value = 2.17e-06 (Fisher's exact test), Q value = 0.00079

Table S8. Gene #15: 'Amp Peak 15(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 15(15Q24.3) MUTATED	8	20	10	10
AMP PEAK 15(15Q24.3) WILD-TYPE	16	6	31	46

Figure S8. Get High-res Image Gene #15: 'Amp Peak 15(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 16(15q26.3) mutation analysis' versus 'CN_CNMF'

P value = 4.78e-05 (Fisher's exact test), Q value = 0.017

Table S9. Gene #16: 'Amp Peak 16(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 16(15Q26.3) MUTATED	8	20	11	14
AMP PEAK 16(15Q26.3) WILD-TYPE	16	6	30	42

Figure S9. Get High-res Image Gene #16: 'Amp Peak 16(15q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(17q25.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000146 (Fisher's exact test), Q value = 0.052

Table S10. Gene #17: 'Amp Peak 17(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 17(17Q25.3) MUTATED	11	11	25	10
AMP PEAK 17(17Q25.3) WILD-TYPE	13	15	16	46

Figure S10. Get High-res Image Gene #17: 'Amp Peak 17(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 19(22q13.2) mutation analysis' versus 'CN_CNMF'

P value = 5.19e-07 (Fisher's exact test), Q value = 0.00019

Table S11. Gene #19: 'Amp Peak 19(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
AMP PEAK 19(22Q13.2) MUTATED	15	22	11	16
AMP PEAK 19(22Q13.2) WILD-TYPE	9	4	30	40

Figure S11. Get High-res Image Gene #19: 'Amp Peak 19(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 2(1p22.1) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000686 (Fisher's exact test), Q value = 0.24

Table S12. Gene #22: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	57	50
DEL PEAK 2(1P22.1) MUTATED	21	11	10
DEL PEAK 2(1P22.1) WILD-TYPE	19	46	40

Figure S12. Get High-res Image Gene #22: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 2(1p22.1) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.93e-05 (Fisher's exact test), Q value = 0.01

Table S13. Gene #22: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	38	51
DEL PEAK 2(1P22.1) MUTATED	26	2	14
DEL PEAK 2(1P22.1) WILD-TYPE	30	36	37

Figure S13. Get High-res Image Gene #22: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 7(4q25) mutation analysis' versus 'CN_CNMF'

P value = 0.000553 (Fisher's exact test), Q value = 0.19

Table S14. Gene #27: 'Del Peak 7(4q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 7(4Q25) MUTATED	5	14	4	10
DEL PEAK 7(4Q25) WILD-TYPE	19	12	37	46

Figure S14. Get High-res Image Gene #27: 'Del Peak 7(4q25) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 10(5q31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000311 (Fisher's exact test), Q value = 0.11

Table S15. Gene #30: 'Del Peak 10(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	40	57	50
DEL PEAK 10(5Q31.3) MUTATED	9	19	31
DEL PEAK 10(5Q31.3) WILD-TYPE	31	38	19

Figure S15. Get High-res Image Gene #30: 'Del Peak 10(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 11(6q25.3) mutation analysis' versus 'CN_CNMF'

P value = 3.05e-08 (Fisher's exact test), Q value = 1.1e-05

Table S16. Gene #31: 'Del Peak 11(6q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 11(6Q25.3) MUTATED	17	17	37	18
DEL PEAK 11(6Q25.3) WILD-TYPE	7	9	4	38

Figure S16. Get High-res Image Gene #31: 'Del Peak 11(6q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6q26) mutation analysis' versus 'CN_CNMF'

P value = 2.62e-07 (Fisher's exact test), Q value = 9.6e-05

Table S17. Gene #32: 'Del Peak 12(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 12(6Q26) MUTATED	17	17	34	16
DEL PEAK 12(6Q26) WILD-TYPE	7	9	7	40

Figure S17. Get High-res Image Gene #32: 'Del Peak 12(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 13(9p23) mutation analysis' versus 'CN_CNMF'

P value = 0.000349 (Fisher's exact test), Q value = 0.12

Table S18. Gene #33: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 13(9P23) MUTATED	18	21	36	28
DEL PEAK 13(9P23) WILD-TYPE	6	5	5	28

Figure S18. Get High-res Image Gene #33: 'Del Peak 13(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 7.72e-07 (Fisher's exact test), Q value = 0.00028

Table S19. Gene #34: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 14(9P21.3) MUTATED	20	24	40	31
DEL PEAK 14(9P21.3) WILD-TYPE	4	2	1	25

Figure S19. Get High-res Image Gene #34: 'Del Peak 14(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 5.42e-06 (Fisher's exact test), Q value = 0.002

Table S20. Gene #35: 'Del Peak 15(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 15(10P15.3) MUTATED	19	20	24	16
DEL PEAK 15(10P15.3) WILD-TYPE	5	6	17	40

Figure S20. Get High-res Image Gene #35: 'Del Peak 15(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(10p15.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.00064 (Fisher's exact test), Q value = 0.22

Table S21. Gene #35: 'Del Peak 15(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	38	51
DEL PEAK 15(10P15.3) MUTATED	41	14	23
DEL PEAK 15(10P15.3) WILD-TYPE	15	24	28

Figure S21. Get High-res Image Gene #35: 'Del Peak 15(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 16(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 6.33e-06 (Fisher's exact test), Q value = 0.0023

Table S22. Gene #36: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 16(10Q23.31) MUTATED	19	24	26	22
DEL PEAK 16(10Q23.31) WILD-TYPE	5	2	15	34

Figure S22. Get High-res Image Gene #36: 'Del Peak 16(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 9.23e-05 (Fisher's exact test), Q value = 0.033

Table S23. Gene #37: 'Del Peak 17(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 17(10Q26.3) MUTATED	17	24	27	24
DEL PEAK 17(10Q26.3) WILD-TYPE	7	2	14	32

Figure S23. Get High-res Image Gene #37: 'Del Peak 17(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(11p11.12) mutation analysis' versus 'CN_CNMF'

P value = 9.39e-05 (Fisher's exact test), Q value = 0.033

Table S24. Gene #38: 'Del Peak 18(11p11.12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 18(11P11.12) MUTATED	16	15	11	12
DEL PEAK 18(11P11.12) WILD-TYPE	8	11	30	44

Figure S24. Get High-res Image Gene #38: 'Del Peak 18(11p11.12) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 19(11q23.3) mutation analysis' versus 'CN_CNMF'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.0049

Table S25. Gene #39: 'Del Peak 19(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	24	26	41	56
DEL PEAK 19(11Q23.3) MUTATED	21	19	20	19
DEL PEAK 19(11Q23.3) WILD-TYPE	3	7	21	37

Figure S25. Get High-res Image Gene #39: 'Del Peak 19(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.
Molecular subtype file = SKCM-Regional_Metastatic.transferedmergedcluster.txt
Number of patients = 147
Number of copy number variation regions = 46
Number of molecular subtypes = 8
Exclude regions that fewer than K tumors have alterations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

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

References

[1] 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)

[2] 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)

[3] GISTIC_version2

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