Dataset Information

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types.

ABSTRACT: Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of cancer samples. Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identified 5 606 570 eQTL-gene pairs in the cis-eQTL analysis and 231 210 eQTL-gene pairs in the trans-eQTL analysis. We further performed survival analysis and identified 22 212 eQTLs associated with patient overall survival. Furthermore, we linked the eQTLs to genome-wide association studies (GWAS) data and identified 337 131 eQTLs that overlap with existing GWAS loci. We developed PancanQTL, a user-friendly database (http://bioinfo.life.hust.edu.cn/PancanQTL/), to store cis-eQTLs, trans-eQTLs, survival-associated eQTLs and GWAS-related eQTLs to enable searching, browsing and downloading. PancanQTL could help the research community understand the effects of inherited variants in tumorigenesis and development.

SUBMITTER: Gong J

PROVIDER: S-EPMC5753226 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types.

Gong Jing J Mei Shufang S Liu Chunjie C Xiang Yu Y Ye Youqiong Y Zhang Zhao Z Feng Jing J Liu Renyan R Diao Lixia L Guo An-Yuan AY Miao Xiaoping X Han Leng L

Nucleic acids research 20180101 D1

Expression quantitative trait locus (eQTL) analysis, which links variations in gene expression to genotypes, is essential to understanding gene regulation and to interpreting disease-associated loci. Currently identified eQTLs are mainly in samples of blood and other normal tissues. However, no database comprehensively provides eQTLs in large number of cancer samples. Using the genotype and expression data of 9196 tumor samples in 33 cancer types from The Cancer Genome Atlas (TCGA), we identifie ...[more]

PMID: 29036324

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Project description:BackgroundMapping expression quantitative trait loci (eQTLs) has provided insight into gene regulation. Compared to cis-eQTLs, the regulatory mechanisms of trans-eQTLs are less known. Previous studies suggest that trans-eQTLs may regulate expression of remote genes by altering the expression of nearby genes. Trans-association has been studied in the mediation analysis with a single mediator. However, prior applications with one mediator are prone to model misspecification due to correlations between genes. Motivated from the observation that trans-eQTLs are more likely to associate with more than one cis-gene than randomly selected SNPs in the GTEx dataset, we developed a computational method to identify trans-eQTLs that are mediated by multiple mediators.ResultsWe proposed two hypothesis tests for testing the total mediation effect (TME) and the component-wise mediation effects (CME), respectively. We demonstrated in simulation studies that the type I error rates were controlled in both tests despite model misspecification. The TME test was more powerful than the CME test when the two mediation effects are in the same direction, while the CME test was more powerful than the TME test when the two mediation effects are in opposite direction. Multiple mediator analysis had increased power to detect mediated trans-eQTLs, especially in large samples. In the HapMap3 data, we identified 11 mediated trans-eQTLs that were not detected by the single mediator analysis in the combined samples of African populations. Moreover, the mediated trans-eQTLs in the HapMap3 samples are more likely to be trait-associated SNPs. In terms of computation, although there is no limit in the number of mediators in our model, analysis takes more time when adding additional mediators. In the analysis of the HapMap3 samples, we included at most 5 cis-gene mediators. Majority of the trios we considered have one or two mediators.ConclusionsTrans-eQTLs are more likely to associate with multiple cis-genes than randomly selected SNPs. Mediation analysis with multiple mediators improves power of identification of mediated trans-eQTLs, especially in large samples.

Dataset Information

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types.

Publications

PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types.

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