Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes<BR>(All

Skin Cutaneous Melanoma: Correlation between copy number variation genes and molecular subtypes
(All_Samples cohort)

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

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 51 peak regions and 8 molecular subtypes across 288 patients, 46 significant findings detected with Q value < 0.25.

Amp Peak 2(1q44) cnvs correlated to 'CN_CNMF'.
Amp Peak 5(5p15.33) cnvs correlated to 'CN_CNMF'.
Amp Peak 6(5q35.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 7(6p25.1) cnvs correlated to 'CN_CNMF', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
Amp Peak 9(7p22.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 10(7q34) cnvs correlated to 'CN_CNMF'.
Amp Peak 11(8q11.22) cnvs correlated to 'CN_CNMF'.
Amp Peak 12(8q24.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 15(11q13.4) cnvs correlated to 'CN_CNMF'.
Amp Peak 17(13q31.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Amp Peak 18(15q24.3) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Amp Peak 19(17q25.3) cnvs correlated to 'CN_CNMF'.
Amp Peak 21(20q13.2) cnvs correlated to 'CN_CNMF'.
Amp Peak 22(22q13.2) cnvs correlated to 'CN_CNMF'.
Del Peak 1(1p36.31) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 2(1p22.1) cnvs correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 8(5q11.2) cnvs correlated to 'CN_CNMF'.
Del Peak 9(5q31.3) cnvs correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
Del Peak 10(6q16.3) cnvs correlated to 'CN_CNMF'.
Del Peak 11(6q26) cnvs correlated to 'CN_CNMF'.
Del Peak 12(6q27) cnvs correlated to 'CN_CNMF'.
Del Peak 14(9p23) cnvs correlated to 'CN_CNMF'.
Del Peak 15(9p21.3) cnvs correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 16(10p15.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 17(10q23.31) cnvs correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
Del Peak 18(10q26.3) cnvs correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
Del Peak 19(11q23.3) cnvs correlated to 'CN_CNMF'.
Del Peak 21(13q34) cnvs correlated to 'CN_CNMF'.
Del Peak 22(14q32.2) cnvs correlated to 'CN_CNMF'.
Del Peak 28(19p13.3) 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 51 regions and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 46 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 15(9p21 3)	223 (77%)	65	1.31e-12 (5.32e-10)	0.000285 (0.104)	0.658 (1.00)	0.836 (1.00)	2.6e-05 (0.01)	0.000182 (0.0672)	0.801 (1.00)	0.772 (1.00)
Amp Peak 7(6p25 1)	157 (55%)	131	7.86e-09 (3.15e-06)	0.00124 (0.446)	0.0327 (1.00)	0.28 (1.00)	0.119 (1.00)	0.187 (1.00)	0.000569 (0.206)	2.41e-05 (0.00932)
Del Peak 16(10p15 3)	161 (56%)	127	2.48e-06 (0.000974)	0.0234 (1.00)	0.979 (1.00)	0.879 (1.00)	7.06e-05 (0.0267)	1.24e-05 (0.00482)	0.603 (1.00)	1 (1.00)
Del Peak 18(10q26 3)	180 (62%)	108	7.73e-07 (0.000306)	0.108 (1.00)	0.42 (1.00)	0.897 (1.00)	8.36e-05 (0.0315)	0.000332 (0.122)	0.55 (1.00)	0.8 (1.00)
Amp Peak 6(5q35 3)	42 (15%)	246	0.000108 (0.0403)	1.02e-05 (0.00396)	0.66 (1.00)	0.722 (1.00)	0.159 (1.00)	0.445 (1.00)	0.113 (1.00)	0.163 (1.00)
Amp Peak 17(13q31 3)	78 (27%)	210	6.89e-11 (2.78e-08)	6.25e-06 (0.00245)	0.973 (1.00)	0.973 (1.00)	0.000842 (0.304)	0.0564 (1.00)	0.474 (1.00)	0.676 (1.00)
Amp Peak 18(15q24 3)	86 (30%)	202	3.06e-05 (0.0117)	0.882 (1.00)	0.79 (1.00)	0.349 (1.00)	0.000115 (0.0426)	0.00246 (0.868)	0.829 (1.00)	0.138 (1.00)
Del Peak 1(1p36 31)	70 (24%)	218	0.000418 (0.153)	4.99e-05 (0.019)	0.858 (1.00)	0.202 (1.00)	0.0199 (1.00)	0.0035 (1.00)	0.145 (1.00)	0.198 (1.00)
Del Peak 2(1p22 1)	73 (25%)	215	0.00191 (0.673)	1.12e-05 (0.00435)	0.945 (1.00)	0.081 (1.00)	9.53e-05 (0.0357)	0.00071 (0.257)	0.854 (1.00)	0.481 (1.00)
Del Peak 9(5q31 3)	104 (36%)	184	9.31e-07 (0.000367)	1.34e-05 (0.00517)	0.225 (1.00)	0.697 (1.00)	0.818 (1.00)	0.903 (1.00)	0.28 (1.00)	0.702 (1.00)
Del Peak 17(10q23 31)	178 (62%)	110	4.13e-10 (1.67e-07)	0.0412 (1.00)	0.42 (1.00)	0.646 (1.00)	0.000193 (0.071)	0.00446 (1.00)	0.526 (1.00)	0.704 (1.00)
Amp Peak 2(1q44)	149 (52%)	139	0.000102 (0.0382)	0.0401 (1.00)	0.67 (1.00)	0.899 (1.00)	0.132 (1.00)	0.7 (1.00)	0.212 (1.00)	1 (1.00)
Amp Peak 5(5p15 33)	82 (28%)	206	6.33e-05 (0.024)	0.247 (1.00)	0.331 (1.00)	0.71 (1.00)	0.46 (1.00)	0.958 (1.00)	0.0713 (1.00)	0.279 (1.00)
Amp Peak 9(7p22 3)	153 (53%)	135	2.02e-09 (8.11e-07)	0.448 (1.00)	0.666 (1.00)	0.442 (1.00)	0.145 (1.00)	0.129 (1.00)	0.953 (1.00)	0.268 (1.00)
Amp Peak 10(7q34)	172 (60%)	116	1.5e-07 (5.98e-05)	0.0689 (1.00)	0.675 (1.00)	0.445 (1.00)	0.0876 (1.00)	0.0686 (1.00)	0.528 (1.00)	0.381 (1.00)
Amp Peak 11(8q11 22)	120 (42%)	168	3.34e-05 (0.0128)	0.105 (1.00)	0.335 (1.00)	0.292 (1.00)	0.0385 (1.00)	0.0425 (1.00)	0.248 (1.00)	1 (1.00)
Amp Peak 12(8q24 3)	139 (48%)	149	9.1e-07 (0.000359)	0.0588 (1.00)	0.919 (1.00)	0.792 (1.00)	0.0659 (1.00)	0.228 (1.00)	0.423 (1.00)	0.462 (1.00)
Amp Peak 15(11q13 4)	48 (17%)	240	0.000494 (0.18)	0.00953 (1.00)	0.549 (1.00)	0.571 (1.00)	0.119 (1.00)	0.201 (1.00)	0.396 (1.00)	0.741 (1.00)
Amp Peak 19(17q25 3)	93 (32%)	195	3.87e-05 (0.0148)	0.00376 (1.00)	0.00985 (1.00)	0.00737 (1.00)	0.0273 (1.00)	0.443 (1.00)	0.184 (1.00)	0.0501 (1.00)
Amp Peak 21(20q13 2)	148 (51%)	140	4.24e-06 (0.00166)	0.0647 (1.00)	0.411 (1.00)	0.979 (1.00)	0.0326 (1.00)	0.152 (1.00)	0.749 (1.00)	0.269 (1.00)
Amp Peak 22(22q13 2)	114 (40%)	174	1.93e-08 (7.7e-06)	0.335 (1.00)	0.388 (1.00)	0.424 (1.00)	0.495 (1.00)	0.83 (1.00)	0.402 (1.00)	0.615 (1.00)
Del Peak 8(5q11 2)	76 (26%)	212	4.14e-07 (0.000164)	0.117 (1.00)	0.409 (1.00)	0.0985 (1.00)	0.547 (1.00)	0.985 (1.00)	0.368 (1.00)	0.781 (1.00)
Del Peak 10(6q16 3)	160 (56%)	128	2.67e-18 (1.08e-15)	0.0452 (1.00)	0.528 (1.00)	0.515 (1.00)	0.00487 (1.00)	0.0885 (1.00)	0.701 (1.00)	0.902 (1.00)
Del Peak 11(6q26)	173 (60%)	115	7.14e-21 (2.91e-18)	0.132 (1.00)	0.453 (1.00)	0.802 (1.00)	0.00188 (0.666)	0.0585 (1.00)	0.407 (1.00)	0.802 (1.00)
Del Peak 12(6q27)	171 (59%)	117	2.4e-18 (9.76e-16)	0.234 (1.00)	0.532 (1.00)	0.978 (1.00)	0.00331 (1.00)	0.133 (1.00)	0.554 (1.00)	0.901 (1.00)
Del Peak 14(9p23)	199 (69%)	89	1.08e-08 (4.3e-06)	0.0414 (1.00)	1 (1.00)	0.846 (1.00)	0.00145 (0.517)	0.00154 (0.548)	0.919 (1.00)	0.353 (1.00)
Del Peak 19(11q23 3)	154 (53%)	134	6.14e-05 (0.0233)	0.0766 (1.00)	0.474 (1.00)	0.136 (1.00)	0.267 (1.00)	0.428 (1.00)	0.253 (1.00)	0.0853 (1.00)
Del Peak 21(13q34)	64 (22%)	224	9.76e-05 (0.0365)	0.00386 (1.00)	0.693 (1.00)	0.97 (1.00)	0.372 (1.00)	0.0423 (1.00)	0.729 (1.00)	0.882 (1.00)
Del Peak 22(14q32 2)	96 (33%)	192	8.37e-05 (0.0315)	0.768 (1.00)	0.0824 (1.00)	0.347 (1.00)	0.00456 (1.00)	0.0214 (1.00)	0.472 (1.00)	0.299 (1.00)
Del Peak 28(19p13 3)	83 (29%)	205	0.000176 (0.065)	0.651 (1.00)	0.00962 (1.00)	0.00939 (1.00)	0.0163 (1.00)	0.038 (1.00)	0.864 (1.00)	0.0784 (1.00)
Amp Peak 1(1p12)	84 (29%)	204	0.0202 (1.00)	0.88 (1.00)	0.635 (1.00)	0.72 (1.00)	0.432 (1.00)	0.842 (1.00)	0.985 (1.00)	0.893 (1.00)
Amp Peak 3(3p13)	71 (25%)	217	0.319 (1.00)	0.321 (1.00)	0.171 (1.00)	0.302 (1.00)	0.23 (1.00)	0.414 (1.00)	0.795 (1.00)	0.886 (1.00)
Amp Peak 4(4q12)	50 (17%)	238	0.019 (1.00)	0.542 (1.00)	0.728 (1.00)	0.0894 (1.00)	0.467 (1.00)	0.959 (1.00)	0.363 (1.00)	0.0152 (1.00)
Amp Peak 8(6q12)	61 (21%)	227	0.294 (1.00)	0.933 (1.00)	0.261 (1.00)	0.487 (1.00)	0.0015 (0.535)	0.093 (1.00)	0.505 (1.00)	0.18 (1.00)
Amp Peak 13(9p24 1)	22 (8%)	266	0.836 (1.00)	0.44 (1.00)	0.449 (1.00)	0.941 (1.00)	0.816 (1.00)	0.329 (1.00)	0.126 (1.00)	0.494 (1.00)
Amp Peak 14(11q13 3)	51 (18%)	237	0.0049 (1.00)	0.0914 (1.00)	0.89 (1.00)	0.582 (1.00)	0.299 (1.00)	0.667 (1.00)	0.659 (1.00)	0.746 (1.00)
Amp Peak 16(12q15)	43 (15%)	245	0.00266 (0.933)	0.955 (1.00)	0.68 (1.00)	0.44 (1.00)	0.872 (1.00)	0.955 (1.00)	0.955 (1.00)	0.608 (1.00)
Amp Peak 20(19p13 2)	57 (20%)	231	0.0339 (1.00)	0.452 (1.00)	0.877 (1.00)	0.0326 (1.00)	0.0133 (1.00)	0.000848 (0.305)	0.0892 (1.00)	0.00507 (1.00)
Del Peak 3(2q37 3)	70 (24%)	218	0.0258 (1.00)	0.149 (1.00)	0.496 (1.00)	0.131 (1.00)	0.00143 (0.511)	0.324 (1.00)	0.0381 (1.00)	0.116 (1.00)
Del Peak 4(3p26 1)	51 (18%)	237	0.314 (1.00)	0.618 (1.00)	0.692 (1.00)	0.845 (1.00)	0.261 (1.00)	0.251 (1.00)	0.528 (1.00)	1 (1.00)
Del Peak 5(3q23)	40 (14%)	248	0.414 (1.00)	0.0184 (1.00)	0.449 (1.00)	0.523 (1.00)	0.455 (1.00)	1 (1.00)	0.495 (1.00)	0.378 (1.00)
Del Peak 6(4p16 3)	64 (22%)	224	0.304 (1.00)	0.32 (1.00)	0.972 (1.00)	0.613 (1.00)	0.2 (1.00)	0.5 (1.00)	0.637 (1.00)	0.376 (1.00)
Del Peak 7(4q34 3)	80 (28%)	208	0.00576 (1.00)	0.199 (1.00)	0.536 (1.00)	0.508 (1.00)	0.209 (1.00)	0.119 (1.00)	0.108 (1.00)	0.00934 (1.00)
Del Peak 13(8p23 3)	75 (26%)	213	0.0127 (1.00)	0.00906 (1.00)	0.515 (1.00)	0.414 (1.00)	0.278 (1.00)	0.871 (1.00)	0.193 (1.00)	0.209 (1.00)
Del Peak 20(12q24 33)	68 (24%)	220	0.118 (1.00)	0.018 (1.00)	0.632 (1.00)	0.817 (1.00)	0.361 (1.00)	0.157 (1.00)	0.967 (1.00)	0.311 (1.00)
Del Peak 23(15q13 3)	61 (21%)	227	0.143 (1.00)	0.0295 (1.00)	0.828 (1.00)	0.729 (1.00)	0.59 (1.00)	0.702 (1.00)	0.398 (1.00)	1 (1.00)
Del Peak 24(15q15 1)	67 (23%)	221	0.0514 (1.00)	0.0314 (1.00)	0.429 (1.00)	0.555 (1.00)	0.626 (1.00)	0.738 (1.00)	0.668 (1.00)	0.311 (1.00)
Del Peak 25(16p13 3)	52 (18%)	236	0.46 (1.00)	0.0603 (1.00)	0.0473 (1.00)	0.761 (1.00)	0.724 (1.00)	0.158 (1.00)	0.603 (1.00)	0.342 (1.00)
Del Peak 26(16q12 1)	96 (33%)	192	0.00645 (1.00)	0.381 (1.00)	0.145 (1.00)	0.231 (1.00)	0.417 (1.00)	0.147 (1.00)	0.782 (1.00)	0.0888 (1.00)
Del Peak 27(16q24 3)	106 (37%)	182	0.0119 (1.00)	0.208 (1.00)	0.363 (1.00)	0.835 (1.00)	0.0695 (1.00)	0.0416 (1.00)	0.282 (1.00)	0.0152 (1.00)
Del Peak 29(22q12 1)	45 (16%)	243	0.0111 (1.00)	0.296 (1.00)	0.671 (1.00)	0.446 (1.00)	0.678 (1.00)	0.626 (1.00)	0.0265 (1.00)	0.132 (1.00)

'Amp Peak 2(1q44) mutation analysis' versus 'CN_CNMF'

P value = 0.000102 (Fisher's exact test), Q value = 0.038

Table S1. Gene #2: 'Amp Peak 2(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 2(1Q44) MUTATED	20	59	24	46
AMP PEAK 2(1Q44) WILD-TYPE	34	36	44	25

Figure S1. Get High-res Image Gene #2: 'Amp Peak 2(1q44) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 6.33e-05 (Fisher's exact test), Q value = 0.024

Table S2. 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	54	95	68	71
AMP PEAK 5(5P15.33) MUTATED	14	37	6	25
AMP PEAK 5(5P15.33) WILD-TYPE	40	58	62	46

Figure S2. Get High-res Image Gene #5: 'Amp Peak 5(5p15.33) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5q35.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000108 (Fisher's exact test), Q value = 0.04

Table S3. Gene #6: 'Amp Peak 6(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 6(5Q35.3) MUTATED	2	23	3	14
AMP PEAK 6(5Q35.3) WILD-TYPE	52	72	65	57

Figure S3. Get High-res Image Gene #6: 'Amp Peak 6(5q35.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 6(5q35.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.004

Table S4. Gene #6: 'Amp Peak 6(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
AMP PEAK 6(5Q35.3) MUTATED	23	12	7
AMP PEAK 6(5Q35.3) WILD-TYPE	48	93	105

Figure S4. Get High-res Image Gene #6: 'Amp Peak 6(5q35.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 7(6p25.1) mutation analysis' versus 'CN_CNMF'

P value = 7.86e-09 (Fisher's exact test), Q value = 3.2e-06

Table S5. Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 7(6P25.1) MUTATED	19	76	29	33
AMP PEAK 7(6P25.1) WILD-TYPE	35	19	39	38

Figure S5. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 7(6p25.1) mutation analysis' versus 'MIRSEQ_CNMF'

P value = 0.000569 (Fisher's exact test), Q value = 0.21

Table S6. Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	122	88	72
AMP PEAK 7(6P25.1) MUTATED	81	35	37
AMP PEAK 7(6P25.1) WILD-TYPE	41	53	35

Figure S6. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #7: 'MIRSEQ_CNMF'

'Amp Peak 7(6p25.1) mutation analysis' versus 'MIRSEQ_CHIERARCHICAL'

P value = 2.41e-05 (Fisher's exact test), Q value = 0.0093

Table S7. Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2
ALL	176	106
AMP PEAK 7(6P25.1) MUTATED	113	40
AMP PEAK 7(6P25.1) WILD-TYPE	63	66

Figure S7. Get High-res Image Gene #7: 'Amp Peak 7(6p25.1) mutation analysis' versus Clinical Feature #8: 'MIRSEQ_CHIERARCHICAL'

'Amp Peak 9(7p22.3) mutation analysis' versus 'CN_CNMF'

P value = 2.02e-09 (Fisher's exact test), Q value = 8.1e-07

Table S8. Gene #9: 'Amp Peak 9(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 9(7P22.3) MUTATED	25	45	23	60
AMP PEAK 9(7P22.3) WILD-TYPE	29	50	45	11

Figure S8. Get High-res Image Gene #9: 'Amp Peak 9(7p22.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.5e-07 (Fisher's exact test), Q value = 6e-05

Table S9. Gene #10: 'Amp Peak 10(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 10(7Q34) MUTATED	24	52	34	62
AMP PEAK 10(7Q34) WILD-TYPE	30	43	34	9

Figure S9. Get High-res Image Gene #10: 'Amp Peak 10(7q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 11(8q11.22) mutation analysis' versus 'CN_CNMF'

P value = 3.34e-05 (Fisher's exact test), Q value = 0.013

Table S10. Gene #11: 'Amp Peak 11(8q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 11(8Q11.22) MUTATED	14	51	17	38
AMP PEAK 11(8Q11.22) WILD-TYPE	40	44	51	33

Figure S10. Get High-res Image Gene #11: 'Amp Peak 11(8q11.22) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 12(8q24.3) mutation analysis' versus 'CN_CNMF'

P value = 9.1e-07 (Fisher's exact test), Q value = 0.00036

Table S11. Gene #12: 'Amp Peak 12(8q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 12(8Q24.3) MUTATED	17	61	19	42
AMP PEAK 12(8Q24.3) WILD-TYPE	37	34	49	29

Figure S11. Get High-res Image Gene #12: 'Amp Peak 12(8q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 15(11q13.4) mutation analysis' versus 'CN_CNMF'

P value = 0.000494 (Fisher's exact test), Q value = 0.18

Table S12. Gene #15: 'Amp Peak 15(11q13.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 15(11Q13.4) MUTATED	10	27	4	7
AMP PEAK 15(11Q13.4) WILD-TYPE	44	68	64	64

Figure S12. Get High-res Image Gene #15: 'Amp Peak 15(11q13.4) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(13q31.3) mutation analysis' versus 'CN_CNMF'

P value = 6.89e-11 (Fisher's exact test), Q value = 2.8e-08

Table S13. Gene #17: 'Amp Peak 17(13q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 17(13Q31.3) MUTATED	16	48	4	10
AMP PEAK 17(13Q31.3) WILD-TYPE	38	47	64	61

Figure S13. Get High-res Image Gene #17: 'Amp Peak 17(13q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 17(13q31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 6.25e-06 (Fisher's exact test), Q value = 0.0024

Table S14. Gene #17: 'Amp Peak 17(13q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
AMP PEAK 17(13Q31.3) MUTATED	35	25	18
AMP PEAK 17(13Q31.3) WILD-TYPE	36	80	94

Figure S14. Get High-res Image Gene #17: 'Amp Peak 17(13q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Amp Peak 18(15q24.3) mutation analysis' versus 'CN_CNMF'

P value = 3.06e-05 (Fisher's exact test), Q value = 0.012

Table S15. Gene #18: 'Amp Peak 18(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 18(15Q24.3) MUTATED	10	29	11	36
AMP PEAK 18(15Q24.3) WILD-TYPE	44	66	57	35

Figure S15. Get High-res Image Gene #18: 'Amp Peak 18(15q24.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 18(15q24.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000115 (Fisher's exact test), Q value = 0.043

Table S16. Gene #18: 'Amp Peak 18(15q24.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
AMP PEAK 18(15Q24.3) MUTATED	2	25	33	24
AMP PEAK 18(15Q24.3) WILD-TYPE	42	56	52	48

Figure S16. Get High-res Image Gene #18: 'Amp Peak 18(15q24.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Amp Peak 19(17q25.3) mutation analysis' versus 'CN_CNMF'

P value = 3.87e-05 (Fisher's exact test), Q value = 0.015

Table S17. Gene #19: 'Amp Peak 19(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 19(17Q25.3) MUTATED	10	43	11	29
AMP PEAK 19(17Q25.3) WILD-TYPE	44	52	57	42

Figure S17. Get High-res Image Gene #19: 'Amp Peak 19(17q25.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Amp Peak 21(20q13.2) mutation analysis' versus 'CN_CNMF'

P value = 4.24e-06 (Fisher's exact test), Q value = 0.0017

Table S18. Gene #21: 'Amp Peak 21(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 21(20Q13.2) MUTATED	20	53	23	52
AMP PEAK 21(20Q13.2) WILD-TYPE	34	42	45	19

Figure S18. Get High-res Image Gene #21: 'Amp Peak 21(20q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

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

P value = 1.93e-08 (Fisher's exact test), Q value = 7.7e-06

Table S19. Gene #22: 'Amp Peak 22(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
AMP PEAK 22(22Q13.2) MUTATED	12	31	21	50
AMP PEAK 22(22Q13.2) WILD-TYPE	42	64	47	21

Figure S19. Get High-res Image Gene #22: 'Amp Peak 22(22q13.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'CN_CNMF'

P value = 0.000418 (Fisher's exact test), Q value = 0.15

Table S20. Gene #23: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 1(1P36.31) MUTATED	16	32	5	17
DEL PEAK 1(1P36.31) WILD-TYPE	38	63	63	54

Figure S20. Get High-res Image Gene #23: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 1(1p36.31) mutation analysis' versus 'METHLYATION_CNMF'

P value = 4.99e-05 (Fisher's exact test), Q value = 0.019

Table S21. Gene #23: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
DEL PEAK 1(1P36.31) MUTATED	31	23	16
DEL PEAK 1(1P36.31) WILD-TYPE	40	82	96

Figure S21. Get High-res Image Gene #23: 'Del Peak 1(1p36.31) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

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

P value = 1.12e-05 (Fisher's exact test), Q value = 0.0043

Table S22. Gene #24: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
DEL PEAK 2(1P22.1) MUTATED	33	15	25
DEL PEAK 2(1P22.1) WILD-TYPE	38	90	87

Figure S22. Get High-res Image Gene #24: '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 = 9.53e-05 (Fisher's exact test), Q value = 0.036

Table S23. Gene #24: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
DEL PEAK 2(1P22.1) MUTATED	10	17	37	9
DEL PEAK 2(1P22.1) WILD-TYPE	34	64	48	63

Figure S23. Get High-res Image Gene #24: 'Del Peak 2(1p22.1) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 8(5q11.2) mutation analysis' versus 'CN_CNMF'

P value = 4.14e-07 (Fisher's exact test), Q value = 0.00016

Table S24. Gene #30: 'Del Peak 8(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 8(5Q11.2) MUTATED	25	17	6	28
DEL PEAK 8(5Q11.2) WILD-TYPE	29	78	62	43

Figure S24. Get High-res Image Gene #30: 'Del Peak 8(5q11.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(5q31.3) mutation analysis' versus 'CN_CNMF'

P value = 9.31e-07 (Fisher's exact test), Q value = 0.00037

Table S25. Gene #31: 'Del Peak 9(5q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 9(5Q31.3) MUTATED	32	23	14	35
DEL PEAK 9(5Q31.3) WILD-TYPE	22	72	54	36

Figure S25. Get High-res Image Gene #31: 'Del Peak 9(5q31.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 9(5q31.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 1.34e-05 (Fisher's exact test), Q value = 0.0052

Table S26. Gene #31: 'Del Peak 9(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
DEL PEAK 9(5Q31.3) MUTATED	11	52	41
DEL PEAK 9(5Q31.3) WILD-TYPE	60	53	71

Figure S26. Get High-res Image Gene #31: 'Del Peak 9(5q31.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 10(6q16.3) mutation analysis' versus 'CN_CNMF'

P value = 2.67e-18 (Fisher's exact test), Q value = 1.1e-15

Table S27. Gene #32: 'Del Peak 10(6q16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 10(6Q16.3) MUTATED	6	77	28	49
DEL PEAK 10(6Q16.3) WILD-TYPE	48	18	40	22

Figure S27. Get High-res Image Gene #32: 'Del Peak 10(6q16.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 11(6q26) mutation analysis' versus 'CN_CNMF'

P value = 7.14e-21 (Fisher's exact test), Q value = 2.9e-18

Table S28. Gene #33: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 11(6Q26) MUTATED	7	84	32	50
DEL PEAK 11(6Q26) WILD-TYPE	47	11	36	21

Figure S28. Get High-res Image Gene #33: 'Del Peak 11(6q26) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 12(6q27) mutation analysis' versus 'CN_CNMF'

P value = 2.4e-18 (Fisher's exact test), Q value = 9.8e-16

Table S29. Gene #34: 'Del Peak 12(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 12(6Q27) MUTATED	7	81	34	49
DEL PEAK 12(6Q27) WILD-TYPE	47	14	34	22

Figure S29. Get High-res Image Gene #34: 'Del Peak 12(6q27) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 14(9p23) mutation analysis' versus 'CN_CNMF'

P value = 1.08e-08 (Fisher's exact test), Q value = 4.3e-06

Table S30. Gene #36: 'Del Peak 14(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 14(9P23) MUTATED	48	76	28	47
DEL PEAK 14(9P23) WILD-TYPE	6	19	40	24

Figure S30. Get High-res Image Gene #36: 'Del Peak 14(9p23) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(9p21.3) mutation analysis' versus 'CN_CNMF'

P value = 1.31e-12 (Fisher's exact test), Q value = 5.3e-10

Table S31. Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 15(9P21.3) MUTATED	51	86	30	56
DEL PEAK 15(9P21.3) WILD-TYPE	3	9	38	15

Figure S31. Get High-res Image Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 15(9p21.3) mutation analysis' versus 'METHLYATION_CNMF'

P value = 0.000285 (Fisher's exact test), Q value = 0.1

Table S32. Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	71	105	112
DEL PEAK 15(9P21.3) MUTATED	63	87	73
DEL PEAK 15(9P21.3) WILD-TYPE	8	18	39

Figure S32. Get High-res Image Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #2: 'METHLYATION_CNMF'

'Del Peak 15(9p21.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 2.6e-05 (Fisher's exact test), Q value = 0.01

Table S33. Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
DEL PEAK 15(9P21.3) MUTATED	35	59	80	47
DEL PEAK 15(9P21.3) WILD-TYPE	9	22	5	25

Figure S33. Get High-res Image Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 15(9p21.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000182 (Fisher's exact test), Q value = 0.067

Table S34. Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	115	88
DEL PEAK 15(9P21.3) MUTATED	67	76	78
DEL PEAK 15(9P21.3) WILD-TYPE	12	39	10

Figure S34. Get High-res Image Gene #37: 'Del Peak 15(9p21.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 16(10p15.3) mutation analysis' versus 'CN_CNMF'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.00097

Table S35. Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 16(10P15.3) MUTATED	34	51	22	54
DEL PEAK 16(10P15.3) WILD-TYPE	20	44	46	17

Figure S35. Get High-res Image Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 16(10p15.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 7.06e-05 (Fisher's exact test), Q value = 0.027

Table S36. Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
DEL PEAK 16(10P15.3) MUTATED	21	40	65	32
DEL PEAK 16(10P15.3) WILD-TYPE	23	41	20	40

Figure S36. Get High-res Image Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 16(10p15.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.0048

Table S37. Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	115	88
DEL PEAK 16(10P15.3) MUTATED	46	47	65
DEL PEAK 16(10P15.3) WILD-TYPE	33	68	23

Figure S37. Get High-res Image Gene #38: 'Del Peak 16(10p15.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

'Del Peak 17(10q23.31) mutation analysis' versus 'CN_CNMF'

P value = 4.13e-10 (Fisher's exact test), Q value = 1.7e-07

Table S38. Gene #39: 'Del Peak 17(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 17(10Q23.31) MUTATED	42	53	23	60
DEL PEAK 17(10Q23.31) WILD-TYPE	12	42	45	11

Figure S38. Get High-res Image Gene #39: 'Del Peak 17(10q23.31) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 17(10q23.31) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 0.000193 (Fisher's exact test), Q value = 0.071

Table S39. Gene #39: 'Del Peak 17(10q23.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
DEL PEAK 17(10Q23.31) MUTATED	23	46	69	38
DEL PEAK 17(10Q23.31) WILD-TYPE	21	35	16	34

Figure S39. Get High-res Image Gene #39: 'Del Peak 17(10q23.31) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 18(10q26.3) mutation analysis' versus 'CN_CNMF'

P value = 7.73e-07 (Fisher's exact test), Q value = 0.00031

Table S40. Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 18(10Q26.3) MUTATED	43	56	26	55
DEL PEAK 18(10Q26.3) WILD-TYPE	11	39	42	16

Figure S40. Get High-res Image Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 18(10q26.3) mutation analysis' versus 'MRNASEQ_CNMF'

P value = 8.36e-05 (Fisher's exact test), Q value = 0.032

Table S41. Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	44	81	85	72
DEL PEAK 18(10Q26.3) MUTATED	23	45	70	39
DEL PEAK 18(10Q26.3) WILD-TYPE	21	36	15	33

Figure S41. Get High-res Image Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #5: 'MRNASEQ_CNMF'

'Del Peak 18(10q26.3) mutation analysis' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000332 (Fisher's exact test), Q value = 0.12

Table S42. Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	79	115	88
DEL PEAK 18(10Q26.3) MUTATED	44	63	70
DEL PEAK 18(10Q26.3) WILD-TYPE	35	52	18

Figure S42. Get High-res Image Gene #40: 'Del Peak 18(10q26.3) mutation analysis' versus Clinical Feature #6: 'MRNASEQ_CHIERARCHICAL'

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

P value = 6.14e-05 (Fisher's exact test), Q value = 0.023

Table S43. Gene #41: 'Del Peak 19(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 19(11Q23.3) MUTATED	23	54	25	52
DEL PEAK 19(11Q23.3) WILD-TYPE	31	41	43	19

Figure S43. Get High-res Image Gene #41: 'Del Peak 19(11q23.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 21(13q34) mutation analysis' versus 'CN_CNMF'

P value = 9.76e-05 (Fisher's exact test), Q value = 0.037

Table S44. Gene #43: 'Del Peak 21(13q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 21(13Q34) MUTATED	9	12	13	30
DEL PEAK 21(13Q34) WILD-TYPE	45	83	55	41

Figure S44. Get High-res Image Gene #43: 'Del Peak 21(13q34) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 22(14q32.2) mutation analysis' versus 'CN_CNMF'

P value = 8.37e-05 (Fisher's exact test), Q value = 0.032

Table S45. Gene #44: 'Del Peak 22(14q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 22(14Q32.2) MUTATED	10	45	13	28
DEL PEAK 22(14Q32.2) WILD-TYPE	44	50	55	43

Figure S45. Get High-res Image Gene #44: 'Del Peak 22(14q32.2) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

'Del Peak 28(19p13.3) mutation analysis' versus 'CN_CNMF'

P value = 0.000176 (Fisher's exact test), Q value = 0.065

Table S46. Gene #50: 'Del Peak 28(19p13.3) mutation analysis' versus Clinical Feature #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	54	95	68	71
DEL PEAK 28(19P13.3) MUTATED	12	27	10	34
DEL PEAK 28(19P13.3) WILD-TYPE	42	68	58	37

Figure S46. Get High-res Image Gene #50: 'Del Peak 28(19p13.3) 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-All_Samples.transferedmergedcluster.txt
Number of patients = 288
Number of copy number variation regions = 51
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.

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] 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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