title: PExFInS: An Integrative Post-GWAS Explorer for Functional Indels and SNPs.
abstract: Expression quantitative trait loci (eQTLs) mapping and linkage disequilibrium (LD) analysis have been widely employed to interpret findings of genome-wide association studies (GWAS). With the availability of deep sequencing data of 423 lymphoblastoid cell lines (LCLs) from six global populations and the microarray expression data, we performed eQTL analysis, identified more than 228 K SNP cis-eQTLs and 21 K indel cis-eQTLs and generated a LCL cis-eQTL database. We demonstrate that the percentages of population-shared and population-specific cis-eQTLs are comparable; while indel cis-eQTLs in the population-specific subsection make more contribution to gene expression variations than those in the population-shared subsection. We found cis-eQTLs, especially the population-shared cis-eQTLs are significantly enriched toward transcription start site. Moreover, the National Human Genome Research Institute cataloged GWAS SNPs are enriched for LCL cis-eQTLs. Specifically, 32.8% GWAS SNPs are LCL cis-eQTLs, among which 12.5% can be tagged by indel cis-eQTLs, suggesting the fundamental contribution of indel cis-eQTLs to GWAS association signals. To search for functional indels and SNPs tagging GWAS SNPs, a pipeline Post-GWAS Explorer for Functional Indels and SNPs (PExFInS) has been developed, integrating LD analysis, functional annotation from public databases, cis-eQTL mapping with our LCL cis-eQTL database and other published cis-eQTL datasets.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Zhongshan
authors.initials: Z
authors.lastname: Cheng
authors.affiliation: Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam Road, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam Road, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Hin
authors.initials: H
authors.lastname: Chu
authors.affiliation: Department of Biochemistry, The University of Hong Kong, Pokfulam Road, Hong Kong.|Center for Genomic Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Cun
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Biochemistry, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: You-Qiang
authors.initials: YQ
authors.lastname: Song
authors.affiliation: Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam Road, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam Road, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Microbiology, The University of Hong Kong, Pokfulam Road, Hong Kong.|State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam Road, Hong Kong.|Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam Road, Hong Kong.|Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam Road, Hong Kong.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D030541:Databases, Genetic; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006801:Humans; D054643:INDEL Mutation; D007938:Leukemia / Q000208:ethnology / Q000235:genetics* / Q000473:pathology; D008214:Lymphocytes / Q000378:metabolism / Q000473:pathology; D008223:Lymphoma / Q000208:ethnology / Q000235:genetics* / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D044469:Racial Groups; D012984:Software; D024363:Transcription Initiation Site