Correlation between copy number variation genes (focal events) and molecular subtypes

Skin Cutaneous Melanoma (Metastatic)

16 April 2014 | analyses__2014_04_16

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 (2014): Correlation between copy number variation genes (focal events) and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1ZP44TK

Overview

Introduction

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

Summary

Testing the association between copy number variation 54 focal events and 10 molecular subtypes across 299 patients, 41 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_1q21.3 cnv correlated to 'CN_CNMF'.
amp_1q44 cnv correlated to 'CN_CNMF'.
amp_5p15.33 cnv correlated to 'CN_CNMF'.
amp_5q35.3 cnv correlated to 'METHLYATION_CNMF'.
amp_6p24.3 cnv correlated to 'CN_CNMF', 'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
amp_7p22.1 cnv correlated to 'CN_CNMF'.
amp_7q34 cnv correlated to 'CN_CNMF'.
amp_8q11.21 cnv correlated to 'CN_CNMF'.
amp_8q24.21 cnv correlated to 'CN_CNMF'.
amp_13q12.3 cnv correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.
amp_15q26.2 cnv correlated to 'CN_CNMF'.
amp_17q25.3 cnv correlated to 'CN_CNMF'.
amp_20q13.33 cnv correlated to 'CN_CNMF'.
amp_22q13.2 cnv correlated to 'CN_CNMF'.
del_1p36.31 cnv correlated to 'METHLYATION_CNMF'.
del_1p22.1 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_5q31.3 cnv correlated to 'METHLYATION_CNMF'.
del_6q22.31 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'CN_CNMF'.
del_9p21.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_10p15.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q23.31 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_10q26.3 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
del_11p11.2 cnv correlated to 'CN_CNMF'.
del_11q23.3 cnv correlated to 'CN_CNMF'.
del_13q12.11 cnv correlated to 'CN_CNMF'.
del_13q34 cnv correlated to 'CN_CNMF'.
del_14q23.3 cnv correlated to 'CN_CNMF'.
del_14q32.2 cnv correlated to 'CN_CNMF'.
del_15q13.3 cnv correlated to 'CN_CNMF'.
del_15q14 cnv correlated to 'CN_CNMF'.
del_15q15.2 cnv correlated to 'CN_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 54 focal events and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 41 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE 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	Fisher's exact test	Fisher's exact test
amp 6p24 3	169 (57%)	130	1.51e-12 (8.15e-10)	0.0017 (0.823)	0.321 (1.00)	0.117 (1.00)	0.0817 (1.00)	0.0155 (1.00)	0.00345 (1.00)	0.000231 (0.116)	0.0152 (1.00)	0.000175 (0.0882)
del 10p15 3	163 (55%)	136	3.55e-08 (1.87e-05)	0.00294 (1.00)	0.818 (1.00)	0.194 (1.00)	4.49e-05 (0.0231)	0.000143 (0.0725)	0.237 (1.00)	0.483 (1.00)	0.463 (1.00)	0.409 (1.00)
amp 13q12 3	85 (28%)	214	1.07e-09 (5.72e-07)	2.04e-05 (0.0106)	0.393 (1.00)	0.961 (1.00)	0.00318 (1.00)	0.0122 (1.00)	0.838 (1.00)	0.845 (1.00)	0.499 (1.00)	0.958 (1.00)
del 1p22 1	76 (25%)	223	0.00112 (0.55)	6.09e-06 (0.00316)	0.583 (1.00)	0.147 (1.00)	9.19e-05 (0.0469)	0.0227 (1.00)	0.324 (1.00)	0.28 (1.00)	0.327 (1.00)	0.564 (1.00)
del 9p21 3	229 (77%)	70	6.24e-07 (0.000328)	0.0019 (0.917)	0.732 (1.00)	0.692 (1.00)	4.39e-06 (0.00229)	0.0341 (1.00)	0.853 (1.00)	0.606 (1.00)	0.535 (1.00)	0.666 (1.00)
del 10q23 31	188 (63%)	111	1.11e-09 (5.94e-07)	0.00702 (1.00)	0.878 (1.00)	0.108 (1.00)	8.47e-05 (0.0434)	0.00081 (0.401)	0.618 (1.00)	0.632 (1.00)	0.892 (1.00)	0.748 (1.00)
del 10q26 3	193 (65%)	106	2.08e-09 (1.1e-06)	0.0465 (1.00)	0.828 (1.00)	0.452 (1.00)	1.6e-05 (0.00831)	0.000861 (0.426)	0.675 (1.00)	0.834 (1.00)	0.312 (1.00)	0.626 (1.00)
amp 1q21 3	158 (53%)	141	2.16e-22 (1.16e-19)	0.0199 (1.00)	0.341 (1.00)	0.906 (1.00)	0.00159 (0.772)	0.0448 (1.00)	0.315 (1.00)	0.149 (1.00)	0.156 (1.00)	0.172 (1.00)
amp 1q44	162 (54%)	137	6.65e-22 (3.58e-19)	0.00753 (1.00)	0.161 (1.00)	0.24 (1.00)	0.0117 (1.00)	0.0139 (1.00)	0.393 (1.00)	0.0291 (1.00)	0.0493 (1.00)	0.0206 (1.00)
amp 5p15 33	91 (30%)	208	0.000135 (0.0685)	0.109 (1.00)	0.687 (1.00)	0.637 (1.00)	0.057 (1.00)	0.501 (1.00)	0.00221 (1.00)	0.0274 (1.00)	0.00242 (1.00)	0.0546 (1.00)
amp 5q35 3	48 (16%)	251	0.00701 (1.00)	0.000116 (0.059)	0.0969 (1.00)	0.0526 (1.00)	0.0314 (1.00)	0.264 (1.00)	0.0309 (1.00)	0.0628 (1.00)	0.0594 (1.00)	0.0201 (1.00)
amp 7p22 1	164 (55%)	135	1.81e-05 (0.00935)	0.625 (1.00)	0.618 (1.00)	0.794 (1.00)	0.0496 (1.00)	0.216 (1.00)	0.622 (1.00)	0.38 (1.00)	0.946 (1.00)	0.593 (1.00)
amp 7q34	177 (59%)	122	1.15e-07 (6.05e-05)	0.304 (1.00)	0.313 (1.00)	0.831 (1.00)	0.156 (1.00)	0.385 (1.00)	0.219 (1.00)	0.236 (1.00)	0.377 (1.00)	0.435 (1.00)
amp 8q11 21	137 (46%)	162	1.07e-06 (0.000561)	0.00341 (1.00)	0.565 (1.00)	0.248 (1.00)	0.0111 (1.00)	0.0681 (1.00)	0.32 (1.00)	0.841 (1.00)	0.233 (1.00)	0.113 (1.00)
amp 8q24 21	158 (53%)	141	9.23e-07 (0.000483)	0.00722 (1.00)	0.751 (1.00)	0.817 (1.00)	0.00863 (1.00)	0.225 (1.00)	0.27 (1.00)	0.531 (1.00)	0.382 (1.00)	0.141 (1.00)
amp 15q26 2	99 (33%)	200	0.000354 (0.177)	0.341 (1.00)	0.932 (1.00)	0.896 (1.00)	0.598 (1.00)	0.422 (1.00)	0.81 (1.00)	0.339 (1.00)	0.953 (1.00)	0.612 (1.00)
amp 17q25 3	100 (33%)	199	0.000184 (0.0925)	0.0242 (1.00)	0.029 (1.00)	0.0832 (1.00)	0.15 (1.00)	0.139 (1.00)	0.269 (1.00)	0.0636 (1.00)	0.0105 (1.00)	0.0196 (1.00)
amp 20q13 33	153 (51%)	146	5.02e-06 (0.00261)	0.0206 (1.00)	0.817 (1.00)	0.83 (1.00)	0.00106 (0.518)	0.0341 (1.00)	0.464 (1.00)	0.156 (1.00)	0.0757 (1.00)	0.319 (1.00)
amp 22q13 2	127 (42%)	172	0.000136 (0.0691)	0.0953 (1.00)	0.962 (1.00)	0.775 (1.00)	0.201 (1.00)	0.361 (1.00)	0.505 (1.00)	0.69 (1.00)	0.419 (1.00)	0.795 (1.00)
del 1p36 31	70 (23%)	229	0.126 (1.00)	6.89e-05 (0.0354)	0.578 (1.00)	0.215 (1.00)	0.044 (1.00)	0.00444 (1.00)	0.901 (1.00)	0.175 (1.00)	0.878 (1.00)	0.461 (1.00)
del 5q31 3	111 (37%)	188	0.000527 (0.263)	0.000226 (0.114)	0.618 (1.00)	0.869 (1.00)	0.349 (1.00)	0.732 (1.00)	0.815 (1.00)	0.277 (1.00)	0.678 (1.00)	0.0941 (1.00)
del 6q22 31	179 (60%)	120	1.31e-09 (7e-07)	0.0414 (1.00)	0.953 (1.00)	0.368 (1.00)	0.00235 (1.00)	0.455 (1.00)	0.293 (1.00)	0.653 (1.00)	0.816 (1.00)	0.32 (1.00)
del 6q26	184 (62%)	115	2.99e-10 (1.6e-07)	0.0419 (1.00)	0.83 (1.00)	0.565 (1.00)	0.000765 (0.379)	0.126 (1.00)	0.164 (1.00)	0.568 (1.00)	0.742 (1.00)	0.698 (1.00)
del 11p11 2	96 (32%)	203	0.000132 (0.0674)	0.00342 (1.00)	0.646 (1.00)	0.744 (1.00)	0.0401 (1.00)	0.0379 (1.00)	0.329 (1.00)	0.693 (1.00)	0.415 (1.00)	0.538 (1.00)
del 11q23 3	161 (54%)	138	3.4e-08 (1.8e-05)	0.255 (1.00)	0.888 (1.00)	0.39 (1.00)	0.0342 (1.00)	0.644 (1.00)	0.149 (1.00)	0.047 (1.00)	0.147 (1.00)	0.0416 (1.00)
del 13q12 11	68 (23%)	231	6.17e-05 (0.0317)	0.111 (1.00)	0.243 (1.00)	0.561 (1.00)	0.794 (1.00)	0.944 (1.00)	0.349 (1.00)	0.239 (1.00)	0.394 (1.00)	0.307 (1.00)
del 13q34	68 (23%)	231	0.000373 (0.187)	0.00131 (0.637)	0.0668 (1.00)	0.451 (1.00)	0.508 (1.00)	0.21 (1.00)	0.789 (1.00)	0.307 (1.00)	0.863 (1.00)	0.235 (1.00)
del 14q23 3	102 (34%)	197	2.89e-08 (1.53e-05)	0.974 (1.00)	0.544 (1.00)	0.338 (1.00)	0.00678 (1.00)	0.598 (1.00)	0.4 (1.00)	0.64 (1.00)	0.303 (1.00)	0.327 (1.00)
del 14q32 2	100 (33%)	199	6.23e-08 (3.29e-05)	0.805 (1.00)	0.505 (1.00)	0.126 (1.00)	0.000862 (0.426)	0.388 (1.00)	0.439 (1.00)	0.686 (1.00)	0.414 (1.00)	0.509 (1.00)
del 15q13 3	73 (24%)	226	8.11e-06 (0.00421)	0.0128 (1.00)	0.0918 (1.00)	0.608 (1.00)	0.0752 (1.00)	0.0542 (1.00)	0.53 (1.00)	1 (1.00)	0.856 (1.00)	0.605 (1.00)
del 15q14	73 (24%)	226	2.19e-08 (1.16e-05)	0.00786 (1.00)	0.804 (1.00)	0.856 (1.00)	0.0667 (1.00)	0.0308 (1.00)	0.797 (1.00)	0.433 (1.00)	0.97 (1.00)	0.463 (1.00)
del 15q15 2	78 (26%)	221	8.92e-10 (4.78e-07)	0.0167 (1.00)	0.473 (1.00)	0.391 (1.00)	0.163 (1.00)	0.0883 (1.00)	0.949 (1.00)	0.676 (1.00)	0.98 (1.00)	0.376 (1.00)
amp 1p12	96 (32%)	203	0.014 (1.00)	0.661 (1.00)	0.7 (1.00)	0.966 (1.00)	0.0746 (1.00)	0.706 (1.00)	0.796 (1.00)	1 (1.00)	0.455 (1.00)	0.992 (1.00)
amp 3p13	78 (26%)	221	0.153 (1.00)	0.305 (1.00)	0.0694 (1.00)	0.115 (1.00)	0.788 (1.00)	0.423 (1.00)	0.947 (1.00)	0.48 (1.00)	1 (1.00)	0.22 (1.00)
amp 4q12	53 (18%)	246	0.000717 (0.357)	0.156 (1.00)	0.0818 (1.00)	0.0551 (1.00)	0.286 (1.00)	0.133 (1.00)	0.0285 (1.00)	0.0244 (1.00)	0.00532 (1.00)	0.0432 (1.00)
amp 6q12	64 (21%)	235	0.005 (1.00)	0.575 (1.00)	0.523 (1.00)	0.11 (1.00)	0.385 (1.00)	0.215 (1.00)	0.127 (1.00)	0.226 (1.00)	0.784 (1.00)	0.328 (1.00)
amp 11q13 3	58 (19%)	241	0.0282 (1.00)	0.4 (1.00)	0.892 (1.00)	0.314 (1.00)	0.206 (1.00)	0.732 (1.00)	0.848 (1.00)	0.269 (1.00)	0.699 (1.00)	0.44 (1.00)
amp 11q13 4	54 (18%)	245	0.00114 (0.558)	0.0623 (1.00)	0.909 (1.00)	0.363 (1.00)	0.0625 (1.00)	0.602 (1.00)	0.504 (1.00)	0.126 (1.00)	0.576 (1.00)	0.262 (1.00)
amp 12q14 1	51 (17%)	248	0.0119 (1.00)	0.391 (1.00)	0.873 (1.00)	0.23 (1.00)	0.052 (1.00)	0.366 (1.00)	0.512 (1.00)	0.962 (1.00)	0.149 (1.00)	0.873 (1.00)
amp 12q15	50 (17%)	249	0.0119 (1.00)	0.726 (1.00)	0.637 (1.00)	0.23 (1.00)	0.364 (1.00)	0.478 (1.00)	0.592 (1.00)	0.639 (1.00)	0.299 (1.00)	0.795 (1.00)
amp 19p13 2	56 (19%)	243	0.108 (1.00)	0.242 (1.00)	0.439 (1.00)	0.736 (1.00)	0.0068 (1.00)	0.047 (1.00)	0.489 (1.00)	0.107 (1.00)	0.424 (1.00)	0.277 (1.00)
del 2q37 3	74 (25%)	225	0.711 (1.00)	0.0624 (1.00)	0.0932 (1.00)	0.0106 (1.00)	0.0147 (1.00)	0.0154 (1.00)	0.0643 (1.00)	0.228 (1.00)	0.152 (1.00)	0.289 (1.00)
del 3p24 3	60 (20%)	239	0.472 (1.00)	0.064 (1.00)	0.36 (1.00)	0.627 (1.00)	0.235 (1.00)	0.352 (1.00)	0.437 (1.00)	0.438 (1.00)	0.385 (1.00)	0.0239 (1.00)
del 3q23	48 (16%)	251	0.147 (1.00)	0.03 (1.00)	0.348 (1.00)	0.363 (1.00)	0.4 (1.00)	0.228 (1.00)	0.829 (1.00)	0.792 (1.00)	0.754 (1.00)	0.31 (1.00)
del 4q34 3	85 (28%)	214	0.0195 (1.00)	0.118 (1.00)	0.508 (1.00)	0.383 (1.00)	0.152 (1.00)	0.0168 (1.00)	0.0136 (1.00)	0.00114 (0.558)	0.0282 (1.00)	0.0147 (1.00)
del 5p15 31	61 (20%)	238	0.788 (1.00)	0.287 (1.00)	0.54 (1.00)	0.632 (1.00)	0.661 (1.00)	0.826 (1.00)	0.663 (1.00)	0.671 (1.00)	0.903 (1.00)	0.0997 (1.00)
del 5q11 2	80 (27%)	219	0.00167 (0.81)	0.187 (1.00)	0.58 (1.00)	0.528 (1.00)	0.326 (1.00)	0.286 (1.00)	0.975 (1.00)	0.395 (1.00)	0.635 (1.00)	0.307 (1.00)
del 8p23 3	69 (23%)	230	0.0805 (1.00)	0.2 (1.00)	0.207 (1.00)	0.19 (1.00)	0.156 (1.00)	0.736 (1.00)	0.0939 (1.00)	0.334 (1.00)	0.161 (1.00)	0.616 (1.00)
del 9p23	206 (69%)	93	0.000866 (0.426)	0.0459 (1.00)	0.451 (1.00)	0.962 (1.00)	0.0017 (0.823)	0.181 (1.00)	0.644 (1.00)	0.0733 (1.00)	0.149 (1.00)	0.154 (1.00)
del 12q23 3	73 (24%)	226	0.000741 (0.368)	0.0501 (1.00)	0.961 (1.00)	0.76 (1.00)	0.52 (1.00)	0.252 (1.00)	0.652 (1.00)	0.354 (1.00)	0.805 (1.00)	0.388 (1.00)
del 16p13 3	56 (19%)	243	0.37 (1.00)	0.0413 (1.00)	0.0131 (1.00)	0.382 (1.00)	0.0501 (1.00)	0.359 (1.00)	0.16 (1.00)	0.441 (1.00)	0.368 (1.00)	0.312 (1.00)
del 16q12 1	97 (32%)	202	0.0906 (1.00)	0.705 (1.00)	0.0212 (1.00)	0.767 (1.00)	0.181 (1.00)	0.34 (1.00)	0.131 (1.00)	0.174 (1.00)	0.312 (1.00)	0.114 (1.00)
del 16q24 3	107 (36%)	192	0.0321 (1.00)	0.843 (1.00)	0.146 (1.00)	0.925 (1.00)	0.015 (1.00)	0.318 (1.00)	0.0501 (1.00)	0.053 (1.00)	0.312 (1.00)	0.0535 (1.00)
del 19p13 3	83 (28%)	216	0.00668 (1.00)	0.439 (1.00)	0.00259 (1.00)	0.0296 (1.00)	0.00287 (1.00)	0.479 (1.00)	0.938 (1.00)	0.272 (1.00)	0.672 (1.00)	0.107 (1.00)

'amp_1q21.3' versus 'CN_CNMF'

P value = 2.16e-22 (Fisher's exact test), Q value = 1.2e-19

Table S1. Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 2(1Q21.3) MUTATED	76	13	37	32
AMP PEAK 2(1Q21.3) WILD-TYPE	9	44	14	74

Figure S1. Get High-res Image Gene #2: 'amp_1q21.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_1q44' versus 'CN_CNMF'

P value = 6.65e-22 (Fisher's exact test), Q value = 3.6e-19

Table S2. Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 3(1Q44) MUTATED	77	14	37	34
AMP PEAK 3(1Q44) WILD-TYPE	8	43	14	72

Figure S2. Get High-res Image Gene #3: 'amp_1q44' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5p15.33' versus 'CN_CNMF'

P value = 0.000135 (Fisher's exact test), Q value = 0.069

Table S3. Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 6(5P15.33) MUTATED	32	25	18	16
AMP PEAK 6(5P15.33) WILD-TYPE	53	32	33	90

Figure S3. Get High-res Image Gene #6: 'amp_5p15.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_5q35.3' versus 'METHLYATION_CNMF'

P value = 0.000116 (Fisher's exact test), Q value = 0.059

Table S4. Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	104	109
AMP PEAK 7(5Q35.3) MUTATED	25	12	10
AMP PEAK 7(5Q35.3) WILD-TYPE	53	92	99

Figure S4. Get High-res Image Gene #7: 'amp_5q35.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_6p24.3' versus 'CN_CNMF'

P value = 1.51e-12 (Fisher's exact test), Q value = 8.1e-10

Table S5. Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 8(6P24.3) MUTATED	67	45	15	42
AMP PEAK 8(6P24.3) WILD-TYPE	18	12	36	64

Figure S5. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_6p24.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.000231 (Fisher's exact test), Q value = 0.12

Table S6. Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	27	164	88
AMP PEAK 8(6P24.3) MUTATED	15	109	35
AMP PEAK 8(6P24.3) WILD-TYPE	12	55	53

Figure S6. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'amp_6p24.3' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000175 (Fisher's exact test), Q value = 0.088

Table S7. Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	25	85	47	122
AMP PEAK 8(6P24.3) MUTATED	14	32	33	80
AMP PEAK 8(6P24.3) WILD-TYPE	11	53	14	42

Figure S7. Get High-res Image Gene #8: 'amp_6p24.3' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'amp_7p22.1' versus 'CN_CNMF'

P value = 1.81e-05 (Fisher's exact test), Q value = 0.0094

Table S8. Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 10(7P22.1) MUTATED	47	34	41	42
AMP PEAK 10(7P22.1) WILD-TYPE	38	23	10	64

Figure S8. Get High-res Image Gene #10: 'amp_7p22.1' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q34' versus 'CN_CNMF'

P value = 1.15e-07 (Fisher's exact test), Q value = 6.1e-05

Table S9. Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 11(7Q34) MUTATED	45	35	47	50
AMP PEAK 11(7Q34) WILD-TYPE	40	22	4	56

Figure S9. Get High-res Image Gene #11: 'amp_7q34' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.21' versus 'CN_CNMF'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.00056

Table S10. Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 12(8Q11.21) MUTATED	44	37	29	27
AMP PEAK 12(8Q11.21) WILD-TYPE	41	20	22	79

Figure S10. Get High-res Image Gene #12: 'amp_8q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q24.21' versus 'CN_CNMF'

P value = 9.23e-07 (Fisher's exact test), Q value = 0.00048

Table S11. Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 13(8Q24.21) MUTATED	53	41	30	34
AMP PEAK 13(8Q24.21) WILD-TYPE	32	16	21	72

Figure S11. Get High-res Image Gene #13: 'amp_8q24.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'CN_CNMF'

P value = 1.07e-09 (Fisher's exact test), Q value = 5.7e-07

Table S12. Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 18(13Q12.3) MUTATED	32	32	10	11
AMP PEAK 18(13Q12.3) WILD-TYPE	53	25	41	95

Figure S12. Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_13q12.3' versus 'METHLYATION_CNMF'

P value = 2.04e-05 (Fisher's exact test), Q value = 0.011

Table S13. Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	104	109
AMP PEAK 18(13Q12.3) MUTATED	38	24	20
AMP PEAK 18(13Q12.3) WILD-TYPE	40	80	89

Figure S13. Get High-res Image Gene #18: 'amp_13q12.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'amp_15q26.2' versus 'CN_CNMF'

P value = 0.000354 (Fisher's exact test), Q value = 0.18

Table S14. Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 19(15Q26.2) MUTATED	27	16	30	26
AMP PEAK 19(15Q26.2) WILD-TYPE	58	41	21	80

Figure S14. Get High-res Image Gene #19: 'amp_15q26.2' versus Molecular Subtype #1: 'CN_CNMF'

'amp_17q25.3' versus 'CN_CNMF'

P value = 0.000184 (Fisher's exact test), Q value = 0.093

Table S15. Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 20(17Q25.3) MUTATED	39	23	19	19
AMP PEAK 20(17Q25.3) WILD-TYPE	46	34	32	87

Figure S15. Get High-res Image Gene #20: 'amp_17q25.3' versus Molecular Subtype #1: 'CN_CNMF'

'amp_20q13.33' versus 'CN_CNMF'

P value = 5.02e-06 (Fisher's exact test), Q value = 0.0026

Table S16. Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 22(20Q13.33) MUTATED	47	36	36	34
AMP PEAK 22(20Q13.33) WILD-TYPE	38	21	15	72

Figure S16. Get High-res Image Gene #22: 'amp_20q13.33' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q13.2' versus 'CN_CNMF'

P value = 0.000136 (Fisher's exact test), Q value = 0.069

Table S17. Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
AMP PEAK 23(22Q13.2) MUTATED	44	20	32	31
AMP PEAK 23(22Q13.2) WILD-TYPE	41	37	19	75

Figure S17. Get High-res Image Gene #23: 'amp_22q13.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_1p36.31' versus 'METHLYATION_CNMF'

P value = 6.89e-05 (Fisher's exact test), Q value = 0.035

Table S18. Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	104	109
DEL PEAK 1(1P36.31) MUTATED	33	19	17
DEL PEAK 1(1P36.31) WILD-TYPE	45	85	92

Figure S18. Get High-res Image Gene #24: 'del_1p36.31' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'METHLYATION_CNMF'

P value = 6.09e-06 (Fisher's exact test), Q value = 0.0032

Table S19. Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	104	109
DEL PEAK 2(1P22.1) MUTATED	36	15	23
DEL PEAK 2(1P22.1) WILD-TYPE	42	89	86

Figure S19. Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_1p22.1' versus 'MRNASEQ_CNMF'

P value = 9.19e-05 (Fisher's exact test), Q value = 0.047

Table S20. Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	81	109
DEL PEAK 2(1P22.1) MUTATED	39	9	26
DEL PEAK 2(1P22.1) WILD-TYPE	62	72	83

Figure S20. Get High-res Image Gene #25: 'del_1p22.1' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_5q31.3' versus 'METHLYATION_CNMF'

P value = 0.000226 (Fisher's exact test), Q value = 0.11

Table S21. Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	78	104	109
DEL PEAK 9(5Q31.3) MUTATED	18	54	37
DEL PEAK 9(5Q31.3) WILD-TYPE	60	50	72

Figure S21. Get High-res Image Gene #32: 'del_5q31.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_6q22.31' versus 'CN_CNMF'

P value = 1.31e-09 (Fisher's exact test), Q value = 7e-07

Table S22. Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 10(6Q22.31) MUTATED	55	46	40	38
DEL PEAK 10(6Q22.31) WILD-TYPE	30	11	11	68

Figure S22. Get High-res Image Gene #33: 'del_6q22.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'CN_CNMF'

P value = 2.99e-10 (Fisher's exact test), Q value = 1.6e-07

Table S23. Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 11(6Q26) MUTATED	60	46	40	38
DEL PEAK 11(6Q26) WILD-TYPE	25	11	11	68

Figure S23. Get High-res Image Gene #34: 'del_6q26' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'CN_CNMF'

P value = 6.24e-07 (Fisher's exact test), Q value = 0.00033

Table S24. Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 14(9P21.3) MUTATED	65	55	44	65
DEL PEAK 14(9P21.3) WILD-TYPE	20	2	7	41

Figure S24. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9p21.3' versus 'MRNASEQ_CNMF'

P value = 4.39e-06 (Fisher's exact test), Q value = 0.0023

Table S25. Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	81	109
DEL PEAK 14(9P21.3) MUTATED	92	49	82
DEL PEAK 14(9P21.3) WILD-TYPE	9	32	27

Figure S25. Get High-res Image Gene #37: 'del_9p21.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'CN_CNMF'

P value = 3.55e-08 (Fisher's exact test), Q value = 1.9e-05

Table S26. Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 15(10P15.3) MUTATED	50	37	41	35
DEL PEAK 15(10P15.3) WILD-TYPE	35	20	10	71

Figure S26. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 4.49e-05 (Fisher's exact test), Q value = 0.023

Table S27. Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	81	109
DEL PEAK 15(10P15.3) MUTATED	73	35	51
DEL PEAK 15(10P15.3) WILD-TYPE	28	46	58

Figure S27. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10p15.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000143 (Fisher's exact test), Q value = 0.073

Table S28. Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	76	138	77
DEL PEAK 15(10P15.3) MUTATED	57	65	37
DEL PEAK 15(10P15.3) WILD-TYPE	19	73	40

Figure S28. Get High-res Image Gene #38: 'del_10p15.3' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'del_10q23.31' versus 'CN_CNMF'

P value = 1.11e-09 (Fisher's exact test), Q value = 5.9e-07

Table S29. Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 16(10Q23.31) MUTATED	51	42	48	47
DEL PEAK 16(10Q23.31) WILD-TYPE	34	15	3	59

Figure S29. Get High-res Image Gene #39: 'del_10q23.31' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q23.31' versus 'MRNASEQ_CNMF'

P value = 8.47e-05 (Fisher's exact test), Q value = 0.043

Table S30. Gene #39: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	81	109
DEL PEAK 16(10Q23.31) MUTATED	80	42	61
DEL PEAK 16(10Q23.31) WILD-TYPE	21	39	48

Figure S30. Get High-res Image Gene #39: 'del_10q23.31' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'CN_CNMF'

P value = 2.08e-09 (Fisher's exact test), Q value = 1.1e-06

Table S31. Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 17(10Q26.3) MUTATED	49	45	48	51
DEL PEAK 17(10Q26.3) WILD-TYPE	36	12	3	55

Figure S31. Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1.6e-05 (Fisher's exact test), Q value = 0.0083

Table S32. Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	101	81	109
DEL PEAK 17(10Q26.3) MUTATED	83	44	61
DEL PEAK 17(10Q26.3) WILD-TYPE	18	37	48

Figure S32. Get High-res Image Gene #40: 'del_10q26.3' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'del_11p11.2' versus 'CN_CNMF'

P value = 0.000132 (Fisher's exact test), Q value = 0.067

Table S33. Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 18(11P11.2) MUTATED	42	13	19	22
DEL PEAK 18(11P11.2) WILD-TYPE	43	44	32	84

Figure S33. Get High-res Image Gene #41: 'del_11p11.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q23.3' versus 'CN_CNMF'

P value = 3.4e-08 (Fisher's exact test), Q value = 1.8e-05

Table S34. Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 19(11Q23.3) MUTATED	66	24	32	39
DEL PEAK 19(11Q23.3) WILD-TYPE	19	33	19	67

Figure S34. Get High-res Image Gene #42: 'del_11q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q12.11' versus 'CN_CNMF'

P value = 6.17e-05 (Fisher's exact test), Q value = 0.032

Table S35. Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 21(13Q12.11) MUTATED	20	6	24	18
DEL PEAK 21(13Q12.11) WILD-TYPE	65	51	27	88

Figure S35. Get High-res Image Gene #44: 'del_13q12.11' versus Molecular Subtype #1: 'CN_CNMF'

'del_13q34' versus 'CN_CNMF'

P value = 0.000373 (Fisher's exact test), Q value = 0.19

Table S36. Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 22(13Q34) MUTATED	20	5	22	21
DEL PEAK 22(13Q34) WILD-TYPE	65	52	29	85

Figure S36. Get High-res Image Gene #45: 'del_13q34' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q23.3' versus 'CN_CNMF'

P value = 2.89e-08 (Fisher's exact test), Q value = 1.5e-05

Table S37. Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 23(14Q23.3) MUTATED	21	32	29	20
DEL PEAK 23(14Q23.3) WILD-TYPE	64	25	22	86

Figure S37. Get High-res Image Gene #46: 'del_14q23.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_14q32.2' versus 'CN_CNMF'

P value = 6.23e-08 (Fisher's exact test), Q value = 3.3e-05

Table S38. Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 24(14Q32.2) MUTATED	23	32	27	18
DEL PEAK 24(14Q32.2) WILD-TYPE	62	25	24	88

Figure S38. Get High-res Image Gene #47: 'del_14q32.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q13.3' versus 'CN_CNMF'

P value = 8.11e-06 (Fisher's exact test), Q value = 0.0042

Table S39. Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 25(15Q13.3) MUTATED	33	20	4	16
DEL PEAK 25(15Q13.3) WILD-TYPE	52	37	47	90

Figure S39. Get High-res Image Gene #48: 'del_15q13.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q14' versus 'CN_CNMF'

P value = 2.19e-08 (Fisher's exact test), Q value = 1.2e-05

Table S40. Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 26(15Q14) MUTATED	35	20	1	17
DEL PEAK 26(15Q14) WILD-TYPE	50	37	50	89

Figure S40. Get High-res Image Gene #49: 'del_15q14' versus Molecular Subtype #1: 'CN_CNMF'

'del_15q15.2' versus 'CN_CNMF'

P value = 8.92e-10 (Fisher's exact test), Q value = 4.8e-07

Table S41. Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	85	57	51	106
DEL PEAK 27(15Q15.2) MUTATED	37	23	1	17
DEL PEAK 27(15Q15.2) WILD-TYPE	48	34	50	89

Figure S41. Get High-res Image Gene #50: 'del_15q15.2' versus Molecular Subtype #1: 'CN_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = SKCM-TM.transferedmergedcluster.txt
Number of patients = 299
Number of significantly focal cnvs = 54
Number of molecular subtypes = 10
Exclude genes 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)

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