This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 39 focal events and 8 clinical features across 48 patients, no significant finding detected with Q value < 0.25.
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No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE | ETHNICITY | ||
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 | Fisher's exact test | |
amp 1q24 2 | 16 (33%) | 32 |
0.276 (1.00) |
0.0151 (0.87) |
0.176 (1.00) |
0.542 (1.00) |
0.0782 (1.00) |
0.371 (1.00) |
0.32 (1.00) |
1 (1.00) |
amp 2p16 1 | 16 (33%) | 32 |
0.166 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.5 (1.00) |
amp 3q27 3 | 14 (29%) | 34 |
0.207 (1.00) |
0.946 (1.00) |
0.696 (1.00) |
0.526 (1.00) |
1 (1.00) |
1 (1.00) |
0.822 (1.00) |
0.294 (1.00) |
amp 3q29 | 15 (31%) | 33 |
0.0223 (0.87) |
0.504 (1.00) |
0.891 (1.00) |
0.351 (1.00) |
0.664 (1.00) |
1 (1.00) |
0.829 (1.00) |
0.0312 (0.974) |
amp 5p13 1 | 8 (17%) | 40 |
0.68 (1.00) |
0.218 (1.00) |
0.71 (1.00) |
0.0841 (1.00) |
0.0193 (0.87) |
1 (1.00) |
0.0939 (1.00) |
|
amp 7p22 3 | 16 (33%) | 32 |
0.0592 (1.00) |
0.768 (1.00) |
0.646 (1.00) |
0.542 (1.00) |
0.676 (1.00) |
0.176 (1.00) |
1 (1.00) |
0.5 (1.00) |
amp 7q21 3 | 15 (31%) | 33 |
0.22 (1.00) |
0.815 (1.00) |
0.88 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.549 (1.00) |
0.671 (1.00) |
0.476 (1.00) |
amp 8q24 23 | 14 (29%) | 34 |
0.917 (1.00) |
0.489 (1.00) |
0.202 (1.00) |
0.41 (1.00) |
0.0621 (1.00) |
0.822 (1.00) |
0.139 (1.00) |
|
amp 12q21 1 | 14 (29%) | 34 |
0.397 (1.00) |
0.708 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.41 (1.00) |
0.131 (1.00) |
0.53 (1.00) |
0.139 (1.00) |
amp 16p12 2 | 10 (21%) | 38 |
0.31 (1.00) |
0.304 (1.00) |
0.512 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.786 (1.00) |
1 (1.00) |
0.695 (1.00) |
amp 18q21 2 | 16 (33%) | 32 |
0.538 (1.00) |
0.387 (1.00) |
0.693 (1.00) |
1 (1.00) |
0.676 (1.00) |
1 (1.00) |
0.0251 (0.872) |
0.5 (1.00) |
amp 19q13 43 | 10 (21%) | 38 |
0.978 (1.00) |
0.741 (1.00) |
0.889 (1.00) |
0.735 (1.00) |
0.63 (1.00) |
1 (1.00) |
0.582 (1.00) |
0.695 (1.00) |
amp xq28 | 8 (17%) | 40 |
0.0219 (0.87) |
0.825 (1.00) |
0.62 (1.00) |
0.71 (1.00) |
0.329 (1.00) |
0.0432 (0.991) |
0.359 (1.00) |
1 (1.00) |
del 1p36 32 | 11 (23%) | 37 |
0.826 (1.00) |
0.932 (1.00) |
0.879 (1.00) |
0.732 (1.00) |
0.659 (1.00) |
0.617 (1.00) |
0.61 (1.00) |
0.43 (1.00) |
del 1p13 1 | 12 (25%) | 36 |
0.338 (1.00) |
0.198 (1.00) |
0.287 (1.00) |
0.111 (1.00) |
0.166 (1.00) |
0.625 (1.00) |
0.619 (1.00) |
0.703 (1.00) |
del 1q43 | 10 (21%) | 38 |
0.868 (1.00) |
0.0888 (1.00) |
0.107 (1.00) |
0.307 (1.00) |
0.318 (1.00) |
0.128 (1.00) |
0.327 (1.00) |
1 (1.00) |
del 2q23 1 | 8 (17%) | 40 |
0.64 (1.00) |
0.638 (1.00) |
0.789 (1.00) |
0.26 (1.00) |
0.585 (1.00) |
0.51 (1.00) |
0.201 (1.00) |
0.394 (1.00) |
del 3p21 31 | 8 (17%) | 40 |
0.672 (1.00) |
0.0617 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.276 (1.00) |
0.0445 (0.991) |
0.274 (1.00) |
0.0939 (1.00) |
del 4q35 1 | 10 (21%) | 38 |
0.406 (1.00) |
0.638 (1.00) |
0.757 (1.00) |
0.735 (1.00) |
1 (1.00) |
1 (1.00) |
0.327 (1.00) |
1 (1.00) |
del 5q33 3 | 4 (8%) | 44 |
0.299 (1.00) |
0.361 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0211 (0.87) |
1 (1.00) |
1 (1.00) |
del 6p21 32 | 6 (12%) | 42 |
0.89 (1.00) |
0.975 (1.00) |
0.483 (1.00) |
0.674 (1.00) |
0.571 (1.00) |
0.388 (1.00) |
0.458 (1.00) |
0.156 (1.00) |
del 6q14 1 | 17 (35%) | 31 |
0.503 (1.00) |
0.796 (1.00) |
0.442 (1.00) |
0.765 (1.00) |
0.396 (1.00) |
0.668 (1.00) |
0.848 (1.00) |
0.3 (1.00) |
del 6q22 32 | 16 (33%) | 32 |
0.819 (1.00) |
0.304 (1.00) |
0.378 (1.00) |
0.764 (1.00) |
0.396 (1.00) |
0.225 (1.00) |
0.32 (1.00) |
0.178 (1.00) |
del 6q23 3 | 16 (33%) | 32 |
0.608 (1.00) |
0.599 (1.00) |
0.627 (1.00) |
1 (1.00) |
1 (1.00) |
0.0407 (0.991) |
0.0153 (0.87) |
0.0735 (1.00) |
del 7q33 | 5 (10%) | 43 |
0.702 (1.00) |
0.129 (1.00) |
0.357 (1.00) |
0.571 (1.00) |
0.146 (1.00) |
0.231 (1.00) |
0.0109 (0.87) |
|
del 8p23 2 | 12 (25%) | 36 |
0.609 (1.00) |
0.748 (1.00) |
0.883 (1.00) |
0.18 (1.00) |
1 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.143 (1.00) |
del 8q12 1 | 9 (19%) | 39 |
0.79 (1.00) |
0.741 (1.00) |
0.13 (1.00) |
0.478 (1.00) |
0.318 (1.00) |
0.565 (1.00) |
0.77 (1.00) |
0.671 (1.00) |
del 9p21 3 | 17 (35%) | 31 |
0.883 (1.00) |
0.267 (1.00) |
0.478 (1.00) |
0.551 (1.00) |
1 (1.00) |
0.186 (1.00) |
0.258 (1.00) |
1 (1.00) |
del 10q23 31 | 7 (15%) | 41 |
0.312 (1.00) |
0.93 (1.00) |
0.106 (1.00) |
0.571 (1.00) |
0.45 (1.00) |
0.737 (1.00) |
0.662 (1.00) |
|
del 12p13 2 | 8 (17%) | 40 |
0.197 (1.00) |
0.131 (1.00) |
0.827 (1.00) |
0.26 (1.00) |
0.329 (1.00) |
0.506 (1.00) |
0.359 (1.00) |
1 (1.00) |
del 13q14 2 | 7 (15%) | 41 |
0.897 (1.00) |
0.381 (1.00) |
0.968 (1.00) |
0.429 (1.00) |
1 (1.00) |
0.267 (1.00) |
0.338 (1.00) |
0.345 (1.00) |
del 15q21 1 | 13 (27%) | 35 |
0.346 (1.00) |
0.538 (1.00) |
0.411 (1.00) |
0.101 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.501 (1.00) |
1 (1.00) |
del 16p13 13 | 6 (12%) | 42 |
0.336 (1.00) |
0.988 (1.00) |
0.077 (1.00) |
0.674 (1.00) |
1 (1.00) |
0.108 (1.00) |
0.708 (1.00) |
1 (1.00) |
del 16q23 1 | 5 (10%) | 43 |
0.568 (1.00) |
0.577 (1.00) |
0.357 (1.00) |
1 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.312 (1.00) |
|
del 17p13 1 | 13 (27%) | 35 |
0.12 (1.00) |
0.685 (1.00) |
0.96 (1.00) |
0.329 (1.00) |
0.377 (1.00) |
0.104 (1.00) |
0.809 (1.00) |
0.00903 (0.87) |
del 17q24 1 | 8 (17%) | 40 |
0.132 (1.00) |
0.771 (1.00) |
1 (1.00) |
0.71 (1.00) |
1 (1.00) |
0.0436 (0.991) |
0.279 (1.00) |
0.394 (1.00) |
del 19p13 2 | 4 (8%) | 44 |
0.389 (1.00) |
0.563 (1.00) |
0.984 (1.00) |
1 (1.00) |
1 (1.00) |
0.262 (1.00) |
1 (1.00) |
0.257 (1.00) |
del 19q13 2 | 5 (10%) | 43 |
0.312 (1.00) |
0.161 (1.00) |
0.357 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.587 (1.00) |
|
del 22q13 31 | 7 (15%) | 41 |
0.947 (1.00) |
0.579 (1.00) |
0.429 (1.00) |
1 (1.00) |
1 (1.00) |
0.488 (1.00) |
1 (1.00) |
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Copy number data file = all_lesions.txt from GISTIC pipeline
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Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/22516373/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/22506396/DLBC-TP.merged_data.txt
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Number of patients = 48
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Number of significantly focal cnvs = 39
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Number of selected clinical features = 8
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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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.