iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies

Constanza Rojo, Qi Zhang, Sündüz Keleş

Research output: Contribution to journalArticle

Abstract

Genome-wide association studies (GWAS) have successfully identified thousands of genetic variants contributing to disease and other phenotypes. However, significant obstacles hamper our ability to elucidate causal variants, identify genes affected by causal variants, and characterize the mechanisms by which genotypes influence phenotypes. The increasing availability of genome-wide functional annotation data is providing unique opportunities to incorporate prior information into the analysis of GWAS to better understand the impact of variants on disease etiology. Although there have been many advances in incorporating prior information into prioritization of trait-associated variants in GWAS, functional annotation data have played a secondary role in the joint analysis of GWAS and molecular (i.e., expression) quantitative trait loci (eQTL) data in assessing evidence for association. To address this, we develop a novel mediation framework, iFunMed, to integrate GWAS and eQTL data with the utilization of publicly available functional annotation data. iFunMed extends the scope of standard mediation analysis by incorporating information from multiple genetic variants at a time and leveraging variant-level summary statistics. Data-driven computational experiments convey how informative annotations improve single-nucleotide polymorphism (SNP) selection performance while emphasizing robustness of iFunMed to noninformative annotations. Application to Framingham Heart Study data indicates that iFunMed is able to boost detection of SNPs with mediation effects that can be attributed to regulatory mechanisms.

Original languageEnglish (US)
Pages (from-to)742-760
Number of pages19
JournalGenetic Epidemiology
Volume43
Issue number7
DOIs
StatePublished - Oct 1 2019

Fingerprint

Quantitative Trait Loci
Genome-Wide Association Study
Single Nucleotide Polymorphism
Phenotype
Genotype
Genome
Genes
Data Curation

Keywords

  • expression quantitative trait locus
  • functional annotation
  • genome-wide association studies
  • mediation analysis
  • variational expectation-maximization

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

Cite this

iFunMed : Integrative functional mediation analysis of GWAS and eQTL studies. / Rojo, Constanza; Zhang, Qi; Keleş, Sündüz.

In: Genetic Epidemiology, Vol. 43, No. 7, 01.10.2019, p. 742-760.

Research output: Contribution to journalArticle

Rojo, Constanza ; Zhang, Qi ; Keleş, Sündüz. / iFunMed : Integrative functional mediation analysis of GWAS and eQTL studies. In: Genetic Epidemiology. 2019 ; Vol. 43, No. 7. pp. 742-760.
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