This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 51 arm-level events and 7 clinical features across 80 patients, 4 significant findings detected with Q value < 0.25.
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3p loss cnv correlated to 'Time to Death'.
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3q loss cnv correlated to 'Time to Death'.
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9p loss cnv correlated to 'YEARS_TO_BIRTH'.
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11p loss cnv correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
||
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 | |
3p loss | 43 (54%) | 37 |
0.000766 (0.137) |
0.322 (1.00) |
0.0583 (1.00) |
0.266 (1.00) |
0.117 (1.00) |
1 (1.00) |
1 (1.00) |
3q loss | 43 (54%) | 37 |
0.000766 (0.137) |
0.322 (1.00) |
0.0586 (1.00) |
0.269 (1.00) |
0.117 (1.00) |
1 (1.00) |
1 (1.00) |
9p loss | 8 (10%) | 72 |
0.0159 (0.517) |
0.0019 (0.205) |
0.605 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.277 (1.00) |
11p loss | 3 (4%) | 77 |
0.0023 (0.205) |
0.305 (1.00) |
1 (1.00) |
0.139 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
1q gain | 8 (10%) | 72 |
0.222 (1.00) |
0.34 (1.00) |
0.366 (1.00) |
0.492 (1.00) |
0.477 (1.00) |
0.288 (1.00) |
1 (1.00) |
2p gain | 10 (12%) | 70 |
0.359 (1.00) |
0.344 (1.00) |
0.36 (1.00) |
0.667 (1.00) |
1 (1.00) |
0.32 (1.00) |
0.337 (1.00) |
2q gain | 8 (10%) | 72 |
0.818 (1.00) |
0.11 (1.00) |
0.62 (1.00) |
0.554 (1.00) |
1 (1.00) |
0.288 (1.00) |
1 (1.00) |
4p gain | 7 (9%) | 73 |
0.523 (1.00) |
0.17 (1.00) |
0.0325 (0.848) |
0.291 (1.00) |
0.379 (1.00) |
1 (1.00) |
0.246 (1.00) |
4q gain | 4 (5%) | 76 |
0.932 (1.00) |
0.0849 (1.00) |
0.00506 (0.361) |
0.0976 (1.00) |
0.267 (1.00) |
0.314 (1.00) |
1 (1.00) |
5p gain | 3 (4%) | 77 |
0.828 (1.00) |
0.447 (1.00) |
0.887 (1.00) |
1 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
5q gain | 3 (4%) | 77 |
0.828 (1.00) |
0.447 (1.00) |
0.889 (1.00) |
1 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
6p gain | 39 (49%) | 41 |
0.204 (1.00) |
0.256 (1.00) |
0.892 (1.00) |
0.873 (1.00) |
0.624 (1.00) |
0.822 (1.00) |
0.615 (1.00) |
6q gain | 16 (20%) | 64 |
0.0445 (0.993) |
0.279 (1.00) |
0.474 (1.00) |
0.301 (1.00) |
1 (1.00) |
0.587 (1.00) |
0.498 (1.00) |
7p gain | 9 (11%) | 71 |
0.125 (1.00) |
0.415 (1.00) |
0.519 (1.00) |
0.427 (1.00) |
0.325 (1.00) |
1 (1.00) |
1 (1.00) |
7q gain | 8 (10%) | 72 |
0.0506 (1.00) |
0.217 (1.00) |
0.392 (1.00) |
0.49 (1.00) |
0.267 (1.00) |
0.724 (1.00) |
1 (1.00) |
8p gain | 33 (41%) | 47 |
0.0333 (0.848) |
0.725 (1.00) |
0.428 (1.00) |
0.571 (1.00) |
0.307 (1.00) |
1 (1.00) |
0.0627 (1.00) |
8q gain | 53 (66%) | 27 |
0.0114 (0.517) |
0.768 (1.00) |
0.911 (1.00) |
0.779 (1.00) |
1 (1.00) |
1 (1.00) |
0.547 (1.00) |
9p gain | 6 (8%) | 74 |
0.723 (1.00) |
0.136 (1.00) |
0.763 (1.00) |
0.221 (1.00) |
1 (1.00) |
0.0811 (1.00) |
1 (1.00) |
9q gain | 5 (6%) | 75 |
0.313 (1.00) |
0.249 (1.00) |
0.575 (1.00) |
0.322 (1.00) |
1 (1.00) |
0.162 (1.00) |
1 (1.00) |
11p gain | 9 (11%) | 71 |
0.505 (1.00) |
0.26 (1.00) |
0.779 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.494 (1.00) |
1 (1.00) |
11q gain | 10 (12%) | 70 |
0.426 (1.00) |
0.436 (1.00) |
0.776 (1.00) |
0.741 (1.00) |
1 (1.00) |
0.741 (1.00) |
1 (1.00) |
12p gain | 3 (4%) | 77 |
0.828 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
12q gain | 3 (4%) | 77 |
0.828 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.778 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
13q gain | 6 (8%) | 74 |
0.994 (1.00) |
0.165 (1.00) |
0.79 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.213 (1.00) |
14q gain | 3 (4%) | 77 |
0.465 (1.00) |
0.603 (1.00) |
0.89 (1.00) |
1 (1.00) |
1 (1.00) |
0.252 (1.00) |
1 (1.00) |
16p gain | 4 (5%) | 76 |
0.543 (1.00) |
0.707 (1.00) |
0.795 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
17p gain | 8 (10%) | 72 |
0.752 (1.00) |
0.365 (1.00) |
0.969 (1.00) |
0.889 (1.00) |
1 (1.00) |
0.724 (1.00) |
1 (1.00) |
17q gain | 9 (11%) | 71 |
0.874 (1.00) |
0.772 (1.00) |
0.87 (1.00) |
0.643 (1.00) |
1 (1.00) |
0.494 (1.00) |
1 (1.00) |
20p gain | 8 (10%) | 72 |
0.581 (1.00) |
0.332 (1.00) |
0.698 (1.00) |
0.491 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
20q gain | 9 (11%) | 71 |
0.177 (1.00) |
0.19 (1.00) |
0.6 (1.00) |
0.381 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
21q gain | 14 (18%) | 66 |
0.061 (1.00) |
0.115 (1.00) |
0.78 (1.00) |
0.634 (1.00) |
0.477 (1.00) |
0.375 (1.00) |
1 (1.00) |
22q gain | 6 (8%) | 74 |
0.535 (1.00) |
0.168 (1.00) |
0.882 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.0811 (1.00) |
1 (1.00) |
xp gain | 10 (12%) | 70 |
0.326 (1.00) |
0.158 (1.00) |
0.963 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.0949 (1.00) |
1 (1.00) |
xq gain | 9 (11%) | 71 |
0.401 (1.00) |
0.209 (1.00) |
0.977 (1.00) |
0.809 (1.00) |
1 (1.00) |
0.169 (1.00) |
1 (1.00) |
1p loss | 19 (24%) | 61 |
0.189 (1.00) |
0.0503 (1.00) |
0.915 (1.00) |
0.83 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.567 (1.00) |
1q loss | 3 (4%) | 77 |
0.338 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
4q loss | 3 (4%) | 77 |
0.531 (1.00) |
0.939 (1.00) |
0.6 (1.00) |
0.295 (1.00) |
1 (1.00) |
1 (1.00) |
0.111 (1.00) |
5q loss | 3 (4%) | 77 |
0.487 (1.00) |
0.462 (1.00) |
0.457 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.0797 (1.00) |
1 (1.00) |
6q loss | 17 (21%) | 63 |
0.108 (1.00) |
0.167 (1.00) |
0.0679 (1.00) |
0.0367 (0.874) |
0.298 (1.00) |
0.583 (1.00) |
0.522 (1.00) |
8p loss | 9 (11%) | 71 |
0.82 (1.00) |
0.61 (1.00) |
0.169 (1.00) |
0.199 (1.00) |
0.379 (1.00) |
1 (1.00) |
1 (1.00) |
8q loss | 3 (4%) | 77 |
0.472 (1.00) |
0.751 (1.00) |
0.302 (1.00) |
1 (1.00) |
0.141 (1.00) |
1 (1.00) |
1 (1.00) |
9q loss | 7 (9%) | 73 |
0.0145 (0.517) |
0.00729 (0.434) |
0.376 (1.00) |
0.445 (1.00) |
1 (1.00) |
1 (1.00) |
0.246 (1.00) |
12p loss | 3 (4%) | 77 |
0.492 (1.00) |
0.761 (1.00) |
0.338 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.578 (1.00) |
1 (1.00) |
13q loss | 3 (4%) | 77 |
0.421 (1.00) |
0.761 (1.00) |
1 (1.00) |
0.138 (1.00) |
1 (1.00) |
0.0797 (1.00) |
1 (1.00) |
15q loss | 4 (5%) | 76 |
0.472 (1.00) |
0.208 (1.00) |
0.796 (1.00) |
0.396 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
16p loss | 3 (4%) | 77 |
0.246 (1.00) |
0.254 (1.00) |
0.0884 (1.00) |
0.214 (1.00) |
0.206 (1.00) |
0.578 (1.00) |
1 (1.00) |
16q loss | 16 (20%) | 64 |
0.0134 (0.517) |
0.125 (1.00) |
0.168 (1.00) |
0.376 (1.00) |
0.204 (1.00) |
0.779 (1.00) |
0.0907 (1.00) |
19p loss | 3 (4%) | 77 |
0.561 (1.00) |
0.879 (1.00) |
0.416 (1.00) |
0.394 (1.00) |
1 (1.00) |
1 (1.00) |
0.111 (1.00) |
19q loss | 3 (4%) | 77 |
0.561 (1.00) |
0.879 (1.00) |
0.416 (1.00) |
0.388 (1.00) |
1 (1.00) |
1 (1.00) |
0.111 (1.00) |
xp loss | 12 (15%) | 68 |
0.456 (1.00) |
0.0119 (0.517) |
0.172 (1.00) |
0.225 (1.00) |
0.522 (1.00) |
0.349 (1.00) |
0.394 (1.00) |
xq loss | 13 (16%) | 67 |
0.647 (1.00) |
0.0248 (0.738) |
0.398 (1.00) |
0.202 (1.00) |
0.563 (1.00) |
0.223 (1.00) |
0.421 (1.00) |
P value = 0.000766 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
3P LOSS MUTATED | 43 | 13 | 0.1 - 52.6 (15.4) |
3P LOSS WILD-TYPE | 37 | 1 | 0.1 - 85.5 (20.2) |
P value = 0.000766 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
3Q LOSS MUTATED | 43 | 13 | 0.1 - 52.6 (15.4) |
3Q LOSS WILD-TYPE | 37 | 1 | 0.1 - 85.5 (20.2) |
P value = 0.0019 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 80 | 61.6 (13.9) |
9P LOSS MUTATED | 8 | 75.4 (9.6) |
9P LOSS WILD-TYPE | 72 | 60.1 (13.6) |
P value = 0.0023 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 80 | 14 | 0.1 - 85.5 (19.1) |
11P LOSS MUTATED | 3 | 3 | 7.9 - 45.9 (13.1) |
11P LOSS WILD-TYPE | 77 | 11 | 0.1 - 85.5 (19.5) |
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Copy number data file = broad_values_by_arm.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/UVM-TP/19783310/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UVM-TP/19775655/UVM-TP.merged_data.txt
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Number of patients = 80
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Number of significantly arm-level cnvs = 51
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Number of selected clinical features = 7
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Exclude regions 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.