Correlation between copy number variation genes (focal events) and selected clinical features
Cholangiocarcinoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1M61J89
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1M61J89
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 23 focal events and 8 clinical features across 36 patients, no significant finding detected with Q value < 0.25.

- No focal cnvs related to clinical features.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 23 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

|  | Clinical Features | Time to Death | YEARS TO BIRTH | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | 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
amp 1p22 3 | 15 (42%) | 21 | 0.547 (0.966) | 0.205 (0.857) | 0.21 (0.857) | 0.372 (0.879) | 0.148 (0.82) | 1 (1.00) | 0.175 (0.82) | 1 (1.00)
amp 1q22 | 24 (67%) | 12 | 0.182 (0.82) | 0.47 (0.908) | 0.0141 (0.438) | 0.00679 (0.416) | 0.631 (0.966) | 1 (1.00) | 0.481 (0.908) | 1 (1.00)
amp 11q13 3 | 8 (22%) | 28 | 0.0683 (0.606) | 0.128 (0.82) | 0.373 (0.879) | 0.564 (0.966) | 0.241 (0.857) | 0.282 (0.879) | 0.709 (1.00) | 0.086 (0.633)
amp 12q13 2 | 10 (28%) | 26 | 0.0115 (0.438) | 0.986 (1.00) | 1 (1.00) | 0.398 (0.904) | 1 (1.00) | 1 (1.00) | 0.285 (0.879) | 0.00624 (0.416)
del 1p36 21 | 30 (83%) | 6 | 0.926 (1.00) | 0.966 (1.00) | 0.182 (0.82) | 0.0692 (0.606) | 1 (1.00) | 1 (1.00) | 0.672 (0.979) | 0.187 (0.82)
del 3p25 3 | 28 (78%) | 8 | 0.222 (0.857) | 0.834 (1.00) | 0.0834 (0.633) | 0.00638 (0.416) | 0.0619 (0.6) | 0.282 (0.879) | 0.709 (1.00) | 0.478 (0.908)
del 3p13 | 28 (78%) | 8 | 0.512 (0.923) | 0.246 (0.857) | 0.084 (0.633) | 0.116 (0.818) | 0.241 (0.857) | 0.0519 (0.6) | 0.422 (0.908) | 0.476 (0.908)
del 4q34 3 | 23 (64%) | 13 | 0.585 (0.966) | 0.152 (0.82) | 0.444 (0.908) | 0.0498 (0.6) | 0.35 (0.879) | 1 (1.00) | 0.301 (0.879) | 0.477 (0.908)
del 5q13 3 | 8 (22%) | 28 | 0.472 (0.908) | 0.924 (1.00) | 0.334 (0.879) | 1 (1.00) | 0.173 (0.82) | 0.0519 (0.6) | 0.422 (0.908) | 0.305 (0.879)
del 6q13 | 21 (58%) | 15 | 0.646 (0.966) | 0.76 (1.00) | 0.452 (0.908) | 0.458 (0.908) | 0.636 (0.966) | 1 (1.00) | 0.741 (1.00) | 0.779 (1.00)
del 6q25 3 | 25 (69%) | 11 | 0.483 (0.908) | 0.236 (0.857) | 0.676 (0.979) | 0.79 (1.00) | 1 (1.00) | 1 (1.00) | 0.483 (0.908) | 0.187 (0.82)
del 8p23 1 | 13 (36%) | 23 | 0.277 (0.879) | 0.382 (0.891) | 0.0782 (0.633) | 0.0167 (0.438) | 0.631 (0.966) | 0.63 (0.966) | 0.169 (0.82) | 1 (1.00)
del 9p21 3 | 23 (64%) | 13 | 0.618 (0.966) | 0.921 (1.00) | 0.458 (0.908) | 0.309 (0.879) | 0.35 (0.879) | 0.36 (0.879) | 0.169 (0.82) | 0.596 (0.966)
del 9q21 11 | 19 (53%) | 17 | 0.398 (0.904) | 0.0167 (0.438) | 0.567 (0.966) | 0.476 (0.908) | 0.636 (0.966) | 0.152 (0.82) | 1 (1.00) | 0.231 (0.857)
del 10q26 12 | 12 (33%) | 24 | 0.781 (1.00) | 0.568 (0.966) | 0.47 (0.908) | 1 (1.00) | 0.296 (0.879) | 0.643 (0.966) | 0.729 (1.00) | 0.788 (1.00)
del 11q25 | 13 (36%) | 23 | 0.0535 (0.6) | 0.339 (0.879) | 0.96 (1.00) | 0.243 (0.857) | 1 (1.00) | 1 (1.00) | 0.493 (0.917) | 1 (1.00)
del 12q24 13 | 8 (22%) | 28 | 0.517 (0.923) | 0.505 (0.92) | 0.0554 (0.6) | 0.484 (0.908) | 0.0619 (0.6) | 0.0313 (0.6) | 0.257 (0.876) | 1 (1.00)
del 13q21 32 | 16 (44%) | 20 | 0.226 (0.857) | 0.372 (0.879) | 0.315 (0.879) | 0.247 (0.857) | 0.344 (0.879) | 0.0574 (0.6) | 1 (1.00) | 0.613 (0.966)
del 14q22 1 | 14 (39%) | 22 | 0.653 (0.969) | 0.673 (0.979) | 0.502 (0.92) | 0.798 (1.00) | 0.147 (0.82) | 0.63 (0.966) | 1 (1.00) | 1 (1.00)
del 14q32 12 | 20 (56%) | 16 | 0.0432 (0.6) | 0.949 (1.00) | 0.358 (0.879) | 0.329 (0.879) | 0.148 (0.82) | 0.639 (0.966) | 0.737 (1.00) | 0.782 (1.00)
del 14q32 11 | 20 (56%) | 16 | 0.0432 (0.6) | 0.949 (1.00) | 0.358 (0.879) | 0.329 (0.879) | 0.148 (0.82) | 0.639 (0.966) | 0.737 (1.00) | 0.78 (1.00)
del 14q32 33 | 20 (56%) | 16 | 0.0432 (0.6) | 0.949 (1.00) | 0.356 (0.879) | 0.329 (0.879) | 0.148 (0.82) | 0.639 (0.966) | 0.737 (1.00) | 0.781 (1.00)
del 16q23 1 | 7 (19%) | 29 | 0.954 (1.00) | 0.889 (1.00) | 0.824 (1.00) | 1 (1.00) | 1 (1.00) | 0.559 (0.966) | 1 (1.00) | 0.684 (0.984)

Methods & Data
Input

- 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/CHOL-TP/15082395/transformed.cor.cli.txt

- Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/15076818/CHOL-TP.merged_data.txt

- Number of patients = 36

- Number of significantly focal cnvs = 23

- Number of selected clinical features = 8

- Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

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

Fisher's exact test

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

Q value calculation

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.

Download Results

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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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