Correlation between copy number variations of arm-level result and selected clinical features
Kidney Chromophobe (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1WQ02P5
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1WQ02P5
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 61 arm-level events and 11 clinical features across 66 patients, 3 significant findings detected with Q value < 0.25.

  • 16p loss cnv correlated to 'NEOPLASM.DISEASESTAGE' and 'PATHOLOGY.N.STAGE'.

  • 16q loss cnv correlated to 'PATHOLOGY.N.STAGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 61 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		NUMBERPACKYEARSSMOKED RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
16p loss 4 (6%) 62 0.519
(1.00) 		0.00037
(0.22) 		0.00668
(1.00) 		3.36e-05
(0.02) 		0.639
(1.00) 		1
(1.00) 		1
(1.00)
16q loss 5 (8%) 61 0.221
(1.00) 		0.0041
(1.00) 		0.0493
(1.00) 		0.000165
(0.0979) 		0.641
(1.00) 		1
(1.00) 		1
(1.00)
3p gain 8 (12%) 58 100
(1.00) 		0.0837
(1.00) 		0.0159
(1.00) 		0.466
(1.00) 		0.0327
(1.00) 		0.256
(1.00) 		0.128
(1.00) 		0.296
(1.00) 		1
(1.00)
3q gain 8 (12%) 58 100
(1.00) 		0.0837
(1.00) 		0.0158
(1.00) 		0.465
(1.00) 		0.0327
(1.00) 		0.254
(1.00) 		0.128
(1.00) 		0.294
(1.00) 		1
(1.00)
4p gain 24 (36%) 42 100
(1.00) 		0.265
(1.00) 		0.143
(1.00) 		0.811
(1.00) 		1
(1.00) 		0.112
(1.00) 		1
(1.00) 		1
(1.00) 		0.0467
(1.00) 		1
(1.00) 		0.287
(1.00)
4q gain 24 (36%) 42 100
(1.00) 		0.265
(1.00) 		0.141
(1.00) 		0.808
(1.00) 		1
(1.00) 		0.113
(1.00) 		1
(1.00) 		1
(1.00) 		0.0467
(1.00) 		1
(1.00) 		0.287
(1.00)
5p gain 8 (12%) 58 100
(1.00) 		0.0661
(1.00) 		0.00148
(0.876) 		0.363
(1.00) 		0.0874
(1.00) 		0.008
(1.00) 		0.455
(1.00) 		1
(1.00) 		1
(1.00)
5q gain 8 (12%) 58 100
(1.00) 		0.0661
(1.00) 		0.00146
(0.866) 		0.363
(1.00) 		0.0874
(1.00) 		0.008
(1.00) 		0.455
(1.00) 		1
(1.00) 		1
(1.00)
7p gain 24 (36%) 42 100
(1.00) 		0.172
(1.00) 		0.361
(1.00) 		0.691
(1.00) 		0.636
(1.00) 		0.112
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.303
(1.00)
7q gain 24 (36%) 42 100
(1.00) 		0.172
(1.00) 		0.362
(1.00) 		0.691
(1.00) 		0.636
(1.00) 		0.112
(1.00) 		0.195
(1.00) 		1
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.303
(1.00)
8p gain 17 (26%) 49 100
(1.00) 		0.142
(1.00) 		0.389
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.588
(1.00)
8q gain 18 (27%) 48 100
(1.00) 		0.15
(1.00) 		0.228
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.588
(1.00)
9p gain 10 (15%) 56 100
(1.00) 		0.979
(1.00) 		0.124
(1.00) 		0.193
(1.00) 		0.306
(1.00) 		1
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.376
(1.00) 		0.535
(1.00)
9q gain 10 (15%) 56 100
(1.00) 		0.979
(1.00) 		0.122
(1.00) 		0.196
(1.00) 		0.306
(1.00) 		1
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.376
(1.00) 		0.535
(1.00)
10p gain 4 (6%) 62 100
(1.00) 		0.34
(1.00) 		0.267
(1.00) 		0.454
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 15 (23%) 51 100
(1.00) 		0.812
(1.00) 		0.739
(1.00) 		0.812
(1.00) 		0.617
(1.00) 		0.385
(1.00) 		1
(1.00) 		0.0467
(1.00) 		0.559
(1.00) 		0.0756
(1.00)
11q gain 15 (23%) 51 100
(1.00) 		0.945
(1.00) 		0.742
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.0467
(1.00) 		0.561
(1.00) 		0.0756
(1.00)
12p gain 19 (29%) 47 100
(1.00) 		0.0137
(1.00) 		0.0771
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.136
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.357
(1.00) 		1
(1.00) 		1
(1.00)
12q gain 20 (30%) 46 100
(1.00) 		0.0696
(1.00) 		0.111
(1.00) 		0.71
(1.00) 		0.33
(1.00) 		0.134
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.806
(1.00) 		1
(1.00)
14q gain 21 (32%) 45 100
(1.00) 		0.144
(1.00) 		0.0951
(1.00) 		0.382
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.609
(1.00)
15q gain 21 (32%) 45 100
(1.00) 		0.283
(1.00) 		0.412
(1.00) 		0.48
(1.00) 		0.35
(1.00) 		0.152
(1.00) 		0.794
(1.00) 		1
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.124
(1.00)
16p gain 21 (32%) 45 100
(1.00) 		0.995
(1.00) 		0.477
(1.00) 		0.402
(1.00) 		0.635
(1.00) 		0.722
(1.00) 		1
(1.00) 		1
(1.00) 		0.0467
(1.00) 		1
(1.00) 		0.124
(1.00)
16q gain 21 (32%) 45 100
(1.00) 		0.995
(1.00) 		0.475
(1.00) 		0.402
(1.00) 		0.635
(1.00) 		0.721
(1.00) 		1
(1.00) 		1
(1.00) 		0.0467
(1.00) 		1
(1.00) 		0.124
(1.00)
18p gain 17 (26%) 49 100
(1.00) 		0.278
(1.00) 		0.294
(1.00) 		0.434
(1.00) 		0.303
(1.00) 		0.508
(1.00) 		0.776
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.57
(1.00)
18q gain 16 (24%) 50 100
(1.00) 		0.525
(1.00) 		0.311
(1.00) 		0.2
(1.00) 		0.303
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.298
(1.00) 		1
(1.00) 		0.305
(1.00)
19p gain 19 (29%) 47 100
(1.00) 		0.0291
(1.00) 		0.0158
(1.00) 		0.519
(1.00) 		0.00246
(1.00) 		0.0836
(1.00) 		0.412
(1.00) 		0.784
(1.00) 		0.258
(1.00) 		0.29
(1.00)
19q gain 17 (26%) 49 100
(1.00) 		0.0137
(1.00) 		0.295
(1.00) 		0.643
(1.00) 		0.136
(1.00) 		0.0618
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.594
(1.00) 		0.29
(1.00)
20p gain 20 (30%) 46 100
(1.00) 		0.128
(1.00) 		0.368
(1.00) 		0.791
(1.00) 		0.35
(1.00) 		0.708
(1.00) 		0.593
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.367
(1.00) 		0.588
(1.00)
20q gain 21 (32%) 45 100
(1.00) 		0.053
(1.00) 		0.136
(1.00) 		0.845
(1.00) 		0.35
(1.00) 		0.709
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.234
(1.00) 		0.368
(1.00) 		0.609
(1.00)
21q gain 4 (6%) 62 100
(1.00) 		0.591
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
22q gain 19 (29%) 47 100
(1.00) 		0.415
(1.00) 		0.489
(1.00) 		0.521
(1.00) 		0.166
(1.00) 		0.355
(1.00) 		0.412
(1.00) 		0.784
(1.00) 		0.794
(1.00) 		0.588
(1.00)
xq gain 6 (9%) 60 100
(1.00) 		0.815
(1.00) 		0.379
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.191
(1.00) 		0.388
(1.00) 		0.458
(1.00) 		0.39
(1.00)
1p loss 53 (80%) 13 100
(1.00) 		0.478
(1.00) 		0.0281
(1.00) 		0.0401
(1.00) 		1
(1.00) 		0.00651
(1.00) 		0.534
(1.00) 		0.438
(1.00) 		0.609
(1.00) 		1
(1.00) 		1
(1.00)
1q loss 52 (79%) 14 100
(1.00) 		0.456
(1.00) 		0.00616
(1.00) 		0.0132
(1.00) 		0.529
(1.00) 		0.0212
(1.00) 		0.367
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
2p loss 46 (70%) 20 100
(1.00) 		0.241
(1.00) 		0.145
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.284
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
2q loss 46 (70%) 20 100
(1.00) 		0.241
(1.00) 		0.143
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.284
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
3p loss 9 (14%) 57 100
(1.00) 		0.0465
(1.00) 		0.0762
(1.00) 		0.0231
(1.00) 		1
(1.00) 		0.658
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.535
(1.00)
3q loss 8 (12%) 58 100
(1.00) 		0.107
(1.00) 		0.142
(1.00) 		0.0529
(1.00) 		1
(1.00) 		0.64
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.535
(1.00)
5p loss 10 (15%) 56 100
(1.00) 		0.642
(1.00) 		0.132
(1.00) 		0.0837
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.159
(1.00) 		0.121
(1.00)
5q loss 10 (15%) 56 100
(1.00) 		0.642
(1.00) 		0.132
(1.00) 		0.0858
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.155
(1.00) 		0.16
(1.00) 		0.121
(1.00)
6p loss 51 (77%) 15 100
(1.00) 		0.379
(1.00) 		0.0811
(1.00) 		0.056
(1.00) 		0.568
(1.00) 		0.169
(1.00) 		0.244
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
6q loss 51 (77%) 15 100
(1.00) 		0.379
(1.00) 		0.083
(1.00) 		0.0546
(1.00) 		0.568
(1.00) 		0.17
(1.00) 		0.244
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
8p loss 9 (14%) 57 100
(1.00) 		0.779
(1.00) 		0.741
(1.00) 		0.436
(1.00) 		1
(1.00) 		1
(1.00) 		0.727
(1.00) 		0.614
(1.00) 		0.566
(1.00)
8q loss 8 (12%) 58 100
(1.00) 		0.575
(1.00) 		0.703
(1.00) 		0.412
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.57
(1.00) 		1
(1.00)
9p loss 10 (15%) 56 100
(1.00) 		0.0116
(1.00) 		1
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.488
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.535
(1.00)
9q loss 10 (15%) 56 100
(1.00) 		0.0116
(1.00) 		1
(1.00) 		1
(1.00) 		0.529
(1.00) 		0.487
(1.00) 		0.508
(1.00) 		1
(1.00) 		0.535
(1.00)
10p loss 48 (73%) 18 100
(1.00) 		0.762
(1.00) 		0.547
(1.00) 		0.393
(1.00) 		1
(1.00) 		0.02
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00)
10q loss 49 (74%) 17 100
(1.00) 		0.953
(1.00) 		0.348
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.0189
(1.00) 		1
(1.00) 		0.146
(1.00) 		0.26
(1.00) 		1
(1.00) 		1
(1.00)
11p loss 7 (11%) 59 100
(1.00) 		0.0527
(1.00) 		0.0959
(1.00) 		0.0802
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.691
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 7 (11%) 59 100
(1.00) 		0.0527
(1.00) 		0.0948
(1.00) 		0.0802
(1.00) 		0.461
(1.00) 		1
(1.00) 		0.691
(1.00) 		1
(1.00) 		1
(1.00)
13q loss 43 (65%) 23 100
(1.00) 		0.0641
(1.00) 		0.448
(1.00) 		0.356
(1.00) 		0.301
(1.00) 		0.536
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.818
(1.00) 		1
(1.00)
17p loss 50 (76%) 16 100
(1.00) 		0.149
(1.00) 		0.0737
(1.00) 		0.042
(1.00) 		0.568
(1.00) 		0.17
(1.00) 		0.158
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
17q loss 50 (76%) 16 100
(1.00) 		0.149
(1.00) 		0.0736
(1.00) 		0.0418
(1.00) 		0.568
(1.00) 		0.172
(1.00) 		0.158
(1.00) 		0.438
(1.00) 		1
(1.00) 		1
(1.00)
18p loss 8 (12%) 58 100
(1.00) 		0.455
(1.00) 		0.446
(1.00) 		0.899
(1.00) 		0.211
(1.00) 		0.658
(1.00) 		0.256
(1.00) 		0.295
(1.00) 		1
(1.00)
18q loss 10 (15%) 56 100
(1.00) 		0.343
(1.00) 		0.138
(1.00) 		0.834
(1.00) 		0.258
(1.00) 		0.659
(1.00) 		0.295
(1.00) 		0.375
(1.00) 		1
(1.00)
19q loss 3 (5%) 63 100
(1.00) 		0.423
(1.00) 		0.0121
(1.00) 		0.191
(1.00) 		0.0289
(1.00) 		1
(1.00) 		0.101
(1.00) 		0.111
(1.00)
20p loss 4 (6%) 62 100
(1.00) 		0.237
(1.00) 		0.14
(1.00) 		0.142
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
20q loss 3 (5%) 63 0.432
(1.00) 		0.0405
(1.00) 		0.0258
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
21q loss 35 (53%) 31 100
(1.00) 		0.375
(1.00) 		0.908
(1.00) 		0.781
(1.00) 		0.0731
(1.00) 		0.0767
(1.00) 		0.805
(1.00) 		0.448
(1.00) 		0.705
(1.00) 		0.543
(1.00) 		0.613
(1.00)
22q loss 8 (12%) 58 100
(1.00) 		0.783
(1.00) 		0.177
(1.00) 		1
(1.00) 		0.211
(1.00) 		0.323
(1.00) 		0.0553
(1.00) 		0.566
(1.00) 		0.39
(1.00)
xq loss 39 (59%) 27 100
(1.00) 		0.0923
(1.00) 		0.303
(1.00) 		0.363
(1.00) 		1
(1.00) 		0.148
(1.00) 		0.136
(1.00) 		0.132
(1.00) 		0.17
(1.00) 		0.818
(1.00) 		1
(1.00)
'16p loss' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.22

Table S1.  Gene #50: '16p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 21 25 14 6
16P LOSS MUTATED 0 0 1 3
16P LOSS WILD-TYPE 21 25 13 3

Figure S1.  Get High-res Image Gene #50: '16p loss' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

'16p loss' versus 'PATHOLOGY.N.STAGE'

P value = 3.36e-05 (Fisher's exact test), Q value = 0.02

Table S2.  Gene #50: '16p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1+N2
ALL 40 5
16P LOSS MUTATED 0 4
16P LOSS WILD-TYPE 40 1

Figure S2.  Get High-res Image Gene #50: '16p loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

'16q loss' versus 'PATHOLOGY.N.STAGE'

P value = 0.000165 (Fisher's exact test), Q value = 0.098

Table S3.  Gene #51: '16q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

nPatients N0 N1+N2
ALL 40 5
16Q LOSS MUTATED 1 4
16Q LOSS WILD-TYPE 39 1

Figure S3.  Get High-res Image Gene #51: '16q loss' versus Clinical Feature #5: 'PATHOLOGY.N.STAGE'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = KICH-TP.merged_data.txt

  • Number of patients = 66

  • Number of significantly arm-level cnvs = 61

  • Number of selected clinical features = 11

  • Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

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] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] 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)
[3] 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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