This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 60 focal events and 5 clinical features across 56 patients, no significant finding detected with Q value < 0.25.
-
No focal cnvs related to clinical features.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RACE | ||
nCNV (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
amp 1q22 | 42 (75%) | 14 |
0.602 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.354 (1.00) |
0.236 (1.00) |
amp 2p14 | 28 (50%) | 28 |
0.263 (1.00) |
0.768 (1.00) |
0.00226 (0.339) |
0.379 (1.00) |
0.147 (1.00) |
amp 2q13 | 29 (52%) | 27 |
0.729 (1.00) |
0.345 (1.00) |
0.0281 (0.895) |
1 (1.00) |
0.594 (1.00) |
amp 3p25 1 | 20 (36%) | 36 |
0.202 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.94 (1.00) |
0.452 (1.00) |
amp 3q26 2 | 37 (66%) | 19 |
0.62 (1.00) |
0.382 (1.00) |
1 (1.00) |
0.48 (1.00) |
0.757 (1.00) |
amp 4p16 3 | 25 (45%) | 31 |
0.18 (1.00) |
0.343 (1.00) |
0.174 (1.00) |
0.0629 (0.943) |
0.357 (1.00) |
amp 5p13 2 | 26 (46%) | 30 |
0.791 (1.00) |
0.902 (1.00) |
0.412 (1.00) |
0.838 (1.00) |
0.316 (1.00) |
amp 6p24 2 | 37 (66%) | 19 |
0.166 (1.00) |
0.0963 (1.00) |
1 (1.00) |
1 (1.00) |
0.759 (1.00) |
amp 8p11 21 | 33 (59%) | 23 |
0.84 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.613 (1.00) |
0.405 (1.00) |
amp 8q11 23 | 38 (68%) | 18 |
0.934 (1.00) |
0.226 (1.00) |
0.146 (1.00) |
0.471 (1.00) |
0.257 (1.00) |
amp 8q24 21 | 42 (75%) | 14 |
0.361 (1.00) |
0.902 (1.00) |
0.76 (1.00) |
0.0685 (0.978) |
0.282 (1.00) |
amp 8q24 21 | 40 (71%) | 16 |
0.107 (1.00) |
0.574 (1.00) |
0.372 (1.00) |
0.198 (1.00) |
0.148 (1.00) |
amp 10q22 2 | 26 (46%) | 30 |
0.463 (1.00) |
0.111 (1.00) |
0.786 (1.00) |
0.698 (1.00) |
0.887 (1.00) |
amp 11q13 1 | 19 (34%) | 37 |
0.339 (1.00) |
0.446 (1.00) |
0.384 (1.00) |
0.939 (1.00) |
0.5 (1.00) |
amp 12q12 | 22 (39%) | 34 |
0.477 (1.00) |
0.512 (1.00) |
0.776 (1.00) |
0.78 (1.00) |
0.107 (1.00) |
amp 12q15 | 17 (30%) | 39 |
0.966 (1.00) |
0.108 (1.00) |
0.554 (1.00) |
0.76 (1.00) |
0.147 (1.00) |
amp 13q31 3 | 25 (45%) | 31 |
0.733 (1.00) |
0.276 (1.00) |
0.579 (1.00) |
0.337 (1.00) |
0.781 (1.00) |
amp 16p11 2 | 20 (36%) | 36 |
0.407 (1.00) |
0.134 (1.00) |
0.582 (1.00) |
0.559 (1.00) |
0.76 (1.00) |
amp 17q12 | 27 (48%) | 29 |
0.801 (1.00) |
0.889 (1.00) |
0.166 (1.00) |
0.698 (1.00) |
1 (1.00) |
amp 17q25 1 | 32 (57%) | 24 |
0.78 (1.00) |
0.0588 (0.929) |
0.587 (1.00) |
0.834 (1.00) |
0.595 (1.00) |
amp 19p13 2 | 19 (34%) | 37 |
0.902 (1.00) |
0.762 (1.00) |
0.772 (1.00) |
0.516 (1.00) |
0.499 (1.00) |
amp 19q12 | 45 (80%) | 11 |
0.484 (1.00) |
0.82 (1.00) |
0.482 (1.00) |
0.622 (1.00) |
0.684 (1.00) |
amp 20q11 21 | 48 (86%) | 8 |
0.474 (1.00) |
0.535 (1.00) |
0.269 (1.00) |
0.38 (1.00) |
0.0491 (0.895) |
amp 20q11 21 | 48 (86%) | 8 |
0.797 (1.00) |
0.87 (1.00) |
0.715 (1.00) |
0.182 (1.00) |
0.0488 (0.895) |
amp xp11 21 | 28 (50%) | 28 |
0.672 (1.00) |
0.0136 (0.626) |
1 (1.00) |
0.268 (1.00) |
1 (1.00) |
del 1p36 21 | 19 (34%) | 37 |
0.87 (1.00) |
0.148 (1.00) |
0.557 (1.00) |
0.0362 (0.895) |
1 (1.00) |
del 2q22 1 | 11 (20%) | 45 |
0.0537 (0.895) |
0.877 (1.00) |
0.308 (1.00) |
0.00092 (0.276) |
0.555 (1.00) |
del 3p14 2 | 37 (66%) | 19 |
0.866 (1.00) |
0.979 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.0507 (0.895) |
del 3q13 31 | 22 (39%) | 34 |
0.262 (1.00) |
0.425 (1.00) |
0.416 (1.00) |
0.47 (1.00) |
0.462 (1.00) |
del 4q22 1 | 37 (66%) | 19 |
0.952 (1.00) |
0.562 (1.00) |
0.384 (1.00) |
0.319 (1.00) |
0.76 (1.00) |
del 4q34 3 | 37 (66%) | 19 |
0.392 (1.00) |
0.646 (1.00) |
0.772 (1.00) |
0.148 (1.00) |
0.227 (1.00) |
del 5q12 1 | 26 (46%) | 30 |
0.665 (1.00) |
0.324 (1.00) |
0.0519 (0.895) |
0.515 (1.00) |
1 (1.00) |
del 6q26 | 10 (18%) | 46 |
0.496 (1.00) |
0.872 (1.00) |
1 (1.00) |
0.361 (1.00) |
0.516 (1.00) |
del 7q11 22 | 12 (21%) | 44 |
0.16 (1.00) |
0.889 (1.00) |
0.512 (1.00) |
0.643 (1.00) |
1 (1.00) |
del 7q36 2 | 20 (36%) | 36 |
0.267 (1.00) |
0.669 (1.00) |
0.776 (1.00) |
0.49 (1.00) |
0.518 (1.00) |
del 8p21 3 | 32 (57%) | 24 |
0.583 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.0897 (1.00) |
del 9p23 | 34 (61%) | 22 |
0.671 (1.00) |
0.0167 (0.626) |
0.776 (1.00) |
0.214 (1.00) |
0.881 (1.00) |
del 9q21 13 | 39 (70%) | 17 |
0.309 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.707 (1.00) |
0.412 (1.00) |
del 9q33 3 | 39 (70%) | 17 |
0.138 (1.00) |
0.284 (1.00) |
0.136 (1.00) |
0.567 (1.00) |
0.867 (1.00) |
del 10q23 31 | 20 (36%) | 36 |
0.619 (1.00) |
0.532 (1.00) |
0.772 (1.00) |
0.561 (1.00) |
0.234 (1.00) |
del 11q14 1 | 26 (46%) | 30 |
0.866 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.207 (1.00) |
0.881 (1.00) |
del 11q23 2 | 26 (46%) | 30 |
0.577 (1.00) |
0.246 (1.00) |
1 (1.00) |
0.205 (1.00) |
0.444 (1.00) |
del 12q23 1 | 20 (36%) | 36 |
0.0807 (1.00) |
0.031 (0.895) |
0.582 (1.00) |
0.821 (1.00) |
1 (1.00) |
del 12q24 31 | 20 (36%) | 36 |
0.133 (1.00) |
0.244 (1.00) |
1 (1.00) |
0.939 (1.00) |
1 (1.00) |
del 13q12 11 | 30 (54%) | 26 |
0.363 (1.00) |
0.344 (1.00) |
0.785 (1.00) |
0.335 (1.00) |
0.601 (1.00) |
del 13q14 2 | 32 (57%) | 24 |
0.947 (1.00) |
0.567 (1.00) |
0.579 (1.00) |
0.582 (1.00) |
0.6 (1.00) |
del 14q21 1 | 28 (50%) | 28 |
0.263 (1.00) |
0.38 (1.00) |
0.098 (1.00) |
0.161 (1.00) |
0.246 (1.00) |
del 15q15 1 | 43 (77%) | 13 |
0.325 (1.00) |
0.217 (1.00) |
0.212 (1.00) |
0.783 (1.00) |
1 (1.00) |
del 16p13 3 | 33 (59%) | 23 |
0.954 (1.00) |
0.967 (1.00) |
0.416 (1.00) |
0.834 (1.00) |
0.0149 (0.626) |
del 16q23 1 | 39 (70%) | 17 |
0.0161 (0.626) |
0.239 (1.00) |
0.136 (1.00) |
0.0148 (0.626) |
0.293 (1.00) |
del 17p13 1 | 42 (75%) | 14 |
0.685 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.922 (1.00) |
0.173 (1.00) |
del 17q21 31 | 27 (48%) | 29 |
0.293 (1.00) |
0.48 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.193 (1.00) |
del 18q22 2 | 26 (46%) | 30 |
0.481 (1.00) |
0.278 (1.00) |
1 (1.00) |
0.315 (1.00) |
0.0132 (0.626) |
del 19p13 3 | 47 (84%) | 9 |
0.403 (1.00) |
0.269 (1.00) |
1 (1.00) |
0.372 (1.00) |
0.0349 (0.895) |
del 19p13 3 | 44 (79%) | 12 |
0.818 (1.00) |
0.749 (1.00) |
0.735 (1.00) |
0.384 (1.00) |
0.0437 (0.895) |
del 19q13 33 | 17 (30%) | 39 |
0.377 (1.00) |
0.837 (1.00) |
0.766 (1.00) |
0.81 (1.00) |
0.483 (1.00) |
del 20p12 1 | 9 (16%) | 47 |
0.723 (1.00) |
0.688 (1.00) |
0.487 (1.00) |
0.665 (1.00) |
0.373 (1.00) |
del 22q13 31 | 40 (71%) | 16 |
0.826 (1.00) |
0.388 (1.00) |
0.766 (1.00) |
0.382 (1.00) |
1 (1.00) |
del xp21 1 | 18 (32%) | 38 |
0.379 (1.00) |
0.304 (1.00) |
1 (1.00) |
0.105 (1.00) |
1 (1.00) |
del xq25 | 23 (41%) | 33 |
0.952 (1.00) |
0.297 (1.00) |
0.588 (1.00) |
0.833 (1.00) |
0.768 (1.00) |
-
Copy number data file = all_lesions.txt from GISTIC pipeline
-
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/22533741/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UCS-TP/22507158/UCS-TP.merged_data.txt
-
Number of patients = 56
-
Number of significantly focal cnvs = 60
-
Number of selected clinical features = 5
-
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.