multi-GPA-Tree: Statistical Approach for Pleiotropy Informed and Functional Annotation Tree Guided Prioritization of GWAS Results

TL;DR

The paper introduces multi-GPA-Tree, a novel statistical method that leverages pleiotropy and functional annotations to improve GWAS result prioritization and interpretability for complex traits.

Contribution

It presents a new tree-based approach that simultaneously identifies SNPs associated with multiple traits and elucidates their functional mechanisms, outperforming existing methods.

Findings

Multi-GPA-Tree outperforms existing methods in simulation studies.

It successfully identifies shared genetic factors across traits.

The method reveals functional annotation patterns linked to risk SNPs.

Abstract

Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), most with small or moderate effect sizes, making them difficult to detect. Second, many complex traits share a common genetic basis due to `pleiotropy' and and though few methods consider it, leveraging pleiotropy can improve statistical power to detect genotype-trait associations with weaker effect sizes. Third, currently available statistical methods are limited in explaining the functional mechanisms through which genetic variants are associated with specific or multiple traits. We propose multi-GPA-Tree to address these challenges. The multi-GPA-Tree approach can identify risk SNPs associated with single as well as multiple traits while also identifying the combinations of functional annotations that can explain the mechanisms through which risk-associated SNPs are linked with the traits. First, we implemented simulation studies to evaluate the proposed multi-GPA-Tree method and compared its performance with an existing statistical approach.The results indicate that multi-GPA-Tree outperforms the existing statistical approach in detecting risk-associated SNPs for multiple traits. Second, we applied multi-GPA-Tree to a systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and to a Crohn's disease (CD) and ulcertive colitis (UC) GWAS, and functional annotation data including GenoSkyline and GenoSkylinePlus. Our results demonstrate that multi-GPA-Tree can be a powerful tool that improves association mapping while facilitating understanding of the underlying genetic architecture of complex traits and potential mechanisms linking risk-associated SNPs with complex traits.