This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.
Testing the association between copy number variation 20 focal events and 10 clinical features across 36 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 |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
RACE | ||
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 | Fisher's exact test | |
amp 1q22 | 24 (67%) | 12 |
0.267 (0.837) |
0.491 (0.922) |
0.0145 (0.556) |
0.00649 (0.457) |
0.631 (0.967) |
1 (1.00) |
0.481 (0.922) |
0.197 (0.804) |
0.0878 (0.675) |
1 (1.00) |
amp 11q13 3 | 8 (22%) | 28 |
0.031 (0.626) |
0.128 (0.761) |
0.37 (0.852) |
0.563 (0.966) |
0.241 (0.837) |
0.282 (0.837) |
0.709 (1.00) |
0.539 (0.945) |
0.127 (0.761) |
0.0865 (0.675) |
amp 12q13 2 | 10 (28%) | 26 |
0.148 (0.761) |
0.986 (1.00) |
1 (1.00) |
0.396 (0.891) |
1 (1.00) |
1 (1.00) |
0.285 (0.837) |
1 (1.00) |
0.819 (1.00) |
0.00667 (0.457) |
del 1p36 21 | 30 (83%) | 6 |
0.973 (1.00) |
1 (1.00) |
0.181 (0.772) |
0.0711 (0.651) |
1 (1.00) |
1 (1.00) |
0.672 (1.00) |
0.0196 (0.56) |
0.748 (1.00) |
0.186 (0.773) |
del 3p25 3 | 28 (78%) | 8 |
0.289 (0.837) |
0.864 (1.00) |
0.0842 (0.675) |
0.00685 (0.457) |
0.0619 (0.651) |
0.282 (0.837) |
0.709 (1.00) |
0.0716 (0.651) |
1 (1.00) |
0.479 (0.922) |
del 3p13 | 28 (78%) | 8 |
0.489 (0.922) |
0.253 (0.837) |
0.0846 (0.675) |
0.115 (0.761) |
0.241 (0.837) |
0.0519 (0.651) |
0.422 (0.917) |
0.0522 (0.651) |
1 (1.00) |
0.481 (0.922) |
del 4q34 3 | 23 (64%) | 13 |
0.719 (1.00) |
0.152 (0.761) |
0.443 (0.922) |
0.05 (0.651) |
0.35 (0.837) |
1 (1.00) |
0.301 (0.837) |
0.29 (0.837) |
0.334 (0.837) |
0.475 (0.922) |
del 5q13 3 | 8 (22%) | 28 |
0.39 (0.886) |
0.939 (1.00) |
0.333 (0.837) |
1 (1.00) |
0.173 (0.769) |
0.0519 (0.651) |
0.422 (0.917) |
0.0143 (0.556) |
0.803 (1.00) |
0.304 (0.837) |
del 6q13 | 21 (58%) | 15 |
0.836 (1.00) |
0.748 (1.00) |
0.452 (0.922) |
0.459 (0.922) |
0.636 (0.967) |
1 (1.00) |
0.741 (1.00) |
0.408 (0.907) |
0.836 (1.00) |
0.777 (1.00) |
del 9p21 3 | 23 (64%) | 13 |
0.99 (1.00) |
0.934 (1.00) |
0.459 (0.922) |
0.309 (0.837) |
0.35 (0.837) |
0.36 (0.837) |
0.169 (0.768) |
0.811 (1.00) |
0.209 (0.835) |
0.596 (0.966) |
del 9q21 11 | 19 (53%) | 17 |
0.532 (0.945) |
0.0167 (0.556) |
0.567 (0.966) |
0.475 (0.922) |
0.636 (0.967) |
0.152 (0.761) |
1 (1.00) |
0.146 (0.761) |
0.861 (1.00) |
0.232 (0.837) |
del 10q26 12 | 12 (33%) | 24 |
0.813 (1.00) |
0.591 (0.966) |
0.471 (0.922) |
1 (1.00) |
0.296 (0.837) |
0.643 (0.967) |
0.729 (1.00) |
0.351 (0.837) |
0.256 (0.837) |
0.788 (1.00) |
del 11q25 | 13 (36%) | 23 |
0.0259 (0.626) |
0.348 (0.837) |
0.959 (1.00) |
0.242 (0.837) |
1 (1.00) |
1 (1.00) |
0.493 (0.922) |
0.29 (0.837) |
0.599 (0.966) |
1 (1.00) |
del 12q24 13 | 8 (22%) | 28 |
0.472 (0.922) |
0.505 (0.927) |
0.056 (0.651) |
0.484 (0.922) |
0.0619 (0.651) |
0.0313 (0.626) |
0.257 (0.837) |
0.538 (0.945) |
0.178 (0.772) |
1 (1.00) |
del 13q21 32 | 16 (44%) | 20 |
0.261 (0.837) |
0.356 (0.837) |
0.318 (0.837) |
0.244 (0.837) |
0.344 (0.837) |
0.0574 (0.651) |
1 (1.00) |
0.0712 (0.651) |
1 (1.00) |
0.612 (0.967) |
del 14q22 1 | 14 (39%) | 22 |
0.572 (0.966) |
0.685 (1.00) |
0.502 (0.927) |
0.796 (1.00) |
0.147 (0.761) |
0.63 (0.967) |
1 (1.00) |
0.51 (0.927) |
1 (1.00) |
1 (1.00) |
del 14q32 11 | 20 (56%) | 16 |
0.164 (0.761) |
0.962 (1.00) |
0.358 (0.837) |
0.329 (0.837) |
0.148 (0.761) |
0.639 (0.967) |
0.737 (1.00) |
0.0989 (0.695) |
0.598 (0.966) |
0.781 (1.00) |
del 14q32 13 | 20 (56%) | 16 |
0.164 (0.761) |
0.962 (1.00) |
0.356 (0.837) |
0.328 (0.837) |
0.148 (0.761) |
0.639 (0.967) |
0.737 (1.00) |
0.101 (0.695) |
0.598 (0.966) |
0.784 (1.00) |
del 14q32 33 | 20 (56%) | 16 |
0.164 (0.761) |
0.962 (1.00) |
0.358 (0.837) |
0.329 (0.837) |
0.148 (0.761) |
0.639 (0.967) |
0.737 (1.00) |
0.1 (0.695) |
0.596 (0.966) |
0.78 (1.00) |
del 16q23 1 | 7 (19%) | 29 |
0.529 (0.945) |
0.889 (1.00) |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
0.559 (0.966) |
1 (1.00) |
0.715 (1.00) |
0.0573 (0.651) |
0.686 (1.00) |
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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/CHOL-TP/22519029/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/22489349/CHOL-TP.merged_data.txt
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Number of patients = 36
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Number of significantly focal cnvs = 20
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Number of selected clinical features = 10
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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.