(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 61 arm-level results and 3 clinical features across 61 patients, 2 significant findings detected with Q value < 0.25.
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18p loss cnv correlated to 'AGE'.
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18q loss cnv correlated to 'AGE'.
Clinical Features |
Time to Death |
AGE | GENDER | ||
nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test | |
18p loss | 7 (11%) | 54 |
0.0213 (1.00) |
0.000571 (0.101) |
0.695 (1.00) |
18q loss | 9 (15%) | 52 |
0.2 (1.00) |
0.00109 (0.191) |
0.71 (1.00) |
1p gain | 8 (13%) | 53 |
0.807 (1.00) |
0.237 (1.00) |
1 (1.00) |
1q gain | 33 (54%) | 28 |
0.71 (1.00) |
0.73 (1.00) |
0.423 (1.00) |
2p gain | 8 (13%) | 53 |
0.738 (1.00) |
0.115 (1.00) |
0.124 (1.00) |
2q gain | 7 (11%) | 54 |
0.867 (1.00) |
0.227 (1.00) |
0.087 (1.00) |
4p gain | 4 (7%) | 57 |
0.931 (1.00) |
0.455 (1.00) |
0.129 (1.00) |
5p gain | 18 (30%) | 43 |
0.304 (1.00) |
0.227 (1.00) |
1 (1.00) |
5q gain | 13 (21%) | 48 |
0.197 (1.00) |
0.201 (1.00) |
1 (1.00) |
6p gain | 12 (20%) | 49 |
0.123 (1.00) |
0.79 (1.00) |
0.509 (1.00) |
6q gain | 8 (13%) | 53 |
0.00574 (1.00) |
0.506 (1.00) |
0.699 (1.00) |
7p gain | 17 (28%) | 44 |
0.816 (1.00) |
0.615 (1.00) |
0.373 (1.00) |
7q gain | 18 (30%) | 43 |
0.828 (1.00) |
0.601 (1.00) |
0.397 (1.00) |
8p gain | 11 (18%) | 50 |
0.112 (1.00) |
0.577 (1.00) |
0.299 (1.00) |
8q gain | 31 (51%) | 30 |
0.271 (1.00) |
0.594 (1.00) |
0.6 (1.00) |
9p gain | 3 (5%) | 58 |
0.822 (1.00) |
0.293 (1.00) |
|
9q gain | 3 (5%) | 58 |
0.822 (1.00) |
0.293 (1.00) |
|
10p gain | 5 (8%) | 56 |
0.166 (1.00) |
0.39 (1.00) |
0.341 (1.00) |
12q gain | 3 (5%) | 58 |
0.894 (1.00) |
0.293 (1.00) |
|
15q gain | 5 (8%) | 56 |
0.814 (1.00) |
0.328 (1.00) |
0.341 (1.00) |
16p gain | 3 (5%) | 58 |
0.0077 (1.00) |
0.149 (1.00) |
1 (1.00) |
17p gain | 3 (5%) | 58 |
0.467 (1.00) |
0.711 (1.00) |
0.293 (1.00) |
17q gain | 16 (26%) | 45 |
0.0844 (1.00) |
0.876 (1.00) |
0.548 (1.00) |
18q gain | 3 (5%) | 58 |
0.937 (1.00) |
0.619 (1.00) |
1 (1.00) |
19p gain | 5 (8%) | 56 |
0.759 (1.00) |
0.62 (1.00) |
0.0524 (1.00) |
19q gain | 7 (11%) | 54 |
0.795 (1.00) |
0.822 (1.00) |
0.087 (1.00) |
20p gain | 12 (20%) | 49 |
0.238 (1.00) |
0.0865 (1.00) |
0.322 (1.00) |
20q gain | 13 (21%) | 48 |
0.361 (1.00) |
0.059 (1.00) |
0.517 (1.00) |
21q gain | 4 (7%) | 57 |
0.696 (1.00) |
0.613 (1.00) |
0.129 (1.00) |
22q gain | 6 (10%) | 55 |
0.16 (1.00) |
0.068 (1.00) |
0.658 (1.00) |
Xq gain | 4 (7%) | 57 |
0.228 (1.00) |
0.223 (1.00) |
1 (1.00) |
1p loss | 11 (18%) | 50 |
0.689 (1.00) |
0.511 (1.00) |
0.504 (1.00) |
1q loss | 3 (5%) | 58 |
0.862 (1.00) |
0.134 (1.00) |
1 (1.00) |
2p loss | 3 (5%) | 58 |
0.293 (1.00) |
||
2q loss | 4 (7%) | 57 |
0.0102 (1.00) |
0.615 (1.00) |
|
3p loss | 5 (8%) | 56 |
0.721 (1.00) |
0.763 (1.00) |
0.341 (1.00) |
3q loss | 3 (5%) | 58 |
0.628 (1.00) |
0.237 (1.00) |
0.293 (1.00) |
4p loss | 9 (15%) | 52 |
0.508 (1.00) |
0.864 (1.00) |
1 (1.00) |
4q loss | 15 (25%) | 46 |
0.515 (1.00) |
0.779 (1.00) |
1 (1.00) |
5q loss | 4 (7%) | 57 |
0.00925 (1.00) |
0.953 (1.00) |
1 (1.00) |
6q loss | 10 (16%) | 51 |
0.258 (1.00) |
0.944 (1.00) |
0.473 (1.00) |
7p loss | 5 (8%) | 56 |
0.489 (1.00) |
0.661 (1.00) |
0.0524 (1.00) |
7q loss | 7 (11%) | 54 |
0.935 (1.00) |
0.429 (1.00) |
0.24 (1.00) |
8p loss | 28 (46%) | 33 |
0.439 (1.00) |
0.262 (1.00) |
0.423 (1.00) |
8q loss | 5 (8%) | 56 |
0.582 (1.00) |
0.855 (1.00) |
0.341 (1.00) |
9p loss | 15 (25%) | 46 |
0.77 (1.00) |
0.266 (1.00) |
1 (1.00) |
9q loss | 13 (21%) | 48 |
0.611 (1.00) |
0.27 (1.00) |
0.753 (1.00) |
10p loss | 3 (5%) | 58 |
0.7 (1.00) |
0.0302 (1.00) |
0.547 (1.00) |
10q loss | 12 (20%) | 49 |
0.514 (1.00) |
0.588 (1.00) |
0.742 (1.00) |
11p loss | 5 (8%) | 56 |
0.691 (1.00) |
0.279 (1.00) |
0.341 (1.00) |
11q loss | 8 (13%) | 53 |
0.244 (1.00) |
0.375 (1.00) |
1 (1.00) |
12p loss | 3 (5%) | 58 |
0.489 (1.00) |
0.509 (1.00) |
1 (1.00) |
13q loss | 22 (36%) | 39 |
0.212 (1.00) |
0.162 (1.00) |
1 (1.00) |
14q loss | 21 (34%) | 40 |
0.64 (1.00) |
0.549 (1.00) |
1 (1.00) |
15q loss | 7 (11%) | 54 |
0.924 (1.00) |
0.363 (1.00) |
1 (1.00) |
16p loss | 11 (18%) | 50 |
0.39 (1.00) |
0.89 (1.00) |
1 (1.00) |
16q loss | 19 (31%) | 42 |
0.902 (1.00) |
0.743 (1.00) |
0.571 (1.00) |
17p loss | 25 (41%) | 36 |
0.245 (1.00) |
0.372 (1.00) |
0.787 (1.00) |
19p loss | 4 (7%) | 57 |
0.23 (1.00) |
0.474 (1.00) |
0.287 (1.00) |
21q loss | 9 (15%) | 52 |
0.0736 (1.00) |
0.76 (1.00) |
0.0203 (1.00) |
22q loss | 9 (15%) | 52 |
0.624 (1.00) |
0.696 (1.00) |
0.0596 (1.00) |
P value = 0.000571 (t-test), Q value = 0.1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 61.8 (14.0) |
18P LOSS MUTATED | 7 | 73.6 (6.4) |
18P LOSS WILD-TYPE | 49 | 60.1 (14.0) |
P value = 0.00109 (t-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 56 | 61.8 (14.0) |
18Q LOSS MUTATED | 9 | 71.6 (6.9) |
18Q LOSS WILD-TYPE | 47 | 60.0 (14.3) |
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Mutation data file = broad_values_by_arm.mutsig.cluster.txt
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Clinical data file = LIHC-TP.clin.merged.picked.txt
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Number of patients = 61
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Number of significantly arm-level cnvs = 61
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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.