Abstract
To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method – Primo – for integrative analysis of GWAS summary statistics with multiple sets of omics QTL summary statistics from different cellular conditions or studies. Primo examines SNPs’ association patterns to complex and omics traits. In gene regions harboring known susceptibility loci, Primo performs conditional association analysis to account for linkage disequilibrium. Primo allows for unknown study heterogeneity and sample correlations. We show two applications using Primo to examine the molecular mechanisms of known susceptibility loci and to detect and interpret pleiotropic effects.
Footnotes
Abbreviations
- GWAS
- genome-wide association studies
- SNP
- single nucleotide polymorphism
- QTL
- quantitative trait locus
- eQTL
- expression quantitative trait locus
- meQTL
- methylation quantitative trait locus
- pQTL
- protein quantitative trait locus
- Primo
- Package in R for Integrative Multi-Omics association analysis
- LD
- linkage disequilibrium
- GTEx
- Genotype-Tissue Expression project
- TCGA
- The Cancer Genome Atlas
- BCAC
- Breast Canter Association Consortium
- FDR
- false discovery rate
- BMI
- body mass index
Copyright
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