This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 46 focal events and 12 clinical features across 90 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 |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
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 | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
amp 1q22 | 17 (19%) | 73 |
0.00231 (0.425) |
0.595 (1.00) |
0.686 (1.00) |
0.687 (1.00) |
0.679 (1.00) |
0.779 (1.00) |
0.506 (1.00) |
1 (1.00) |
0.132 (0.776) |
0.0645 (0.736) |
0.496 (1.00) |
0.613 (1.00) |
amp 4p16 3 | 41 (46%) | 49 |
0.136 (0.776) |
0.789 (1.00) |
0.934 (1.00) |
0.972 (1.00) |
0.75 (1.00) |
0.505 (1.00) |
0.599 (1.00) |
0.215 (0.85) |
0.139 (0.776) |
0.877 (1.00) |
1 (1.00) |
0.693 (1.00) |
amp 4q35 1 | 29 (32%) | 61 |
0.0564 (0.736) |
0.604 (1.00) |
0.214 (0.85) |
0.333 (1.00) |
0.159 (0.838) |
0.164 (0.843) |
0.402 (1.00) |
0.257 (0.891) |
0.463 (1.00) |
0.246 (0.882) |
1 (1.00) |
1 (1.00) |
amp 5p15 33 | 65 (72%) | 25 |
0.967 (1.00) |
0.675 (1.00) |
0.582 (1.00) |
0.592 (1.00) |
0.721 (1.00) |
0.469 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.805 (1.00) |
1 (1.00) |
0.0827 (0.736) |
0.403 (1.00) |
amp 5q35 3 | 63 (70%) | 27 |
0.206 (0.843) |
0.685 (1.00) |
0.77 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.878 (1.00) |
1 (1.00) |
0.694 (1.00) |
amp 6p21 31 | 19 (21%) | 71 |
0.778 (1.00) |
0.00597 (0.61) |
0.864 (1.00) |
0.635 (1.00) |
0.68 (1.00) |
0.188 (0.843) |
0.104 (0.748) |
1 (1.00) |
0.0424 (0.736) |
0.407 (1.00) |
0.104 (0.748) |
0.374 (1.00) |
amp 6q24 3 | 19 (21%) | 71 |
0.977 (1.00) |
0.355 (1.00) |
0.723 (1.00) |
0.365 (1.00) |
0.115 (0.748) |
0.792 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.406 (1.00) |
0.0912 (0.748) |
0.0897 (0.748) |
0.645 (1.00) |
amp 7p22 1 | 54 (60%) | 36 |
0.579 (1.00) |
0.683 (1.00) |
0.0915 (0.748) |
0.0966 (0.748) |
0.305 (0.959) |
1 (1.00) |
0.295 (0.945) |
0.788 (1.00) |
0.602 (1.00) |
0.475 (1.00) |
1 (1.00) |
1 (1.00) |
amp 9q31 3 | 34 (38%) | 56 |
0.00944 (0.651) |
0.861 (1.00) |
0.0264 (0.736) |
0.0776 (0.736) |
0.0413 (0.736) |
0.498 (1.00) |
0.174 (0.843) |
0.563 (1.00) |
0.0682 (0.736) |
0.206 (0.843) |
1 (1.00) |
0.439 (1.00) |
amp 12q14 1 | 70 (78%) | 20 |
0.538 (1.00) |
0.614 (1.00) |
0.89 (1.00) |
0.877 (1.00) |
0.683 (1.00) |
0.791 (1.00) |
0.528 (1.00) |
1 (1.00) |
0.674 (1.00) |
0.625 (1.00) |
0.546 (1.00) |
0.171 (0.843) |
amp 14q11 2 | 27 (30%) | 63 |
0.388 (1.00) |
0.067 (0.736) |
0.385 (1.00) |
0.394 (1.00) |
0.0585 (0.736) |
0.631 (1.00) |
0.254 (0.891) |
0.518 (1.00) |
0.439 (1.00) |
0.0567 (0.736) |
0.649 (1.00) |
0.407 (1.00) |
amp 16p13 3 | 50 (56%) | 40 |
0.205 (0.843) |
0.968 (1.00) |
0.798 (1.00) |
0.925 (1.00) |
1 (1.00) |
0.119 (0.749) |
0.425 (1.00) |
1 (1.00) |
0.736 (1.00) |
0.168 (0.843) |
0.72 (1.00) |
1 (1.00) |
amp 16q22 1 | 56 (62%) | 34 |
0.905 (1.00) |
0.68 (1.00) |
0.686 (1.00) |
0.661 (1.00) |
0.737 (1.00) |
0.257 (0.891) |
0.0303 (0.736) |
0.773 (1.00) |
0.217 (0.85) |
0.321 (0.988) |
0.0526 (0.736) |
1 (1.00) |
amp 16q24 2 | 49 (54%) | 41 |
0.18 (0.843) |
0.903 (1.00) |
0.739 (1.00) |
0.526 (1.00) |
1 (1.00) |
0.187 (0.843) |
0.188 (0.843) |
1 (1.00) |
1 (1.00) |
0.515 (1.00) |
0.731 (1.00) |
0.699 (1.00) |
amp 17q25 3 | 18 (20%) | 72 |
0.186 (0.843) |
0.232 (0.853) |
0.789 (1.00) |
0.495 (1.00) |
0.68 (1.00) |
0.588 (1.00) |
0.754 (1.00) |
0.136 (0.776) |
0.877 (1.00) |
0.265 (0.891) |
0.472 (1.00) |
0.664 (1.00) |
amp 19p13 12 | 58 (64%) | 32 |
0.212 (0.85) |
0.129 (0.776) |
0.137 (0.776) |
0.188 (0.843) |
0.484 (1.00) |
1 (1.00) |
0.0576 (0.736) |
1 (1.00) |
0.814 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.23 (0.853) |
amp 19q12 | 56 (62%) | 34 |
0.0515 (0.736) |
0.0457 (0.736) |
0.0813 (0.736) |
0.117 (0.748) |
0.737 (1.00) |
0.498 (1.00) |
0.0303 (0.736) |
1 (1.00) |
0.366 (1.00) |
0.979 (1.00) |
1 (1.00) |
0.226 (0.853) |
amp xp11 22 | 49 (54%) | 41 |
0.838 (1.00) |
0.906 (1.00) |
0.671 (1.00) |
0.858 (1.00) |
0.502 (1.00) |
0.505 (1.00) |
0.6 (1.00) |
0.213 (0.85) |
0.785 (1.00) |
0.399 (1.00) |
1 (1.00) |
0.0399 (0.736) |
amp xq28 | 46 (51%) | 44 |
0.401 (1.00) |
0.707 (1.00) |
0.881 (1.00) |
0.936 (1.00) |
1 (1.00) |
1 (1.00) |
0.441 (1.00) |
0.804 (1.00) |
0.376 (1.00) |
0.554 (1.00) |
0.742 (1.00) |
1 (1.00) |
del 1p36 23 | 38 (42%) | 52 |
0.187 (0.843) |
0.49 (1.00) |
0.613 (1.00) |
0.467 (1.00) |
0.736 (1.00) |
0.823 (1.00) |
1 (1.00) |
0.598 (1.00) |
0.296 (0.945) |
0.939 (1.00) |
0.507 (1.00) |
0.407 (1.00) |
del 1q43 | 18 (20%) | 72 |
0.915 (1.00) |
0.948 (1.00) |
0.636 (1.00) |
0.181 (0.843) |
0.399 (1.00) |
0.782 (1.00) |
0.745 (1.00) |
0.0536 (0.736) |
0.948 (1.00) |
0.269 (0.891) |
1 (1.00) |
0.587 (1.00) |
del 2q22 1 | 18 (20%) | 72 |
0.0679 (0.736) |
0.948 (1.00) |
0.436 (1.00) |
0.736 (1.00) |
1 (1.00) |
1 (1.00) |
0.331 (1.00) |
0.0525 (0.736) |
0.948 (1.00) |
0.814 (1.00) |
1 (1.00) |
1 (1.00) |
del 2q37 3 | 21 (23%) | 69 |
0.446 (1.00) |
0.8 (1.00) |
0.184 (0.843) |
0.977 (1.00) |
1 (1.00) |
1 (1.00) |
0.549 (1.00) |
0.0802 (0.736) |
0.849 (1.00) |
0.77 (1.00) |
1 (1.00) |
0.277 (0.909) |
del 3q13 31 | 25 (28%) | 65 |
0.116 (0.748) |
0.474 (1.00) |
0.361 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.0464 (0.736) |
0.55 (1.00) |
0.693 (1.00) |
0.217 (0.85) |
0.883 (1.00) |
0.315 (0.978) |
0.374 (1.00) |
del 4q34 3 | 25 (28%) | 65 |
0.00224 (0.425) |
0.479 (1.00) |
0.0985 (0.748) |
0.0861 (0.748) |
1 (1.00) |
1 (1.00) |
0.562 (1.00) |
0.691 (1.00) |
0.00774 (0.61) |
0.611 (1.00) |
0.628 (1.00) |
1 (1.00) |
del 4q34 3 | 28 (31%) | 62 |
0.015 (0.736) |
0.717 (1.00) |
0.206 (0.843) |
0.168 (0.843) |
1 (1.00) |
0.815 (1.00) |
0.251 (0.891) |
0.158 (0.838) |
0.0344 (0.736) |
0.361 (1.00) |
0.65 (1.00) |
0.412 (1.00) |
del 4q35 1 | 30 (33%) | 60 |
0.0131 (0.722) |
0.535 (1.00) |
0.262 (0.891) |
0.205 (0.843) |
1 (1.00) |
0.485 (1.00) |
0.0241 (0.736) |
0.394 (1.00) |
0.082 (0.736) |
0.716 (1.00) |
0.686 (1.00) |
0.669 (1.00) |
del 6p24 3 | 20 (22%) | 70 |
0.22 (0.85) |
0.197 (0.843) |
0.224 (0.853) |
0.756 (1.00) |
1 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.0712 (0.736) |
0.263 (0.891) |
0.854 (1.00) |
1 (1.00) |
1 (1.00) |
del 6q26 | 21 (23%) | 69 |
0.102 (0.748) |
0.116 (0.748) |
0.0218 (0.736) |
0.0456 (0.736) |
0.697 (1.00) |
0.301 (0.954) |
1 (1.00) |
0.0826 (0.736) |
0.126 (0.776) |
0.671 (1.00) |
1 (1.00) |
1 (1.00) |
del 7q36 3 | 11 (12%) | 79 |
0.00753 (0.61) |
0.402 (1.00) |
0.134 (0.776) |
0.0454 (0.736) |
1 (1.00) |
1 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.0241 (0.736) |
0.896 (1.00) |
0.338 (1.00) |
1 (1.00) |
del 9p23 | 24 (27%) | 66 |
0.0638 (0.736) |
0.749 (1.00) |
1 (1.00) |
0.744 (1.00) |
0.444 (1.00) |
0.803 (1.00) |
0.231 (0.853) |
0.685 (1.00) |
0.731 (1.00) |
0.0961 (0.748) |
1 (1.00) |
0.412 (1.00) |
del 9p21 3 | 27 (30%) | 63 |
0.0544 (0.736) |
0.35 (1.00) |
0.957 (1.00) |
0.948 (1.00) |
0.27 (0.891) |
1 (1.00) |
0.154 (0.832) |
0.52 (1.00) |
0.912 (1.00) |
0.065 (0.736) |
0.697 (1.00) |
0.669 (1.00) |
del 10q23 1 | 11 (12%) | 79 |
0.856 (1.00) |
0.242 (0.876) |
0.868 (1.00) |
0.518 (1.00) |
0.607 (1.00) |
0.742 (1.00) |
1 (1.00) |
0.0525 (0.736) |
0.106 (0.748) |
0.338 (1.00) |
0.367 (1.00) |
1 (1.00) |
del 11p15 5 | 27 (30%) | 63 |
0.292 (0.944) |
0.609 (1.00) |
0.495 (1.00) |
0.981 (1.00) |
0.139 (0.776) |
0.23 (0.853) |
0.771 (1.00) |
0.231 (0.853) |
0.583 (1.00) |
0.147 (0.804) |
1 (1.00) |
1 (1.00) |
del 11q14 1 | 25 (28%) | 65 |
0.373 (1.00) |
0.202 (0.843) |
0.117 (0.748) |
0.427 (1.00) |
1 (1.00) |
0.322 (0.988) |
1 (1.00) |
0.128 (0.776) |
0.593 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 12q14 2 | 5 (6%) | 85 |
0.0311 (0.736) |
0.311 (0.97) |
0.391 (1.00) |
0.471 (1.00) |
1 (1.00) |
0.656 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.504 (1.00) |
1 (1.00) |
1 (1.00) |
|
del 13q14 2 | 42 (47%) | 48 |
0.108 (0.748) |
0.269 (0.891) |
0.201 (0.843) |
0.69 (1.00) |
0.75 (1.00) |
0.828 (1.00) |
1 (1.00) |
0.22 (0.85) |
0.908 (1.00) |
0.939 (1.00) |
0.497 (1.00) |
0.694 (1.00) |
del 14q21 2 | 20 (22%) | 70 |
0.619 (1.00) |
0.58 (1.00) |
0.813 (1.00) |
0.894 (1.00) |
0.11 (0.748) |
0.599 (1.00) |
0.339 (1.00) |
0.0711 (0.736) |
1 (1.00) |
0.0645 (0.736) |
0.233 (0.853) |
0.344 (1.00) |
del 16p13 3 | 7 (8%) | 83 |
0.114 (0.748) |
0.386 (1.00) |
0.615 (1.00) |
0.538 (1.00) |
0.584 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0744 (0.736) |
1 (1.00) |
0.0815 (0.736) |
0.134 (0.776) |
del 16q23 1 | 11 (12%) | 79 |
0.00333 (0.459) |
0.108 (0.748) |
0.357 (1.00) |
0.157 (0.838) |
0.35 (1.00) |
1 (1.00) |
0.68 (1.00) |
1 (1.00) |
0.0461 (0.736) |
0.173 (0.843) |
1 (1.00) |
1 (1.00) |
del 17q11 2 | 24 (27%) | 66 |
0.0277 (0.736) |
0.975 (1.00) |
0.19 (0.843) |
0.0989 (0.748) |
0.706 (1.00) |
0.0243 (0.736) |
0.759 (1.00) |
0.683 (1.00) |
0.105 (0.748) |
0.583 (1.00) |
1 (1.00) |
1 (1.00) |
del 17q21 31 | 26 (29%) | 64 |
0.0328 (0.736) |
0.742 (1.00) |
0.38 (1.00) |
0.286 (0.93) |
1 (1.00) |
0.055 (0.736) |
1 (1.00) |
0.516 (1.00) |
0.198 (0.843) |
0.747 (1.00) |
1 (1.00) |
0.658 (1.00) |
del 17q24 2 | 24 (27%) | 66 |
0.0198 (0.736) |
0.971 (1.00) |
0.0116 (0.71) |
0.306 (0.959) |
0.26 (0.891) |
0.0802 (0.736) |
0.377 (1.00) |
0.684 (1.00) |
0.0402 (0.736) |
0.187 (0.843) |
1 (1.00) |
1 (1.00) |
del 18q21 2 | 36 (40%) | 54 |
0.84 (1.00) |
0.556 (1.00) |
0.582 (1.00) |
0.919 (1.00) |
0.735 (1.00) |
0.118 (0.748) |
0.59 (1.00) |
0.435 (1.00) |
0.601 (1.00) |
0.504 (1.00) |
0.282 (0.92) |
1 (1.00) |
del 20p12 1 | 12 (13%) | 78 |
0.116 (0.748) |
0.357 (1.00) |
0.454 (1.00) |
0.425 (1.00) |
0.35 (1.00) |
0.206 (0.843) |
0.69 (1.00) |
1 (1.00) |
0.001 (0.425) |
0.173 (0.843) |
0.365 (1.00) |
0.203 (0.843) |
del 22q12 1 | 50 (56%) | 40 |
0.0645 (0.736) |
0.0943 (0.748) |
0.183 (0.843) |
0.145 (0.801) |
0.745 (1.00) |
0.267 (0.891) |
0.793 (1.00) |
1 (1.00) |
0.786 (1.00) |
0.26 (0.891) |
1 (1.00) |
0.243 (0.876) |
-
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/ACC-TP/19778622/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/19775006/ACC-TP.merged_data.txt
-
Number of patients = 90
-
Number of significantly focal cnvs = 46
-
Number of selected clinical features = 12
-
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.