This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 21 focal events and 7 clinical features across 80 patients, 10 significant findings detected with Q value < 0.25.
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amp_6p24.3 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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amp_8q11.22 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3p25.2 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3p25.1 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3p22.2 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3p14.2 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3q24 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3q29 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_3q29 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
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del_8p11.22 cnv correlated to 'DAYS_TO_DEATH_OR_LAST_FUP'.
Table 1. Get Full Table Overview of the association between significant copy number variation of 21 focal 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 | |
amp 6p24 3 | 47 (59%) | 33 |
0.00431 (0.0634) |
0.125 (0.46) |
0.222 (0.573) |
0.124 (0.46) |
0.32 (0.627) |
0.818 (1.00) |
1 (1.00) |
amp 8q11 22 | 48 (60%) | 32 |
0.000136 (0.0025) |
0.398 (0.72) |
0.306 (0.614) |
0.211 (0.569) |
0.286 (0.595) |
0.646 (0.931) |
0.265 (0.591) |
del 3p25 2 | 42 (52%) | 38 |
4.36e-06 (0.000214) |
0.216 (0.569) |
0.0423 (0.368) |
0.238 (0.573) |
0.113 (0.456) |
0.823 (1.00) |
1 (1.00) |
del 3p25 1 | 42 (52%) | 38 |
4.36e-06 (0.000214) |
0.216 (0.569) |
0.0425 (0.368) |
0.234 (0.573) |
0.113 (0.456) |
0.823 (1.00) |
1 (1.00) |
del 3p22 2 | 42 (52%) | 38 |
4.36e-06 (0.000214) |
0.216 (0.569) |
0.0422 (0.368) |
0.237 (0.573) |
0.113 (0.456) |
0.823 (1.00) |
1 (1.00) |
del 3p14 2 | 43 (54%) | 37 |
9.35e-06 (0.000344) |
0.172 (0.526) |
0.0528 (0.431) |
0.172 (0.526) |
0.113 (0.456) |
0.655 (0.934) |
1 (1.00) |
del 3q24 | 44 (55%) | 36 |
1.89e-05 (0.000398) |
0.287 (0.595) |
0.037 (0.368) |
0.109 (0.456) |
0.117 (0.456) |
0.824 (1.00) |
1 (1.00) |
del 3q29 | 44 (55%) | 36 |
1.89e-05 (0.000398) |
0.287 (0.595) |
0.0371 (0.368) |
0.107 (0.456) |
0.117 (0.456) |
0.824 (1.00) |
1 (1.00) |
del 3q29 | 44 (55%) | 36 |
1.89e-05 (0.000398) |
0.287 (0.595) |
0.0381 (0.368) |
0.109 (0.456) |
0.117 (0.456) |
0.824 (1.00) |
1 (1.00) |
del 8p11 22 | 19 (24%) | 61 |
0.00399 (0.0634) |
0.0801 (0.456) |
0.0821 (0.456) |
0.368 (0.694) |
0.204 (0.569) |
0.296 (0.604) |
0.145 (0.497) |
amp 8q24 22 | 61 (76%) | 19 |
0.0233 (0.312) |
0.582 (0.894) |
0.86 (1.00) |
0.495 (0.827) |
0.562 (0.88) |
0.427 (0.747) |
1 (1.00) |
del 1p36 12 | 25 (31%) | 55 |
0.0849 (0.456) |
0.0766 (0.456) |
0.538 (0.86) |
0.643 (0.931) |
0.131 (0.47) |
0.807 (1.00) |
1 (1.00) |
del 1p12 | 18 (22%) | 62 |
0.271 (0.594) |
0.212 (0.569) |
0.707 (0.98) |
1 (1.00) |
0.265 (0.591) |
0.172 (0.526) |
0.503 (0.831) |
del 2q37 2 | 4 (5%) | 76 |
0.387 (0.72) |
0.599 (0.899) |
0.531 (0.857) |
0.661 (0.934) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 5q23 1 | 4 (5%) | 76 |
0.191 (0.569) |
0.401 (0.72) |
0.675 (0.945) |
0.814 (1.00) |
1 (1.00) |
0.309 (0.614) |
1 (1.00) |
del 6q25 3 | 26 (32%) | 54 |
0.15 (0.5) |
0.339 (0.653) |
0.774 (1.00) |
0.217 (0.569) |
0.59 (0.894) |
0.634 (0.931) |
0.256 (0.591) |
del 11q24 3 | 7 (9%) | 73 |
0.393 (0.72) |
0.074 (0.456) |
0.964 (1.00) |
0.866 (1.00) |
1 (1.00) |
0.456 (0.789) |
1 (1.00) |
del 16q22 1 | 18 (22%) | 62 |
0.102 (0.456) |
0.489 (0.827) |
0.231 (0.573) |
0.136 (0.478) |
0.265 (0.591) |
0.584 (0.894) |
0.105 (0.456) |
del 16q23 3 | 19 (24%) | 61 |
0.104 (0.456) |
0.509 (0.831) |
0.342 (0.653) |
0.161 (0.525) |
0.265 (0.591) |
0.79 (1.00) |
0.118 (0.456) |
del 17q12 | 3 (4%) | 77 |
0.0675 (0.456) |
0.617 (0.916) |
0.414 (0.734) |
0.557 (0.88) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 18q22 2 | 4 (5%) | 76 |
0.491 (0.827) |
0.955 (1.00) |
0.859 (1.00) |
0.816 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 0.00431 (logrank test), Q value = 0.063
Table S1. Gene #1: 'amp_6p24.3' 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) |
AMP PEAK 1(6P24.3) MUTATED | 47 | 8 | 0.1 - 85.5 (27.0) |
AMP PEAK 1(6P24.3) WILD-TYPE | 32 | 14 | 0.2 - 61.2 (20.4) |
Figure S1. Get High-res Image Gene #1: 'amp_6p24.3' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.000136 (logrank test), Q value = 0.0025
Table S2. Gene #2: 'amp_8q11.22' 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) |
AMP PEAK 2(8Q11.22) MUTATED | 47 | 20 | 0.1 - 82.2 (23.3) |
AMP PEAK 2(8Q11.22) WILD-TYPE | 32 | 2 | 0.2 - 85.5 (31.3) |
Figure S2. Get High-res Image Gene #2: 'amp_8q11.22' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 4.36e-06 (logrank test), Q value = 0.00021
Table S3. Gene #7: 'del_3p25.2' 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) |
DEL PEAK 4(3P25.2) MUTATED | 41 | 20 | 0.1 - 61.2 (21.0) |
DEL PEAK 4(3P25.2) WILD-TYPE | 38 | 2 | 0.2 - 85.5 (27.5) |
Figure S3. Get High-res Image Gene #7: 'del_3p25.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 4.36e-06 (logrank test), Q value = 0.00021
Table S4. Gene #8: 'del_3p25.1' 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) |
DEL PEAK 5(3P25.1) MUTATED | 41 | 20 | 0.1 - 61.2 (21.0) |
DEL PEAK 5(3P25.1) WILD-TYPE | 38 | 2 | 0.2 - 85.5 (27.5) |
Figure S4. Get High-res Image Gene #8: 'del_3p25.1' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 4.36e-06 (logrank test), Q value = 0.00021
Table S5. Gene #9: 'del_3p22.2' 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) |
DEL PEAK 6(3P22.2) MUTATED | 41 | 20 | 0.1 - 61.2 (21.0) |
DEL PEAK 6(3P22.2) WILD-TYPE | 38 | 2 | 0.2 - 85.5 (27.5) |
Figure S5. Get High-res Image Gene #9: 'del_3p22.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 9.35e-06 (logrank test), Q value = 0.00034
Table S6. Gene #10: 'del_3p14.2' 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) |
DEL PEAK 7(3P14.2) MUTATED | 42 | 20 | 0.1 - 61.2 (22.1) |
DEL PEAK 7(3P14.2) WILD-TYPE | 37 | 2 | 0.2 - 85.5 (27.5) |
Figure S6. Get High-res Image Gene #10: 'del_3p14.2' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 1.89e-05 (logrank test), Q value = 4e-04
Table S7. Gene #11: 'del_3q24' 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) |
DEL PEAK 8(3Q24) MUTATED | 43 | 20 | 0.1 - 61.2 (23.3) |
DEL PEAK 8(3Q24) WILD-TYPE | 36 | 2 | 0.2 - 85.5 (27.3) |
Figure S7. Get High-res Image Gene #11: 'del_3q24' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 1.89e-05 (logrank test), Q value = 4e-04
Table S8. Gene #12: 'del_3q29' 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) |
DEL PEAK 9(3Q29) MUTATED | 43 | 20 | 0.1 - 61.2 (23.3) |
DEL PEAK 9(3Q29) WILD-TYPE | 36 | 2 | 0.2 - 85.5 (27.3) |
Figure S8. Get High-res Image Gene #12: 'del_3q29' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 1.89e-05 (logrank test), Q value = 4e-04
Table S9. Gene #13: 'del_3q29' 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) |
DEL PEAK 10(3Q29) MUTATED | 43 | 20 | 0.1 - 61.2 (23.3) |
DEL PEAK 10(3Q29) WILD-TYPE | 36 | 2 | 0.2 - 85.5 (27.3) |
Figure S9. Get High-res Image Gene #13: 'del_3q29' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

P value = 0.00399 (logrank test), Q value = 0.063
Table S10. Gene #16: 'del_8p11.22' 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) |
DEL PEAK 13(8P11.22) MUTATED | 19 | 10 | 0.1 - 61.2 (23.3) |
DEL PEAK 13(8P11.22) WILD-TYPE | 60 | 12 | 0.2 - 85.5 (26.4) |
Figure S10. Get High-res Image Gene #16: 'del_8p11.22' versus Clinical Feature #1: 'DAYS_TO_DEATH_OR_LAST_FUP'

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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /cromwell_root/fc-f5144117-2d5a-42c2-8998-5b38e52db5d9/852a61f5-e734-402b-a7d5-7b508460e2ea/correlate_genomic_events_all/1ec834d1-534b-4843-b535-2942ce5ba9b8/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 focal cnvs = 21
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Number of selected clinical features = 7
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Exclude genes 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.