This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.
Testing the association between copy number variation 52 arm-level events and 8 clinical features across 48 patients, one significant finding detected with Q value < 0.25.
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9p gain cnv correlated to 'HISTOLOGICAL_TYPE'.
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 | |
9p gain | 7 (15%) | 41 |
0.945 (1.00) |
0.156 (0.834) |
0.413 (1.00) |
0.687 (1.00) |
0.0566 (0.589) |
0.00041 (0.171) |
0.492 (1.00) |
0.345 (1.00) |
1q gain | 6 (12%) | 42 |
0.286 (0.995) |
0.374 (1.00) |
0.245 (0.989) |
1 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.14 (0.834) |
1 (1.00) |
2p gain | 6 (12%) | 42 |
0.986 (1.00) |
0.0952 (0.732) |
1 (1.00) |
0.214 (0.989) |
0.108 (0.732) |
0.701 (1.00) |
0.156 (0.834) |
|
2q gain | 6 (12%) | 42 |
0.986 (1.00) |
0.0952 (0.732) |
1 (1.00) |
0.214 (0.989) |
0.108 (0.732) |
0.705 (1.00) |
0.156 (0.834) |
|
3p gain | 10 (21%) | 38 |
0.098 (0.732) |
1 (1.00) |
0.562 (1.00) |
0.735 (1.00) |
0.63 (1.00) |
0.786 (1.00) |
0.585 (1.00) |
0.241 (0.989) |
3q gain | 13 (27%) | 35 |
0.0508 (0.589) |
0.585 (1.00) |
0.565 (1.00) |
0.746 (1.00) |
0.377 (1.00) |
1 (1.00) |
0.651 (1.00) |
0.263 (0.989) |
5p gain | 7 (15%) | 41 |
0.607 (1.00) |
0.32 (1.00) |
1 (1.00) |
0.0566 (0.589) |
0.0124 (0.481) |
0.736 (1.00) |
0.0552 (0.589) |
|
5q gain | 6 (12%) | 42 |
0.981 (1.00) |
0.156 (0.834) |
0.674 (1.00) |
0.0348 (0.589) |
0.0071 (0.376) |
1 (1.00) |
0.0278 (0.589) |
|
6p gain | 6 (12%) | 42 |
0.275 (0.989) |
0.852 (1.00) |
0.199 (0.988) |
1 (1.00) |
0.635 (1.00) |
0.703 (1.00) |
0.631 (1.00) |
|
6q gain | 4 (8%) | 44 |
0.423 (1.00) |
0.926 (1.00) |
0.114 (0.732) |
1 (1.00) |
1 (1.00) |
0.223 (0.989) |
1 (1.00) |
|
7p gain | 14 (29%) | 34 |
0.145 (0.834) |
0.901 (1.00) |
0.562 (1.00) |
1 (1.00) |
1 (1.00) |
0.253 (0.989) |
0.822 (1.00) |
0.726 (1.00) |
7q gain | 12 (25%) | 36 |
0.292 (0.995) |
0.347 (1.00) |
0.561 (1.00) |
1 (1.00) |
1 (1.00) |
0.493 (1.00) |
0.617 (1.00) |
1 (1.00) |
8p gain | 7 (15%) | 41 |
0.774 (1.00) |
0.0393 (0.589) |
0.429 (1.00) |
0.276 (0.989) |
0.146 (0.834) |
0.343 (1.00) |
0.00724 (0.376) |
|
8q gain | 8 (17%) | 40 |
0.672 (1.00) |
0.0278 (0.589) |
0.71 (1.00) |
0.0841 (0.732) |
0.0199 (0.562) |
0.273 (0.989) |
0.00162 (0.312) |
|
9q gain | 7 (15%) | 41 |
0.898 (1.00) |
0.136 (0.834) |
0.412 (1.00) |
0.223 (0.989) |
0.0566 (0.589) |
0.0117 (0.481) |
0.49 (1.00) |
0.345 (1.00) |
10p gain | 4 (8%) | 44 |
0.402 (1.00) |
0.926 (1.00) |
0.114 (0.732) |
1 (1.00) |
1 (1.00) |
0.664 (1.00) |
1 (1.00) |
|
10q gain | 4 (8%) | 44 |
0.423 (1.00) |
0.444 (1.00) |
0.614 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.257 (0.989) |
|
11p gain | 9 (19%) | 39 |
0.747 (1.00) |
0.711 (1.00) |
0.793 (1.00) |
0.0276 (0.589) |
1 (1.00) |
0.0633 (0.642) |
0.554 (1.00) |
0.0321 (0.589) |
11q gain | 13 (27%) | 35 |
0.819 (1.00) |
0.493 (1.00) |
0.783 (1.00) |
0.101 (0.732) |
0.655 (1.00) |
0.221 (0.989) |
0.81 (1.00) |
0.263 (0.989) |
12p gain | 7 (15%) | 41 |
0.216 (0.989) |
0.357 (1.00) |
0.972 (1.00) |
1 (1.00) |
0.276 (0.989) |
0.0532 (0.589) |
1 (1.00) |
0.345 (1.00) |
12q gain | 9 (19%) | 39 |
0.0546 (0.589) |
0.588 (1.00) |
0.253 (0.989) |
0.713 (1.00) |
0.605 (1.00) |
0.0203 (0.562) |
0.769 (1.00) |
0.199 (0.988) |
13q gain | 5 (10%) | 43 |
0.647 (1.00) |
0.344 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.422 (1.00) |
0.587 (1.00) |
|
16p gain | 7 (15%) | 41 |
0.281 (0.989) |
0.77 (1.00) |
0.928 (1.00) |
1 (1.00) |
1 (1.00) |
0.265 (0.989) |
1 (1.00) |
1 (1.00) |
16q gain | 7 (15%) | 41 |
0.0742 (0.732) |
0.953 (1.00) |
0.616 (1.00) |
0.687 (1.00) |
1 (1.00) |
0.266 (0.989) |
1 (1.00) |
1 (1.00) |
17q gain | 3 (6%) | 45 |
0.196 (0.988) |
0.241 (0.989) |
0.239 (0.989) |
1 (1.00) |
0.383 (1.00) |
0.11 (0.732) |
0.563 (1.00) |
|
18p gain | 13 (27%) | 35 |
0.0492 (0.589) |
0.291 (0.995) |
0.648 (1.00) |
0.746 (1.00) |
0.377 (1.00) |
0.803 (1.00) |
0.0851 (0.732) |
0.71 (1.00) |
18q gain | 13 (27%) | 35 |
0.0492 (0.589) |
0.291 (0.995) |
0.644 (1.00) |
0.746 (1.00) |
0.377 (1.00) |
0.804 (1.00) |
0.0836 (0.732) |
0.71 (1.00) |
19p gain | 3 (6%) | 45 |
0.445 (1.00) |
0.0844 (0.732) |
1 (1.00) |
0.391 (1.00) |
1 (1.00) |
1 (1.00) |
0.15 (0.834) |
|
19q gain | 3 (6%) | 45 |
0.445 (1.00) |
0.0844 (0.732) |
1 (1.00) |
0.391 (1.00) |
1 (1.00) |
1 (1.00) |
0.15 (0.834) |
|
20p gain | 5 (10%) | 43 |
0.745 (1.00) |
0.636 (1.00) |
0.0538 (0.589) |
1 (1.00) |
0.563 (1.00) |
0.425 (1.00) |
0.587 (1.00) |
|
20q gain | 4 (8%) | 44 |
0.56 (1.00) |
0.255 (0.989) |
0.114 (0.732) |
1 (1.00) |
0.478 (1.00) |
0.66 (1.00) |
0.257 (0.989) |
|
21q gain | 10 (21%) | 38 |
0.977 (1.00) |
0.328 (1.00) |
0.48 (1.00) |
0.307 (1.00) |
0.63 (1.00) |
0.279 (0.989) |
0.779 (1.00) |
0.695 (1.00) |
xp gain | 6 (12%) | 42 |
0.926 (1.00) |
0.64 (1.00) |
0.305 (1.00) |
1 (1.00) |
1 (1.00) |
0.0172 (0.562) |
1 (1.00) |
0.0278 (0.589) |
xq gain | 7 (15%) | 41 |
0.935 (1.00) |
0.248 (0.989) |
0.305 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.0285 (0.589) |
1 (1.00) |
0.0552 (0.589) |
1p loss | 3 (6%) | 45 |
0.445 (1.00) |
0.36 (1.00) |
0.587 (1.00) |
1 (1.00) |
0.193 (0.988) |
1 (1.00) |
1 (1.00) |
|
3p loss | 4 (8%) | 44 |
0.502 (1.00) |
0.455 (1.00) |
0.614 (1.00) |
0.488 (1.00) |
0.0949 (0.732) |
0.342 (1.00) |
0.0432 (0.589) |
|
3q loss | 3 (6%) | 45 |
0.561 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.391 (1.00) |
0.0521 (0.589) |
0.319 (1.00) |
0.0127 (0.481) |
|
4p loss | 3 (6%) | 45 |
0.502 (1.00) |
0.327 (1.00) |
0.239 (0.989) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
4q loss | 4 (8%) | 44 |
0.49 (1.00) |
0.455 (1.00) |
0.114 (0.732) |
1 (1.00) |
1 (1.00) |
0.662 (1.00) |
1 (1.00) |
|
6q loss | 7 (15%) | 41 |
0.851 (1.00) |
0.826 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.0839 (0.732) |
0.337 (1.00) |
0.0552 (0.589) |
8p loss | 8 (17%) | 40 |
0.929 (1.00) |
0.782 (1.00) |
0.26 (0.989) |
1 (1.00) |
0.333 (1.00) |
0.741 (1.00) |
0.394 (1.00) |
|
8q loss | 4 (8%) | 44 |
0.402 (1.00) |
0.14 (0.834) |
0.614 (1.00) |
1 (1.00) |
0.259 (0.989) |
1 (1.00) |
0.257 (0.989) |
|
13q loss | 3 (6%) | 45 |
0.527 (1.00) |
0.898 (1.00) |
1 (1.00) |
0.391 (1.00) |
0.0519 (0.589) |
0.32 (1.00) |
0.15 (0.834) |
|
15q loss | 7 (15%) | 41 |
0.22 (0.989) |
0.737 (1.00) |
0.106 (0.732) |
0.573 (1.00) |
1 (1.00) |
1 (1.00) |
0.662 (1.00) |
|
16q loss | 4 (8%) | 44 |
0.435 (1.00) |
0.94 (1.00) |
0.114 (0.732) |
1 (1.00) |
1 (1.00) |
0.223 (0.989) |
0.56 (1.00) |
|
17p loss | 9 (19%) | 39 |
0.186 (0.97) |
0.843 (1.00) |
0.891 (1.00) |
0.151 (0.834) |
0.605 (1.00) |
0.0197 (0.562) |
0.552 (1.00) |
0.00424 (0.312) |
17q loss | 4 (8%) | 44 |
0.47 (1.00) |
0.49 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.00402 (0.312) |
0.346 (1.00) |
0.00254 (0.312) |
|
18p loss | 5 (10%) | 43 |
0.602 (1.00) |
0.853 (1.00) |
0.88 (1.00) |
0.649 (1.00) |
1 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.587 (1.00) |
18q loss | 5 (10%) | 43 |
0.768 (1.00) |
0.166 (0.875) |
1 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.675 (1.00) |
0.0918 (0.732) |
|
22q loss | 3 (6%) | 45 |
0.502 (1.00) |
0.782 (1.00) |
0.239 (0.989) |
1 (1.00) |
1 (1.00) |
0.11 (0.732) |
0.563 (1.00) |
|
xp loss | 5 (10%) | 43 |
0.0498 (0.589) |
0.447 (1.00) |
0.0538 (0.589) |
1 (1.00) |
1 (1.00) |
0.424 (1.00) |
1 (1.00) |
|
xq loss | 4 (8%) | 44 |
0.0045 (0.312) |
1 (1.00) |
0.114 (0.732) |
1 (1.00) |
1 (1.00) |
0.22 (0.989) |
0.56 (1.00) |
P value = 0.00041 (Fisher's exact test), Q value = 0.17
nPatients | DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL) | PRIMARY DLBCL OF THE CNS | PRIMARY MEDIASTINAL (THYMIC) DLBCL |
---|---|---|---|
ALL | 41 | 3 | 4 |
9P GAIN MUTATED | 3 | 0 | 4 |
9P GAIN WILD-TYPE | 38 | 3 | 0 |
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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/DLBC-TP/22516374/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
-
Number of patients = 48
-
Number of significantly arm-level cnvs = 52
-
Number of selected clinical features = 8
-
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.