(primary solid tumor cohort)
This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 21 arm-level results and 3 clinical features across 146 patients, no significant finding detected with Q value < 0.25.
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No arm-level cnvs related to clinical features.
Table 1. Get Full Table Overview of the association between significant copy number variation of 21 arm-level results and 3 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
|
Clinical Features |
Time to Death |
AGE |
RADIATIONS RADIATION REGIMENINDICATION |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
| 1q gain | 4 (3%) | 142 |
1 (1.00) |
0.299 (1.00) |
1 (1.00) |
| 3p gain | 4 (3%) | 142 |
1 (1.00) |
0.646 (1.00) |
1 (1.00) |
| 3q gain | 6 (4%) | 140 |
1 (1.00) |
0.329 (1.00) |
1 (1.00) |
| 7p gain | 15 (10%) | 131 |
1 (1.00) |
0.0153 (0.963) |
1 (1.00) |
| 7q gain | 12 (8%) | 134 |
1 (1.00) |
0.0682 (1.00) |
1 (1.00) |
| 8p gain | 6 (4%) | 140 |
1 (1.00) |
0.537 (1.00) |
1 (1.00) |
| 8q gain | 13 (9%) | 133 |
1 (1.00) |
0.603 (1.00) |
1 (1.00) |
| 9q gain | 3 (2%) | 143 |
1 (1.00) |
0.276 (1.00) |
1 (1.00) |
| 6q loss | 7 (5%) | 139 |
1 (1.00) |
0.258 (1.00) |
1 (1.00) |
| 8p loss | 38 (26%) | 108 |
1 (1.00) |
0.0476 (1.00) |
0.327 (1.00) |
| 8q loss | 4 (3%) | 142 |
1 (1.00) |
0.635 (1.00) |
1 (1.00) |
| 10p loss | 5 (3%) | 141 |
1 (1.00) |
0.91 (1.00) |
1 (1.00) |
| 10q loss | 4 (3%) | 142 |
1 (1.00) |
0.396 (1.00) |
1 (1.00) |
| 12p loss | 7 (5%) | 139 |
1 (1.00) |
0.674 (1.00) |
1 (1.00) |
| 13q loss | 11 (8%) | 135 |
1 (1.00) |
0.82 (1.00) |
1 (1.00) |
| 16q loss | 18 (12%) | 128 |
1 (1.00) |
0.146 (1.00) |
1 (1.00) |
| 17p loss | 17 (12%) | 129 |
1 (1.00) |
0.529 (1.00) |
1 (1.00) |
| 18p loss | 14 (10%) | 132 |
1 (1.00) |
0.621 (1.00) |
1 (1.00) |
| 18q loss | 19 (13%) | 127 |
1 (1.00) |
0.3 (1.00) |
1 (1.00) |
| 20p loss | 4 (3%) | 142 |
1 (1.00) |
0.451 (1.00) |
0.131 (1.00) |
| 22q loss | 5 (3%) | 141 |
1 (1.00) |
0.274 (1.00) |
0.162 (1.00) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = PRAD-TP.clin.merged.picked.txt
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Number of patients = 146
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Number of significantly arm-level cnvs = 21
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Number of selected clinical features = 3
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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 continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.