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 8 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 |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
GENDER | 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 | |
amp 1q22 | 17 (19%) | 73 |
0.00287 (0.471) |
0.595 (1.00) |
0.682 (1.00) |
0.689 (1.00) |
0.679 (1.00) |
0.779 (1.00) |
0.498 (1.00) |
0.613 (1.00) |
amp 4p16 3 | 41 (46%) | 49 |
0.207 (0.876) |
0.789 (1.00) |
0.934 (1.00) |
0.973 (1.00) |
0.75 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.693 (1.00) |
amp 4q35 1 | 29 (32%) | 61 |
0.0403 (0.73) |
0.604 (1.00) |
0.213 (0.891) |
0.332 (1.00) |
0.159 (0.876) |
0.164 (0.876) |
1 (1.00) |
1 (1.00) |
amp 5p15 33 | 65 (72%) | 25 |
0.97 (1.00) |
0.675 (1.00) |
0.586 (1.00) |
0.593 (1.00) |
0.721 (1.00) |
0.469 (1.00) |
0.082 (0.744) |
0.403 (1.00) |
amp 5q35 3 | 63 (70%) | 27 |
0.175 (0.876) |
0.685 (1.00) |
0.767 (1.00) |
0.905 (1.00) |
1 (1.00) |
0.631 (1.00) |
1 (1.00) |
0.694 (1.00) |
amp 6p21 31 | 19 (21%) | 71 |
0.651 (1.00) |
0.00597 (0.549) |
0.863 (1.00) |
0.636 (1.00) |
0.68 (1.00) |
0.188 (0.876) |
0.103 (0.744) |
0.374 (1.00) |
amp 6q24 3 | 19 (21%) | 71 |
0.9 (1.00) |
0.355 (1.00) |
0.722 (1.00) |
0.366 (1.00) |
0.115 (0.744) |
0.792 (1.00) |
0.0901 (0.744) |
0.645 (1.00) |
amp 7p22 1 | 54 (60%) | 36 |
0.667 (1.00) |
0.683 (1.00) |
0.0921 (0.744) |
0.098 (0.744) |
0.305 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
amp 9q31 3 | 34 (38%) | 56 |
0.0104 (0.568) |
0.861 (1.00) |
0.0241 (0.73) |
0.0781 (0.744) |
0.0413 (0.73) |
0.498 (1.00) |
1 (1.00) |
0.439 (1.00) |
amp 12q14 1 | 70 (78%) | 20 |
0.569 (1.00) |
0.614 (1.00) |
0.887 (1.00) |
0.875 (1.00) |
0.683 (1.00) |
0.791 (1.00) |
0.543 (1.00) |
0.171 (0.876) |
amp 14q11 2 | 27 (30%) | 63 |
0.504 (1.00) |
0.067 (0.744) |
0.384 (1.00) |
0.392 (1.00) |
0.0585 (0.744) |
0.631 (1.00) |
0.649 (1.00) |
0.407 (1.00) |
amp 16p13 3 | 50 (56%) | 40 |
0.279 (0.968) |
0.968 (1.00) |
0.798 (1.00) |
0.923 (1.00) |
1 (1.00) |
0.119 (0.744) |
0.72 (1.00) |
1 (1.00) |
amp 16q22 1 | 56 (62%) | 34 |
0.74 (1.00) |
0.68 (1.00) |
0.688 (1.00) |
0.658 (1.00) |
0.737 (1.00) |
0.257 (0.963) |
0.0519 (0.744) |
1 (1.00) |
amp 16q24 2 | 49 (54%) | 41 |
0.118 (0.744) |
0.903 (1.00) |
0.739 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.187 (0.876) |
0.731 (1.00) |
0.699 (1.00) |
amp 17q25 3 | 18 (20%) | 72 |
0.335 (1.00) |
0.232 (0.907) |
0.789 (1.00) |
0.49 (1.00) |
0.68 (1.00) |
0.588 (1.00) |
0.473 (1.00) |
0.664 (1.00) |
amp 19p13 12 | 58 (64%) | 32 |
0.277 (0.968) |
0.129 (0.792) |
0.137 (0.8) |
0.189 (0.876) |
0.484 (1.00) |
1 (1.00) |
1 (1.00) |
0.23 (0.907) |
amp 19q12 | 56 (62%) | 34 |
0.0804 (0.744) |
0.0457 (0.73) |
0.082 (0.744) |
0.116 (0.744) |
0.737 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.226 (0.907) |
amp xp11 22 | 49 (54%) | 41 |
0.727 (1.00) |
0.906 (1.00) |
0.671 (1.00) |
0.857 (1.00) |
0.502 (1.00) |
0.505 (1.00) |
1 (1.00) |
0.0399 (0.73) |
amp xq28 | 46 (51%) | 44 |
0.315 (1.00) |
0.707 (1.00) |
0.884 (1.00) |
0.935 (1.00) |
1 (1.00) |
1 (1.00) |
0.744 (1.00) |
1 (1.00) |
del 1p36 23 | 38 (42%) | 52 |
0.176 (0.876) |
0.49 (1.00) |
0.619 (1.00) |
0.469 (1.00) |
0.736 (1.00) |
0.823 (1.00) |
0.507 (1.00) |
0.407 (1.00) |
del 1q43 | 18 (20%) | 72 |
0.953 (1.00) |
0.948 (1.00) |
0.636 (1.00) |
0.178 (0.876) |
0.399 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.587 (1.00) |
del 2q22 1 | 18 (20%) | 72 |
0.0804 (0.744) |
0.948 (1.00) |
0.433 (1.00) |
0.737 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 2q37 3 | 21 (23%) | 69 |
0.489 (1.00) |
0.8 (1.00) |
0.182 (0.876) |
0.978 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.277 (0.968) |
del 3q13 31 | 25 (28%) | 65 |
0.0865 (0.744) |
0.474 (1.00) |
0.362 (1.00) |
0.657 (1.00) |
1 (1.00) |
0.0464 (0.73) |
0.316 (1.00) |
0.374 (1.00) |
del 4q34 3 | 25 (28%) | 65 |
0.00237 (0.471) |
0.479 (1.00) |
0.0991 (0.744) |
0.0866 (0.744) |
1 (1.00) |
1 (1.00) |
0.628 (1.00) |
1 (1.00) |
del 4q34 3 | 28 (31%) | 62 |
0.0359 (0.73) |
0.717 (1.00) |
0.207 (0.876) |
0.166 (0.876) |
1 (1.00) |
0.815 (1.00) |
0.647 (1.00) |
0.412 (1.00) |
del 4q35 1 | 30 (33%) | 60 |
0.0124 (0.572) |
0.535 (1.00) |
0.265 (0.963) |
0.204 (0.876) |
1 (1.00) |
0.485 (1.00) |
0.686 (1.00) |
0.669 (1.00) |
del 6p24 3 | 20 (22%) | 70 |
0.224 (0.907) |
0.197 (0.876) |
0.223 (0.907) |
0.756 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 6q26 | 21 (23%) | 69 |
0.109 (0.744) |
0.116 (0.744) |
0.0225 (0.73) |
0.0456 (0.73) |
0.697 (1.00) |
0.301 (1.00) |
1 (1.00) |
1 (1.00) |
del 7q36 3 | 11 (12%) | 79 |
0.00918 (0.568) |
0.402 (1.00) |
0.134 (0.796) |
0.0464 (0.73) |
1 (1.00) |
1 (1.00) |
0.337 (1.00) |
1 (1.00) |
del 9p23 | 24 (27%) | 66 |
0.0476 (0.73) |
0.749 (1.00) |
1 (1.00) |
0.745 (1.00) |
0.444 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.412 (1.00) |
del 9p21 3 | 27 (30%) | 63 |
0.0409 (0.73) |
0.35 (1.00) |
0.956 (1.00) |
0.948 (1.00) |
0.27 (0.963) |
1 (1.00) |
0.697 (1.00) |
0.669 (1.00) |
del 10q23 1 | 11 (12%) | 79 |
0.767 (1.00) |
0.242 (0.921) |
0.866 (1.00) |
0.514 (1.00) |
0.607 (1.00) |
0.742 (1.00) |
0.366 (1.00) |
1 (1.00) |
del 11p15 5 | 27 (30%) | 63 |
0.379 (1.00) |
0.609 (1.00) |
0.493 (1.00) |
0.982 (1.00) |
0.139 (0.8) |
0.23 (0.907) |
1 (1.00) |
1 (1.00) |
del 11q14 1 | 25 (28%) | 65 |
0.443 (1.00) |
0.202 (0.876) |
0.118 (0.744) |
0.425 (1.00) |
1 (1.00) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
del 12q14 2 | 5 (6%) | 85 |
0.0281 (0.73) |
0.311 (1.00) |
0.392 (1.00) |
0.466 (1.00) |
1 (1.00) |
0.656 (1.00) |
1 (1.00) |
1 (1.00) |
del 13q14 2 | 42 (47%) | 48 |
0.0857 (0.744) |
0.269 (0.963) |
0.204 (0.876) |
0.695 (1.00) |
0.75 (1.00) |
0.828 (1.00) |
0.498 (1.00) |
0.694 (1.00) |
del 14q21 2 | 20 (22%) | 70 |
0.631 (1.00) |
0.58 (1.00) |
0.812 (1.00) |
0.893 (1.00) |
0.11 (0.744) |
0.599 (1.00) |
0.235 (0.909) |
0.344 (1.00) |
del 16p13 3 | 7 (8%) | 83 |
0.106 (0.744) |
0.386 (1.00) |
0.616 (1.00) |
0.539 (1.00) |
0.584 (1.00) |
1 (1.00) |
0.0793 (0.744) |
0.134 (0.796) |
del 16q23 1 | 11 (12%) | 79 |
0.00384 (0.471) |
0.108 (0.744) |
0.359 (1.00) |
0.158 (0.876) |
0.35 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
del 17q11 2 | 24 (27%) | 66 |
0.0306 (0.73) |
0.975 (1.00) |
0.189 (0.876) |
0.0989 (0.744) |
0.706 (1.00) |
0.0243 (0.73) |
1 (1.00) |
1 (1.00) |
del 17q21 31 | 26 (29%) | 64 |
0.0757 (0.744) |
0.742 (1.00) |
0.377 (1.00) |
0.287 (0.98) |
1 (1.00) |
0.055 (0.744) |
1 (1.00) |
0.658 (1.00) |
del 17q24 2 | 24 (27%) | 66 |
0.0238 (0.73) |
0.971 (1.00) |
0.0108 (0.568) |
0.305 (1.00) |
0.26 (0.963) |
0.0802 (0.744) |
1 (1.00) |
1 (1.00) |
del 18q21 2 | 36 (40%) | 54 |
0.725 (1.00) |
0.556 (1.00) |
0.582 (1.00) |
0.92 (1.00) |
0.735 (1.00) |
0.118 (0.744) |
0.282 (0.969) |
1 (1.00) |
del 20p12 1 | 12 (13%) | 78 |
0.113 (0.744) |
0.357 (1.00) |
0.458 (1.00) |
0.426 (1.00) |
0.35 (1.00) |
0.206 (0.876) |
0.362 (1.00) |
0.203 (0.876) |
del 22q12 1 | 50 (56%) | 40 |
0.0993 (0.744) |
0.0943 (0.744) |
0.185 (0.876) |
0.146 (0.827) |
0.745 (1.00) |
0.267 (0.963) |
1 (1.00) |
0.243 (0.921) |
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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/ACC-TP/15081748/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/ACC-TP/15074660/ACC-TP.merged_data.txt
-
Number of patients = 90
-
Number of significantly focal cnvs = 46
-
Number of selected clinical features = 8
-
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.