This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 40 focal events and 7 clinical features across 47 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 |
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 | |
amp 1q24 2 | 15 (32%) | 32 |
0.276 (0.966) |
0.0113 (0.768) |
0.355 (0.966) |
0.0782 (0.966) |
0.454 (1.00) |
0.546 (1.00) |
1 (1.00) |
amp 2p16 1 | 15 (32%) | 32 |
0.166 (0.966) |
0.964 (1.00) |
0.355 (0.966) |
1 (1.00) |
0.271 (0.966) |
1 (1.00) |
0.481 (1.00) |
amp 3q27 3 | 14 (30%) | 33 |
0.207 (0.966) |
0.981 (1.00) |
0.528 (1.00) |
1 (1.00) |
1 (1.00) |
0.827 (1.00) |
0.465 (1.00) |
amp 3q29 | 15 (32%) | 32 |
0.0223 (0.768) |
0.53 (1.00) |
0.355 (0.966) |
0.667 (1.00) |
1 (1.00) |
0.83 (1.00) |
0.0341 (0.768) |
amp 5p13 1 | 8 (17%) | 39 |
0.68 (1.00) |
0.218 (0.966) |
0.715 (1.00) |
0.089 (0.966) |
0.0209 (0.768) |
1 (1.00) |
0.176 (0.966) |
amp 7p22 3 | 16 (34%) | 31 |
0.0592 (0.966) |
0.796 (1.00) |
0.547 (1.00) |
0.681 (1.00) |
0.137 (0.966) |
1 (1.00) |
0.725 (1.00) |
amp 7q21 3 | 15 (32%) | 32 |
0.22 (0.966) |
0.837 (1.00) |
0.758 (1.00) |
1 (1.00) |
0.453 (1.00) |
0.679 (1.00) |
0.481 (1.00) |
amp 8q24 23 | 14 (30%) | 33 |
0.917 (1.00) |
0.463 (1.00) |
0.205 (0.966) |
0.658 (1.00) |
0.0644 (0.966) |
0.827 (1.00) |
0.14 (0.966) |
amp 12q21 1 | 14 (30%) | 33 |
0.397 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.658 (1.00) |
0.141 (0.966) |
0.542 (1.00) |
0.14 (0.966) |
amp 16p12 2 | 10 (21%) | 37 |
0.31 (0.966) |
0.317 (0.966) |
1 (1.00) |
1 (1.00) |
0.789 (1.00) |
1 (1.00) |
0.7 (1.00) |
amp 18q21 2 | 16 (34%) | 31 |
0.538 (1.00) |
0.4 (1.00) |
1 (1.00) |
0.681 (1.00) |
1 (1.00) |
0.0248 (0.768) |
0.725 (1.00) |
amp 19q13 43 | 10 (21%) | 37 |
0.978 (1.00) |
0.755 (1.00) |
1 (1.00) |
0.636 (1.00) |
1 (1.00) |
0.591 (1.00) |
0.7 (1.00) |
amp xq27 3 | 7 (15%) | 40 |
0.162 (0.966) |
0.811 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.0306 (0.768) |
0.227 (0.966) |
1 (1.00) |
del 1p36 32 | 11 (23%) | 36 |
0.826 (1.00) |
0.96 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.617 (1.00) |
0.61 (1.00) |
0.435 (1.00) |
del 1p13 1 | 11 (23%) | 36 |
0.338 (0.966) |
0.159 (0.966) |
0.181 (0.966) |
0.171 (0.966) |
0.615 (1.00) |
0.459 (1.00) |
0.703 (1.00) |
del 1q43 | 10 (21%) | 37 |
0.868 (1.00) |
0.101 (0.966) |
0.475 (1.00) |
0.319 (0.966) |
0.135 (0.966) |
0.337 (0.966) |
1 (1.00) |
del 2q23 1 | 8 (17%) | 39 |
0.64 (1.00) |
0.61 (1.00) |
0.269 (0.966) |
0.587 (1.00) |
0.517 (1.00) |
0.204 (0.966) |
0.403 (1.00) |
del 3p21 31 | 8 (17%) | 39 |
0.672 (1.00) |
0.0677 (0.966) |
1 (1.00) |
0.286 (0.966) |
0.0461 (0.922) |
0.274 (0.966) |
0.176 (0.966) |
del 4q35 1 | 10 (21%) | 37 |
0.406 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.332 (0.966) |
1 (1.00) |
del 5q33 3 | 4 (9%) | 43 |
0.299 (0.966) |
0.35 (0.966) |
1 (1.00) |
1 (1.00) |
0.0214 (0.768) |
1 (1.00) |
1 (1.00) |
del 6p21 32 | 6 (13%) | 41 |
0.89 (1.00) |
0.975 (1.00) |
0.678 (1.00) |
0.57 (1.00) |
0.397 (1.00) |
0.46 (1.00) |
0.164 (0.966) |
del 6q14 1 | 17 (36%) | 30 |
0.503 (1.00) |
0.765 (1.00) |
0.768 (1.00) |
0.234 (0.966) |
0.673 (1.00) |
1 (1.00) |
0.306 (0.966) |
del 6q22 32 | 15 (32%) | 32 |
0.819 (1.00) |
0.273 (0.966) |
1 (1.00) |
0.399 (1.00) |
0.165 (0.966) |
0.551 (1.00) |
0.158 (0.966) |
del 6q23 3 | 15 (32%) | 32 |
0.608 (1.00) |
0.553 (1.00) |
0.758 (1.00) |
1 (1.00) |
0.0357 (0.768) |
0.0296 (0.768) |
0.0341 (0.768) |
del 7q33 | 5 (11%) | 42 |
0.702 (1.00) |
0.124 (0.966) |
0.362 (0.966) |
1 (1.00) |
0.154 (0.966) |
0.232 (0.966) |
0.0118 (0.768) |
del 8p23 2 | 11 (23%) | 36 |
0.609 (1.00) |
0.811 (1.00) |
0.0809 (0.966) |
1 (1.00) |
0.246 (0.966) |
0.792 (1.00) |
0.118 (0.966) |
del 8q12 1 | 9 (19%) | 38 |
0.79 (1.00) |
0.766 (1.00) |
0.711 (1.00) |
0.316 (0.966) |
0.575 (1.00) |
0.776 (1.00) |
0.674 (1.00) |
del 9p21 3 | 17 (36%) | 30 |
0.883 (1.00) |
0.288 (0.966) |
0.543 (1.00) |
1 (1.00) |
0.187 (0.966) |
0.261 (0.966) |
1 (1.00) |
del 10q23 31 | 8 (17%) | 39 |
0.47 (1.00) |
0.561 (1.00) |
0.0592 (0.966) |
1 (1.00) |
0.341 (0.966) |
0.545 (1.00) |
1 (1.00) |
del 12p13 2 | 8 (17%) | 39 |
0.197 (0.966) |
0.137 (0.966) |
0.269 (0.966) |
0.325 (0.966) |
0.523 (1.00) |
0.361 (0.966) |
1 (1.00) |
del 13q14 2 | 6 (13%) | 41 |
0.897 (1.00) |
0.3 (0.966) |
0.204 (0.966) |
1 (1.00) |
0.214 (0.966) |
0.462 (1.00) |
0.164 (0.966) |
del 15q21 1 | 13 (28%) | 34 |
0.346 (0.966) |
0.584 (1.00) |
0.102 (0.966) |
0.355 (0.966) |
1 (1.00) |
0.419 (1.00) |
1 (1.00) |
del 16p13 13 | 5 (11%) | 42 |
0.336 (0.966) |
0.931 (1.00) |
0.362 (0.966) |
1 (1.00) |
0.0766 (0.966) |
0.433 (1.00) |
1 (1.00) |
del 16q23 1 | 5 (11%) | 42 |
0.568 (1.00) |
0.605 (1.00) |
0.362 (0.966) |
1 (1.00) |
1 (1.00) |
0.167 (0.966) |
0.309 (0.966) |
del 17p13 1 | 12 (26%) | 35 |
0.12 (0.966) |
0.733 (1.00) |
0.179 (0.966) |
0.355 (0.966) |
0.0843 (0.966) |
0.803 (1.00) |
0.00544 (0.768) |
del 17q24 1 | 7 (15%) | 40 |
0.132 (0.966) |
0.686 (1.00) |
0.436 (1.00) |
1 (1.00) |
0.0312 (0.768) |
0.336 (0.966) |
0.35 (0.966) |
del 19p13 2 | 4 (9%) | 43 |
0.389 (1.00) |
0.58 (1.00) |
1 (1.00) |
1 (1.00) |
0.267 (0.966) |
1 (1.00) |
0.266 (0.966) |
del 19q13 2 | 5 (11%) | 42 |
0.312 (0.966) |
0.167 (0.966) |
0.362 (0.966) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.59 (1.00) |
del 22q13 31 | 7 (15%) | 40 |
0.947 (1.00) |
0.601 (1.00) |
0.436 (1.00) |
1 (1.00) |
1 (1.00) |
0.494 (1.00) |
1 (1.00) |
del xq28 | 3 (6%) | 44 |
0.174 (0.966) |
0.728 (1.00) |
0.242 (0.966) |
1 (1.00) |
1 (1.00) |
0.582 (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/19780778/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/19775131/DLBC-TP.merged_data.txt
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Number of patients = 47
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Number of significantly focal cnvs = 40
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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.
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.