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PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs
Zhongshan Cheng1, Hin Chu1,2,3,4, Yanhui Fan5,6
1Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.
Scientific Reports
|November 28, 2015
Summary
This study identifies over 228K SNP cis-eQTLs and 21K indel cis-eQTLs in lymphoblastoid cell lines, revealing their contribution to gene expression and genome-wide association study signals.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- Genome-Wide Association Studies (GWAS) require interpretation of genetic variants.
- Expression quantitative trait loci (eQTL) mapping and linkage disequilibrium (LD) analysis are key tools for this interpretation.
Purpose of the Study:
- To create a comprehensive cis-eQTL database for lymphoblastoid cell lines (LCLs) across global populations.
- To investigate the contribution of single nucleotide polymorphisms (SNPs) and insertion-deletion (indel) cis-eQTLs to gene expression variation and GWAS signals.
Main Methods:
- Performed cis-eQTL analysis on deep sequencing and microarray expression data from 423 LCLs across six populations.
- Generated a LCL cis-eQTL database, including SNP and indel cis-eQTLs.
- Developed the Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) pipeline integrating LD, functional annotation, and eQTL data.
Main Results:
- Identified >228K SNP cis-eQTLs and >21K indel cis-eQTLs.
- Found comparable percentages of population-shared and population-specific cis-eQTLs, with specific indels contributing more to expression variation.
- Observed significant enrichment of cis-eQTLs, particularly population-shared ones, near transcription start sites.
- Demonstrated that 32.8% of GWAS SNPs are LCL cis-eQTLs, with 12.5% tagged by indel cis-eQTLs.
Conclusions:
- Indel cis-eQTLs play a fundamental role in GWAS association signals.
- The developed PExFInS pipeline aids in identifying functional indels and SNPs associated with GWAS findings.
- The LCL cis-eQTL database provides a valuable resource for interpreting genetic variation.
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