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

Testicular Germ Cell Tumors (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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/C19K496N

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 47 focal events and 8 molecular subtypes across 150 patients, 42 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_7q11.22 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.
amp_8q11.23 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
amp_8q23.3 cnv correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
amp_16q21 cnv correlated to 'CN_CNMF'.
amp_22q11.21 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_6p22.3 cnv correlated to 'CN_CNMF'.
del_6q26 cnv correlated to 'METHLYATION_CNMF'.
del_9q33.3 cnv correlated to 'CN_CNMF'.
del_9q34.2 cnv correlated to 'CN_CNMF'.
del_10p15.3 cnv correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.
del_10q23.1 cnv correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_10q26.3 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.
del_11p15.5 cnv correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.
del_11q12.3 cnv correlated to 'CN_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.
del_11q24.2 cnv correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.
del_19q13.41 cnv correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
del_xp21.1 cnv correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 47 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 42 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	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
del 19q13 41	58 (39%)	92	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)	1e-05 (0.00364)
del 11q12 3	114 (76%)	36	1e-05 (0.00364)	0.186 (1.00)	7e-05 (0.024)	1e-05 (0.00364)	3e-05 (0.0104)	0.00029 (0.0969)	0.00748 (1.00)	0.00728 (1.00)
del 10q26 3	76 (51%)	74	0.00047 (0.154)	1e-05 (0.00364)	1e-05 (0.00364)	0.00015 (0.0507)	0.588 (1.00)	0.0347 (1.00)	0.0384 (1.00)	0.0111 (1.00)
amp 8q11 23	122 (81%)	28	4e-05 (0.0139)	0.00966 (1.00)	1e-05 (0.00364)	4e-05 (0.0139)	0.0126 (1.00)	0.0261 (1.00)	0.0239 (1.00)	0.0829 (1.00)
amp 22q11 21	57 (38%)	93	1e-05 (0.00364)	0.00719 (1.00)	0.00013 (0.0441)	1e-05 (0.00364)	0.0702 (1.00)	0.236 (1.00)	0.331 (1.00)	0.0443 (1.00)
del 10q23 1	71 (47%)	79	0.00596 (1.00)	1e-05 (0.00364)	4e-05 (0.0139)	0.00022 (0.0737)	0.357 (1.00)	0.0487 (1.00)	0.0834 (1.00)	0.0363 (1.00)
amp 7q11 22	120 (80%)	30	0.0006 (0.196)	0.0393 (1.00)	5e-05 (0.0172)	0.00229 (0.701)	0.0159 (1.00)	0.00368 (1.00)	0.0153 (1.00)	0.0467 (1.00)
amp 8q23 3	108 (72%)	42	0.184 (1.00)	0.00328 (0.977)	0.00035 (0.116)	0.00058 (0.19)	0.00603 (1.00)	0.0208 (1.00)	0.0354 (1.00)	0.143 (1.00)
del 10p15 3	84 (56%)	66	0.00124 (0.391)	0.00036 (0.119)	0.0002 (0.0674)	0.00113 (0.359)	0.9 (1.00)	0.0596 (1.00)	0.234 (1.00)	0.279 (1.00)
del 11p15 5	94 (63%)	56	0.0251 (1.00)	0.256 (1.00)	0.003 (0.9)	0.00402 (1.00)	0.0002 (0.0674)	0.00037 (0.122)	0.00125 (0.392)	0.0163 (1.00)
del 11q24 2	122 (81%)	28	7e-05 (0.024)	0.725 (1.00)	0.00897 (1.00)	0.00068 (0.22)	0.00094 (0.301)	0.0379 (1.00)	0.019 (1.00)	0.0431 (1.00)
amp 16q21	21 (14%)	129	8e-05 (0.0272)	0.373 (1.00)	0.00282 (0.854)	0.0076 (1.00)	0.0346 (1.00)	0.00285 (0.861)	0.0011 (0.351)	0.0407 (1.00)
del 6p22 3	24 (16%)	126	7e-05 (0.024)	0.0157 (1.00)	0.00386 (1.00)	0.0126 (1.00)	0.322 (1.00)	0.0777 (1.00)	0.116 (1.00)	0.224 (1.00)
del 6q26	26 (17%)	124	0.0324 (1.00)	0.00075 (0.242)	0.00592 (1.00)	0.00135 (0.421)	0.468 (1.00)	0.29 (1.00)	0.246 (1.00)	0.459 (1.00)
del 9q33 3	60 (40%)	90	0.00037 (0.122)	0.394 (1.00)	0.118 (1.00)	0.0156 (1.00)	0.32 (1.00)	0.00252 (0.769)	0.0262 (1.00)	0.0538 (1.00)
del 9q34 2	60 (40%)	90	0.00029 (0.0969)	0.276 (1.00)	0.0954 (1.00)	0.00396 (1.00)	0.509 (1.00)	0.0125 (1.00)	0.0754 (1.00)	0.182 (1.00)
del xp21 1	28 (19%)	122	0.0585 (1.00)	0.00067 (0.218)	0.0453 (1.00)	0.0523 (1.00)	0.357 (1.00)	0.245 (1.00)	0.082 (1.00)	0.158 (1.00)
amp 1q21 2	69 (46%)	81	0.0778 (1.00)	0.718 (1.00)	0.87 (1.00)	0.00085 (0.274)	0.0178 (1.00)	0.445 (1.00)	0.673 (1.00)	0.194 (1.00)
amp 2p24 1	62 (41%)	88	0.00407 (1.00)	0.00087 (0.279)	0.0191 (1.00)	0.0441 (1.00)	0.188 (1.00)	0.19 (1.00)	0.202 (1.00)	0.316 (1.00)
amp 3q27 3	49 (33%)	101	0.0776 (1.00)	0.102 (1.00)	0.00254 (0.772)	0.00771 (1.00)	0.152 (1.00)	0.183 (1.00)	0.259 (1.00)	0.233 (1.00)
amp 4q12	20 (13%)	130	0.00849 (1.00)	0.661 (1.00)	0.393 (1.00)	0.394 (1.00)	0.863 (1.00)	0.69 (1.00)	0.129 (1.00)	0.429 (1.00)
amp 7p22 1	126 (84%)	24	0.0863 (1.00)	0.0779 (1.00)	0.0289 (1.00)	0.103 (1.00)	0.042 (1.00)	0.0362 (1.00)	0.191 (1.00)	0.177 (1.00)
amp 12p13 33	145 (97%)	5	0.053 (1.00)	0.102 (1.00)	0.0826 (1.00)	0.684 (1.00)
amp 12p12 1	147 (98%)	3	0.0549 (1.00)	0.109 (1.00)	0.444 (1.00)	0.558 (1.00)
amp 12p11 21	144 (96%)	6	0.108 (1.00)	0.0391 (1.00)	0.036 (1.00)	0.497 (1.00)	0.11 (1.00)	0.469 (1.00)	0.188 (1.00)	0.236 (1.00)
amp 12q15	100 (67%)	50	0.527 (1.00)	0.93 (1.00)	0.813 (1.00)	0.734 (1.00)	0.325 (1.00)	0.564 (1.00)	0.837 (1.00)	0.628 (1.00)
amp 20q11 21	51 (34%)	99	0.0048 (1.00)	0.00292 (0.879)	0.00301 (0.9)	0.0342 (1.00)	0.0121 (1.00)	0.0487 (1.00)	0.0304 (1.00)	0.0279 (1.00)
del 1p36 31	34 (23%)	116	0.282 (1.00)	0.733 (1.00)	0.00228 (0.7)	0.0507 (1.00)	0.115 (1.00)	0.0778 (1.00)	0.127 (1.00)	0.33 (1.00)
del 1p31 1	27 (18%)	123	0.00709 (1.00)	0.601 (1.00)	0.247 (1.00)	0.723 (1.00)	0.396 (1.00)	0.42 (1.00)	0.498 (1.00)	0.866 (1.00)
del 1q42 12	9 (6%)	141	0.0386 (1.00)	0.52 (1.00)	0.562 (1.00)	0.195 (1.00)	0.133 (1.00)	0.188 (1.00)	0.114 (1.00)	0.0605 (1.00)
del 2q37 3	15 (10%)	135	0.457 (1.00)	0.0408 (1.00)	0.0576 (1.00)	0.173 (1.00)	0.676 (1.00)	0.0283 (1.00)	0.117 (1.00)	0.215 (1.00)
del 3p26 2	41 (27%)	109	0.76 (1.00)	0.0207 (1.00)	0.00133 (0.416)	0.00382 (1.00)	0.0497 (1.00)	0.0743 (1.00)	0.0907 (1.00)	0.0391 (1.00)
del 4q22 2	110 (73%)	40	0.0211 (1.00)	0.0321 (1.00)	0.00897 (1.00)	0.00144 (0.448)	0.116 (1.00)	0.108 (1.00)	0.624 (1.00)	0.506 (1.00)
del 5p15 2	101 (67%)	49	0.187 (1.00)	0.489 (1.00)	0.214 (1.00)	0.457 (1.00)	0.685 (1.00)	0.222 (1.00)	0.34 (1.00)	0.368 (1.00)
del 5p14 3	103 (69%)	47	0.264 (1.00)	0.318 (1.00)	0.18 (1.00)	0.294 (1.00)	0.528 (1.00)	0.123 (1.00)	0.237 (1.00)	0.304 (1.00)
del 5q12 1	105 (70%)	45	0.0895 (1.00)	0.104 (1.00)	0.0302 (1.00)	0.00745 (1.00)	0.501 (1.00)	0.0489 (1.00)	0.1 (1.00)	0.155 (1.00)
del 7q11 22	4 (3%)	146	0.315 (1.00)	0.00722 (1.00)	0.00916 (1.00)	0.0301 (1.00)
del 7q36 1	15 (10%)	135	0.0509 (1.00)	0.889 (1.00)	0.201 (1.00)	0.00989 (1.00)	0.455 (1.00)	0.724 (1.00)	0.0837 (1.00)	0.18 (1.00)
del 9p24 3	70 (47%)	80	0.0909 (1.00)	0.896 (1.00)	1 (1.00)	0.805 (1.00)	0.284 (1.00)	0.768 (1.00)	0.32 (1.00)	0.374 (1.00)
del 9p23	66 (44%)	84	0.0383 (1.00)	0.915 (1.00)	0.908 (1.00)	0.523 (1.00)	0.325 (1.00)	0.804 (1.00)	0.293 (1.00)	0.41 (1.00)
del 11p12	99 (66%)	51	0.0556 (1.00)	0.111 (1.00)	0.00163 (0.504)	0.00523 (1.00)	0.00338 (1.00)	0.00373 (1.00)	0.0296 (1.00)	0.0483 (1.00)
del 13q34	113 (75%)	37	0.0441 (1.00)	0.554 (1.00)	0.0828 (1.00)	0.00191 (0.588)	0.418 (1.00)	0.276 (1.00)	0.00349 (1.00)	0.0274 (1.00)
del 16q23 1	66 (44%)	84	0.00118 (0.373)	0.234 (1.00)	0.357 (1.00)	0.393 (1.00)	0.292 (1.00)	0.437 (1.00)	0.162 (1.00)	0.251 (1.00)
del 18p11 32	118 (79%)	32	0.699 (1.00)	0.132 (1.00)	0.0503 (1.00)	0.247 (1.00)	0.124 (1.00)	0.098 (1.00)	0.0844 (1.00)	0.108 (1.00)
del 18q22 2	125 (83%)	25	0.0586 (1.00)	0.143 (1.00)	0.109 (1.00)	0.133 (1.00)	0.155 (1.00)	0.2 (1.00)	0.0207 (1.00)	0.00596 (1.00)
del 20p12 1	29 (19%)	121	0.335 (1.00)	0.336 (1.00)	0.31 (1.00)	0.095 (1.00)	0.492 (1.00)	0.187 (1.00)	0.111 (1.00)	0.0741 (1.00)
del xq27 3	30 (20%)	120	0.00113 (0.359)	0.00157 (0.487)	0.0942 (1.00)	0.0627 (1.00)	0.591 (1.00)	0.383 (1.00)	0.101 (1.00)	0.604 (1.00)

'amp_7q11.22' versus 'CN_CNMF'

P value = 6e-04 (Fisher's exact test), Q value = 0.2

Table S1. Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 6(7Q11.22) MUTATED	35	43	42
AMP PEAK 6(7Q11.22) WILD-TYPE	13	1	16

Figure S1. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #1: 'CN_CNMF'

'amp_7q11.22' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.017

Table S2. Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 6(7Q11.22) MUTATED	63	35	22
AMP PEAK 6(7Q11.22) WILD-TYPE	7	5	18

Figure S2. Get High-res Image Gene #6: 'amp_7q11.22' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S3. Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 7(8Q11.23) MUTATED	35	44	43
AMP PEAK 7(8Q11.23) WILD-TYPE	13	0	15

Figure S3. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #1: 'CN_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S4. Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 7(8Q11.23) MUTATED	67	31	24
AMP PEAK 7(8Q11.23) WILD-TYPE	3	9	16

Figure S4. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q11.23' versus 'MRNASEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S5. Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 7(8Q11.23) MUTATED	40	27	8	18	6	19	4
AMP PEAK 7(8Q11.23) WILD-TYPE	3	0	4	6	2	4	9

Figure S5. Get High-res Image Gene #7: 'amp_8q11.23' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_8q23.3' versus 'MRNASEQ_CNMF'

P value = 0.00035 (Fisher's exact test), Q value = 0.12

Table S6. Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 8(8Q23.3) MUTATED	60	28	20
AMP PEAK 8(8Q23.3) WILD-TYPE	10	12	20

Figure S6. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_8q23.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00058 (Fisher's exact test), Q value = 0.19

Table S7. Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 8(8Q23.3) MUTATED	38	22	9	15	5	16	3
AMP PEAK 8(8Q23.3) WILD-TYPE	5	5	3	9	3	7	10

Figure S7. Get High-res Image Gene #8: 'amp_8q23.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'amp_16q21' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.027

Table S8. Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 13(16Q21) MUTATED	2	2	17
AMP PEAK 13(16Q21) WILD-TYPE	46	42	41

Figure S8. Get High-res Image Gene #13: 'amp_16q21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S9. Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
AMP PEAK 15(22Q11.21) MUTATED	13	30	14
AMP PEAK 15(22Q11.21) WILD-TYPE	35	14	44

Figure S9. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #1: 'CN_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.044

Table S10. Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
AMP PEAK 15(22Q11.21) MUTATED	39	10	8
AMP PEAK 15(22Q11.21) WILD-TYPE	31	30	32

Figure S10. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_22q11.21' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S11. Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
AMP PEAK 15(22Q11.21) MUTATED	16	23	4	5	1	5	3
AMP PEAK 15(22Q11.21) WILD-TYPE	27	4	8	19	7	18	10

Figure S11. Get High-res Image Gene #15: 'amp_22q11.21' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_6p22.3' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S12. Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 10(6P22.3) MUTATED	2	3	19
DEL PEAK 10(6P22.3) WILD-TYPE	46	41	39

Figure S12. Get High-res Image Gene #25: 'del_6p22.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_6q26' versus 'METHLYATION_CNMF'

P value = 0.00075 (Fisher's exact test), Q value = 0.24

Table S13. Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 11(6Q26) MUTATED	2	14	10
DEL PEAK 11(6Q26) WILD-TYPE	54	35	35

Figure S13. Get High-res Image Gene #26: 'del_6q26' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_9q33.3' versus 'CN_CNMF'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S14. Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 16(9Q33.3) MUTATED	12	13	35
DEL PEAK 16(9Q33.3) WILD-TYPE	36	31	23

Figure S14. Get High-res Image Gene #31: 'del_9q33.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_9q34.2' versus 'CN_CNMF'

P value = 0.00029 (Fisher's exact test), Q value = 0.097

Table S15. Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 17(9Q34.2) MUTATED	12	13	35
DEL PEAK 17(9Q34.2) WILD-TYPE	36	31	23

Figure S15. Get High-res Image Gene #32: 'del_9q34.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_10p15.3' versus 'METHLYATION_CNMF'

P value = 0.00036 (Fisher's exact test), Q value = 0.12

Table S16. Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 18(10P15.3) MUTATED	21	37	26
DEL PEAK 18(10P15.3) WILD-TYPE	35	12	19

Figure S16. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10p15.3' versus 'MRNASEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.067

Table S17. Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 18(10P15.3) MUTATED	28	32	24
DEL PEAK 18(10P15.3) WILD-TYPE	42	8	16

Figure S17. Get High-res Image Gene #33: 'del_10p15.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S18. Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 19(10Q23.1) MUTATED	15	37	19
DEL PEAK 19(10Q23.1) WILD-TYPE	41	12	26

Figure S18. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q23.1' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.014

Table S19. Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 19(10Q23.1) MUTATED	22	31	18
DEL PEAK 19(10Q23.1) WILD-TYPE	48	9	22

Figure S19. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q23.1' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00022 (Fisher's exact test), Q value = 0.074

Table S20. Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 19(10Q23.1) MUTATED	14	8	9	12	5	19	4
DEL PEAK 19(10Q23.1) WILD-TYPE	29	19	3	12	3	4	9

Figure S20. Get High-res Image Gene #34: 'del_10q23.1' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_10q26.3' versus 'CN_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.15

Table S21. Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 20(10Q26.3) MUTATED	18	17	41
DEL PEAK 20(10Q26.3) WILD-TYPE	30	27	17

Figure S21. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_10q26.3' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S22. Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 20(10Q26.3) MUTATED	16	38	22
DEL PEAK 20(10Q26.3) WILD-TYPE	40	11	23

Figure S22. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_10q26.3' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S23. Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 20(10Q26.3) MUTATED	24	33	19
DEL PEAK 20(10Q26.3) WILD-TYPE	46	7	21

Figure S23. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_10q26.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.051

Table S24. Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 20(10Q26.3) MUTATED	16	8	10	13	6	19	4
DEL PEAK 20(10Q26.3) WILD-TYPE	27	19	2	11	2	4	9

Figure S24. Get High-res Image Gene #35: 'del_10q26.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11p15.5' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.067

Table S25. Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	21	16	25
DEL PEAK 21(11P15.5) MUTATED	10	15	4	22
DEL PEAK 21(11P15.5) WILD-TYPE	2	6	12	3

Figure S25. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11p15.5' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00037 (Fisher's exact test), Q value = 0.12

Table S26. Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	15	15
DEL PEAK 21(11P15.5) MUTATED	36	11	4
DEL PEAK 21(11P15.5) WILD-TYPE	8	4	11

Figure S26. Get High-res Image Gene #36: 'del_11p15.5' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q12.3' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S27. Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 23(11Q12.3) MUTATED	30	43	41
DEL PEAK 23(11Q12.3) WILD-TYPE	18	1	17

Figure S27. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q12.3' versus 'MRNASEQ_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S28. Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 23(11Q12.3) MUTATED	62	32	20
DEL PEAK 23(11Q12.3) WILD-TYPE	8	8	20

Figure S28. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_11q12.3' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S29. Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 23(11Q12.3) MUTATED	35	27	9	14	6	20	3
DEL PEAK 23(11Q12.3) WILD-TYPE	8	0	3	10	2	3	10

Figure S29. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_11q12.3' versus 'MIRSEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.01

Table S30. Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	21	16	25
DEL PEAK 23(11Q12.3) MUTATED	9	20	6	24
DEL PEAK 23(11Q12.3) WILD-TYPE	3	1	10	1

Figure S30. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_11q12.3' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.097

Table S31. Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	15	15
DEL PEAK 23(11Q12.3) MUTATED	39	14	6
DEL PEAK 23(11Q12.3) WILD-TYPE	5	1	9

Figure S31. Get High-res Image Gene #38: 'del_11q12.3' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_11q24.2' versus 'CN_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.024

Table S32. Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 24(11Q24.2) MUTATED	33	44	45
DEL PEAK 24(11Q24.2) WILD-TYPE	15	0	13

Figure S32. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #1: 'CN_CNMF'

'del_11q24.2' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00068 (Fisher's exact test), Q value = 0.22

Table S33. Gene #39: 'del_11q24.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 24(11Q24.2) MUTATED	35	27	10	18	7	20	5
DEL PEAK 24(11Q24.2) WILD-TYPE	8	0	2	6	1	3	8

Figure S33. Get High-res Image Gene #39: 'del_11q24.2' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S34. Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	48	44	58
DEL PEAK 29(19Q13.41) MUTATED	14	7	37
DEL PEAK 29(19Q13.41) WILD-TYPE	34	37	21

Figure S34. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #1: 'CN_CNMF'

'del_19q13.41' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S35. Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 29(19Q13.41) MUTATED	2	37	19
DEL PEAK 29(19Q13.41) WILD-TYPE	54	12	26

Figure S35. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'del_19q13.41' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S36. Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	70	40	40
DEL PEAK 29(19Q13.41) MUTATED	1	33	24
DEL PEAK 29(19Q13.41) WILD-TYPE	69	7	16

Figure S36. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'del_19q13.41' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S37. Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	43	27	12	24	8	23	13
DEL PEAK 29(19Q13.41) MUTATED	0	1	11	14	5	20	7
DEL PEAK 29(19Q13.41) WILD-TYPE	43	26	1	10	3	3	6

Figure S37. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S38. Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	12	21	16	25
DEL PEAK 29(19Q13.41) MUTATED	0	15	8	1
DEL PEAK 29(19Q13.41) WILD-TYPE	12	6	8	24

Figure S38. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'del_19q13.41' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S39. Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	44	15	15
DEL PEAK 29(19Q13.41) MUTATED	2	14	8
DEL PEAK 29(19Q13.41) WILD-TYPE	42	1	7

Figure S39. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'del_19q13.41' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S40. Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	13	20	19
DEL PEAK 29(19Q13.41) MUTATED	1	11	0	12
DEL PEAK 29(19Q13.41) WILD-TYPE	21	2	20	7

Figure S40. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'del_19q13.41' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.0036

Table S41. Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	11	8	15	11	5	13	11
DEL PEAK 29(19Q13.41) MUTATED	0	0	14	6	3	1	0
DEL PEAK 29(19Q13.41) WILD-TYPE	11	8	1	5	2	12	11

Figure S41. Get High-res Image Gene #44: 'del_19q13.41' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'del_xp21.1' versus 'METHLYATION_CNMF'

P value = 0.00067 (Fisher's exact test), Q value = 0.22

Table S42. Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	56	49	45
DEL PEAK 31(XP21.1) MUTATED	5	6	17
DEL PEAK 31(XP21.1) WILD-TYPE	51	43	28

Figure S42. Get High-res Image Gene #46: 'del_xp21.1' versus Molecular Subtype #2: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = TGCT-TP.transferedmergedcluster.txt
Number of patients = 150
Number of significantly focal cnvs = 47
Number of molecular subtypes = 8
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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