This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 51 arm-level events and 7 clinical features across 80 patients, 10 significant findings detected with Q value < 0.25.
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4q gain cnv correlated to 'PATHOLOGIC_STAGE'.
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6q gain cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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8p gain cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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8q gain cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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3p loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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3q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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6q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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9p loss cnv correlated to 'YEARS_TO_BIRTH'.
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9q loss cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP' and 'YEARS_TO_BIRTH'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 51 arm-level events and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 10 significant findings detected.
Clinical Features |
DAYS TO DEATH OR LAST FUP |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
||
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 | |
9q loss | 7 (9%) | 73 |
0.00119 (0.0936) |
0.00206 (0.0936) |
0.772 (1.00) |
0.762 (1.00) |
1 (1.00) |
0.456 (1.00) |
0.249 (1.00) |
4q gain | 5 (6%) | 75 |
0.567 (1.00) |
0.0296 (0.662) |
0.00324 (0.129) |
0.0366 (0.662) |
0.325 (1.00) |
0.647 (1.00) |
0.182 (0.917) |
6q gain | 20 (25%) | 60 |
0.00494 (0.177) |
0.0906 (0.789) |
0.428 (1.00) |
0.372 (1.00) |
0.562 (1.00) |
0.602 (1.00) |
1 (1.00) |
8p gain | 32 (40%) | 48 |
0.0021 (0.0936) |
0.864 (1.00) |
0.583 (1.00) |
0.323 (1.00) |
0.298 (1.00) |
0.818 (1.00) |
0.555 (1.00) |
8q gain | 54 (68%) | 26 |
0.00153 (0.0936) |
0.639 (1.00) |
0.81 (1.00) |
0.813 (1.00) |
0.286 (1.00) |
1 (1.00) |
0.547 (1.00) |
3p loss | 42 (52%) | 38 |
4.36e-06 (0.00156) |
0.216 (0.976) |
0.0408 (0.662) |
0.237 (1.00) |
0.113 (0.844) |
0.823 (1.00) |
1 (1.00) |
3q loss | 44 (55%) | 36 |
1.89e-05 (0.00338) |
0.287 (1.00) |
0.0365 (0.662) |
0.108 (0.844) |
0.117 (0.856) |
0.824 (1.00) |
1 (1.00) |
6q loss | 14 (18%) | 66 |
0.000324 (0.0386) |
0.0701 (0.789) |
0.0819 (0.789) |
0.0775 (0.789) |
0.204 (0.958) |
0.373 (1.00) |
0.452 (1.00) |
9p loss | 8 (10%) | 72 |
0.0133 (0.397) |
0.00185 (0.0936) |
0.579 (1.00) |
0.885 (1.00) |
1 (1.00) |
0.72 (1.00) |
0.28 (1.00) |
1q gain | 10 (12%) | 70 |
0.577 (1.00) |
0.55 (1.00) |
0.835 (1.00) |
0.82 (1.00) |
0.522 (1.00) |
0.0903 (0.789) |
1 (1.00) |
2p gain | 10 (12%) | 70 |
0.72 (1.00) |
0.353 (1.00) |
0.374 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.313 (1.00) |
0.341 (1.00) |
2q gain | 8 (10%) | 72 |
0.806 (1.00) |
0.113 (0.844) |
0.595 (1.00) |
0.489 (1.00) |
1 (1.00) |
0.28 (1.00) |
1 (1.00) |
4p gain | 8 (10%) | 72 |
0.848 (1.00) |
0.407 (1.00) |
0.0673 (0.789) |
0.687 (1.00) |
0.429 (1.00) |
0.72 (1.00) |
0.28 (1.00) |
5p gain | 4 (5%) | 76 |
0.928 (1.00) |
0.149 (0.892) |
0.577 (1.00) |
0.511 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
5q gain | 4 (5%) | 76 |
0.928 (1.00) |
0.149 (0.892) |
0.575 (1.00) |
0.514 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
6p gain | 40 (50%) | 40 |
0.0339 (0.662) |
0.388 (1.00) |
0.537 (1.00) |
0.722 (1.00) |
0.617 (1.00) |
0.821 (1.00) |
1 (1.00) |
7p gain | 8 (10%) | 72 |
0.142 (0.891) |
0.505 (1.00) |
0.692 (1.00) |
0.554 (1.00) |
0.325 (1.00) |
0.72 (1.00) |
1 (1.00) |
7q gain | 7 (9%) | 73 |
0.0605 (0.789) |
0.269 (1.00) |
0.557 (1.00) |
0.442 (1.00) |
0.267 (1.00) |
0.456 (1.00) |
1 (1.00) |
9p gain | 4 (5%) | 76 |
0.929 (1.00) |
0.44 (1.00) |
0.268 (1.00) |
0.0634 (0.789) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
9q gain | 3 (4%) | 77 |
0.288 (1.00) |
0.457 (1.00) |
0.194 (0.935) |
0.0354 (0.662) |
1 (1.00) |
0.574 (1.00) |
1 (1.00) |
11p gain | 9 (11%) | 71 |
0.871 (1.00) |
0.256 (1.00) |
0.79 (1.00) |
0.894 (1.00) |
1 (1.00) |
0.488 (1.00) |
1 (1.00) |
11q gain | 9 (11%) | 71 |
0.364 (1.00) |
0.66 (1.00) |
0.426 (1.00) |
0.563 (1.00) |
1 (1.00) |
0.488 (1.00) |
1 (1.00) |
12p gain | 3 (4%) | 77 |
0.914 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.574 (1.00) |
1 (1.00) |
12q gain | 3 (4%) | 77 |
0.914 (1.00) |
0.564 (1.00) |
1 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.574 (1.00) |
1 (1.00) |
13q gain | 6 (8%) | 74 |
0.847 (1.00) |
0.159 (0.892) |
0.787 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.216 (0.976) |
14q gain | 3 (4%) | 77 |
0.0817 (0.789) |
0.608 (1.00) |
0.885 (1.00) |
1 (1.00) |
1 (1.00) |
0.255 (1.00) |
1 (1.00) |
16p gain | 3 (4%) | 77 |
0.534 (1.00) |
0.158 (0.892) |
1 (1.00) |
0.773 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
17p gain | 9 (11%) | 71 |
0.427 (1.00) |
0.787 (1.00) |
0.867 (1.00) |
1 (1.00) |
1 (1.00) |
0.488 (1.00) |
1 (1.00) |
17q gain | 10 (12%) | 70 |
0.598 (1.00) |
0.785 (1.00) |
0.792 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.313 (1.00) |
1 (1.00) |
20p gain | 8 (10%) | 72 |
0.16 (0.892) |
0.333 (1.00) |
0.732 (1.00) |
0.552 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 9 (11%) | 71 |
0.0397 (0.662) |
0.192 (0.935) |
0.643 (1.00) |
0.462 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
21q gain | 14 (18%) | 66 |
0.173 (0.899) |
0.113 (0.844) |
0.812 (1.00) |
0.678 (1.00) |
0.477 (1.00) |
0.254 (1.00) |
1 (1.00) |
22q gain | 6 (8%) | 74 |
0.777 (1.00) |
0.168 (0.894) |
0.883 (1.00) |
0.462 (1.00) |
1 (1.00) |
0.0792 (0.789) |
1 (1.00) |
xp gain | 10 (12%) | 70 |
0.125 (0.859) |
0.161 (0.892) |
0.947 (1.00) |
0.663 (1.00) |
1 (1.00) |
0.0903 (0.789) |
1 (1.00) |
xq gain | 9 (11%) | 71 |
0.219 (0.978) |
0.211 (0.976) |
0.953 (1.00) |
0.722 (1.00) |
1 (1.00) |
0.163 (0.892) |
1 (1.00) |
1p loss | 18 (22%) | 62 |
0.325 (1.00) |
0.0569 (0.789) |
0.707 (1.00) |
1 (1.00) |
0.265 (1.00) |
0.785 (1.00) |
0.503 (1.00) |
1q loss | 4 (5%) | 76 |
0.288 (1.00) |
0.0543 (0.789) |
0.428 (1.00) |
1 (1.00) |
0.267 (1.00) |
1 (1.00) |
1 (1.00) |
4q loss | 3 (4%) | 77 |
0.709 (1.00) |
0.949 (1.00) |
0.59 (1.00) |
0.291 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (0.844) |
5q loss | 3 (4%) | 77 |
0.282 (1.00) |
0.449 (1.00) |
0.413 (1.00) |
0.561 (1.00) |
1 (1.00) |
0.0757 (0.789) |
1 (1.00) |
8p loss | 7 (9%) | 73 |
0.515 (1.00) |
0.0859 (0.789) |
0.078 (0.789) |
0.869 (1.00) |
0.325 (1.00) |
0.692 (1.00) |
0.249 (1.00) |
11p loss | 3 (4%) | 77 |
0.0192 (0.528) |
0.305 (1.00) |
1 (1.00) |
0.132 (0.859) |
1 (1.00) |
0.574 (1.00) |
1 (1.00) |
12p loss | 3 (4%) | 77 |
0.715 (1.00) |
0.768 (1.00) |
0.372 (1.00) |
0.135 (0.859) |
1 (1.00) |
0.574 (1.00) |
1 (1.00) |
13q loss | 3 (4%) | 77 |
0.274 (1.00) |
0.768 (1.00) |
1 (1.00) |
0.134 (0.859) |
1 (1.00) |
0.0757 (0.789) |
1 (1.00) |
15q loss | 5 (6%) | 75 |
0.755 (1.00) |
0.526 (1.00) |
0.945 (1.00) |
0.71 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
16p loss | 7 (9%) | 73 |
0.6 (1.00) |
0.165 (0.892) |
0.135 (0.859) |
0.263 (1.00) |
0.267 (1.00) |
1 (1.00) |
0.182 (0.917) |
16q loss | 16 (20%) | 64 |
0.131 (0.859) |
0.152 (0.892) |
0.125 (0.859) |
0.376 (1.00) |
0.204 (0.958) |
0.564 (1.00) |
0.0813 (0.789) |
17p loss | 3 (4%) | 77 |
0.0395 (0.662) |
0.174 (0.899) |
0.0709 (0.789) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
19p loss | 3 (4%) | 77 |
0.632 (1.00) |
0.868 (1.00) |
0.334 (1.00) |
0.382 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (0.844) |
19q loss | 3 (4%) | 77 |
0.632 (1.00) |
0.868 (1.00) |
0.333 (1.00) |
0.379 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (0.844) |
xp loss | 11 (14%) | 69 |
0.911 (1.00) |
0.0119 (0.386) |
0.785 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.313 (1.00) |
1 (1.00) |
xq loss | 12 (15%) | 68 |
0.587 (1.00) |
0.0266 (0.662) |
0.88 (1.00) |
0.913 (1.00) |
0.522 (1.00) |
0.192 (0.935) |
1 (1.00) |
P value = 0.00324 (Fisher's exact test), Q value = 0.13
Table S1. Gene #5: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'
nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|
ALL | 11 | 27 | 25 | 10 | 1 | 4 |
4Q GAIN MUTATED | 0 | 0 | 1 | 2 | 1 | 1 |
4Q GAIN WILD-TYPE | 11 | 27 | 24 | 8 | 0 | 3 |
Figure S1. Get High-res Image Gene #5: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

P value = 0.00494 (logrank test), Q value = 0.18
Table S2. Gene #9: '6q gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
6Q GAIN MUTATED | 20 | 0 | 0.6 - 82.2 (27.3) |
6Q GAIN WILD-TYPE | 59 | 22 | 0.1 - 85.5 (24.4) |
Figure S2. Get High-res Image Gene #9: '6q gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.0021 (logrank test), Q value = 0.094
Table S3. Gene #12: '8p gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
8P GAIN MUTATED | 31 | 15 | 1.3 - 82.2 (24.0) |
8P GAIN WILD-TYPE | 48 | 7 | 0.1 - 85.5 (26.6) |
Figure S3. Get High-res Image Gene #12: '8p gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00153 (logrank test), Q value = 0.094
Table S4. Gene #13: '8q gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
8Q GAIN MUTATED | 53 | 20 | 0.1 - 82.2 (23.3) |
8Q GAIN WILD-TYPE | 26 | 2 | 0.2 - 85.5 (36.4) |
Figure S4. Get High-res Image Gene #13: '8q gain' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 4.36e-06 (logrank test), Q value = 0.0016
Table S5. Gene #33: '3p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
3P LOSS MUTATED | 41 | 20 | 0.1 - 61.2 (21.0) |
3P LOSS WILD-TYPE | 38 | 2 | 0.2 - 85.5 (27.5) |
Figure S5. Get High-res Image Gene #33: '3p loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 1.89e-05 (logrank test), Q value = 0.0034
Table S6. Gene #34: '3q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
3Q LOSS MUTATED | 43 | 20 | 0.1 - 61.2 (23.3) |
3Q LOSS WILD-TYPE | 36 | 2 | 0.2 - 85.5 (27.3) |
Figure S6. Get High-res Image Gene #34: '3q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.000324 (logrank test), Q value = 0.039
Table S7. Gene #37: '6q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
6Q LOSS MUTATED | 14 | 8 | 1.4 - 36.6 (23.7) |
6Q LOSS WILD-TYPE | 65 | 14 | 0.1 - 85.5 (26.2) |
Figure S7. Get High-res Image Gene #37: '6q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00185 (Wilcoxon-test), Q value = 0.094
Table S8. Gene #39: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 79 | 61.5 (14.0) |
9P LOSS MUTATED | 8 | 75.4 (9.6) |
9P LOSS WILD-TYPE | 71 | 60.0 (13.6) |
Figure S8. Get High-res Image Gene #39: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

P value = 0.00119 (logrank test), Q value = 0.094
Table S9. Gene #40: '9q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 79 | 22 | 0.1 - 85.5 (26.1) |
9Q LOSS MUTATED | 7 | 4 | 1.6 - 24.0 (19.7) |
9Q LOSS WILD-TYPE | 72 | 18 | 0.1 - 85.5 (27.3) |
Figure S9. Get High-res Image Gene #40: '9q loss' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00206 (Wilcoxon-test), Q value = 0.094
Table S10. Gene #40: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 79 | 61.5 (14.0) |
9Q LOSS MUTATED | 7 | 76.3 (10.0) |
9Q LOSS WILD-TYPE | 72 | 60.1 (13.5) |
Figure S10. Get High-res Image Gene #40: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

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Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
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Processed Copy number data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/bc5d8513-6b0c-49b6-b076-3d7f4a228ff8/correlate_genomic_events_all/46b76953-a313-4baa-a6bd-91b46d0a3069/call-preprocess_genomic_event/transformed.cor.cli.txt
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Clinical data file = /cromwell_root/fc-2289d790-de74-4808-9b0a-cefafc34d859/0d7c7dcf-18e0-4b2d-afc0-a0b2ee1e45ff/preprocess_clinical_workflow/70152ac6-f707-4277-8d60-8770b1b366c6/call-preprocess_clinical/TCGA-UVM-TP.clin.merged.picked.txt
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Number of patients = 80
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Number of significantly arm-level cnvs = 51
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Number of selected clinical features = 7
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Exclude regions that fewer than K tumors have mutations, K = 3
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
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
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.