(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 34 arm-level results and 6 clinical features across 26 patients, one significant finding detected with Q value < 0.25.
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15q gain cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.
Clinical Features |
Time to Death |
AGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | ||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | t-test | t-test | |
15q gain | 3 (12%) | 23 |
1 (1.00) |
0.818 (1.00) |
1 (1.00) |
0.000729 (0.0984) |
||
1p gain | 5 (19%) | 21 |
0.617 (1.00) |
0.0415 (1.00) |
1 (1.00) |
0.94 (1.00) |
||
1q gain | 10 (38%) | 16 |
0.414 (1.00) |
0.00733 (0.983) |
0.625 (1.00) |
0.869 (1.00) |
||
3p gain | 3 (12%) | 23 |
1 (1.00) |
0.742 (1.00) |
0.408 (1.00) |
0.594 (1.00) |
||
3q gain | 16 (62%) | 10 |
1 (1.00) |
0.242 (1.00) |
1 (1.00) |
0.545 (1.00) |
||
5p gain | 8 (31%) | 18 |
0.617 (1.00) |
0.438 (1.00) |
0.563 (1.00) |
0.952 (1.00) |
||
6p gain | 3 (12%) | 23 |
1 (1.00) |
0.745 (1.00) |
1 (1.00) |
0.227 (1.00) |
||
8p gain | 3 (12%) | 23 |
1 (1.00) |
0.561 (1.00) |
0.408 (1.00) |
0.792 (1.00) |
||
8q gain | 5 (19%) | 21 |
0.617 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.916 (1.00) |
||
10p gain | 3 (12%) | 23 |
0.0455 (1.00) |
0.332 (1.00) |
1 (1.00) |
0.291 (1.00) |
||
12p gain | 5 (19%) | 21 |
1 (1.00) |
0.485 (1.00) |
1 (1.00) |
0.639 (1.00) |
||
12q gain | 3 (12%) | 23 |
1 (1.00) |
0.723 (1.00) |
0.408 (1.00) |
0.792 (1.00) |
||
16p gain | 4 (15%) | 22 |
0.617 (1.00) |
0.944 (1.00) |
0.511 (1.00) |
0.792 (1.00) |
||
16q gain | 3 (12%) | 23 |
0.617 (1.00) |
0.165 (1.00) |
0.408 (1.00) |
|||
18p gain | 3 (12%) | 23 |
0.617 (1.00) |
0.336 (1.00) |
0.0523 (1.00) |
0.399 (1.00) |
||
20p gain | 8 (31%) | 18 |
1 (1.00) |
0.818 (1.00) |
0.563 (1.00) |
0.624 (1.00) |
||
20q gain | 9 (35%) | 17 |
1 (1.00) |
0.923 (1.00) |
1 (1.00) |
0.55 (1.00) |
||
22q gain | 4 (15%) | 22 |
0.617 (1.00) |
0.275 (1.00) |
0.511 (1.00) |
0.238 (1.00) |
||
3p loss | 7 (27%) | 19 |
0.414 (1.00) |
0.586 (1.00) |
1 (1.00) |
0.962 (1.00) |
||
4p loss | 10 (38%) | 16 |
0.414 (1.00) |
0.666 (1.00) |
0.625 (1.00) |
0.367 (1.00) |
||
4q loss | 3 (12%) | 23 |
0.617 (1.00) |
0.43 (1.00) |
0.408 (1.00) |
0.657 (1.00) |
||
5q loss | 8 (31%) | 18 |
0.414 (1.00) |
0.179 (1.00) |
0.277 (1.00) |
0.926 (1.00) |
||
8p loss | 7 (27%) | 19 |
0.414 (1.00) |
0.257 (1.00) |
1 (1.00) |
0.692 (1.00) |
||
10p loss | 5 (19%) | 21 |
0.617 (1.00) |
0.563 (1.00) |
0.155 (1.00) |
0.246 (1.00) |
||
10q loss | 5 (19%) | 21 |
0.0455 (1.00) |
0.582 (1.00) |
0.155 (1.00) |
0.0824 (1.00) |
||
11p loss | 5 (19%) | 21 |
0.414 (1.00) |
0.229 (1.00) |
0.155 (1.00) |
0.15 (1.00) |
||
11q loss | 5 (19%) | 21 |
0.414 (1.00) |
0.933 (1.00) |
0.155 (1.00) |
0.323 (1.00) |
||
12p loss | 4 (15%) | 22 |
0.0455 (1.00) |
0.077 (1.00) |
1 (1.00) |
0.436 (1.00) |
||
13q loss | 8 (31%) | 18 |
0.414 (1.00) |
0.907 (1.00) |
0.0721 (1.00) |
0.673 (1.00) |
||
17p loss | 7 (27%) | 19 |
0.414 (1.00) |
0.451 (1.00) |
0.287 (1.00) |
0.732 (1.00) |
||
17q loss | 3 (12%) | 23 |
0.221 (1.00) |
0.383 (1.00) |
0.408 (1.00) |
0.874 (1.00) |
||
18p loss | 3 (12%) | 23 |
0.617 (1.00) |
0.726 (1.00) |
0.408 (1.00) |
0.227 (1.00) |
||
18q loss | 4 (15%) | 22 |
0.414 (1.00) |
0.491 (1.00) |
0.511 (1.00) |
0.075 (1.00) |
||
21q loss | 6 (23%) | 20 |
0.617 (1.00) |
0.92 (1.00) |
0.542 (1.00) |
0.0689 (1.00) |
P value = 0.000729 (t-test), Q value = 0.098
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 25 | 1.8 (1.1) |
15Q GAIN MUTATED | 3 | 1.0 (0.0) |
15Q GAIN WILD-TYPE | 22 | 2.0 (1.1) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = CESC-TP.clin.merged.picked.txt
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Number of patients = 26
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Number of significantly arm-level cnvs = 34
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Number of selected clinical features = 6
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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.