Pathways of Distinction Analysis: a new technique for multi-SNP analysis of GWAS data

TL;DR

Pathways of Distinction Analysis (PoDA) is a novel multi-SNP GWAS method that identifies disease-related pathways by analyzing system-level genetic differences, including epistatic interactions, without requiring independent SNP effects.

Contribution

PoDA introduces a new approach for pathway-based GWAS analysis that captures complex interactions and system-level differences, surpassing traditional single-SNP methods.

Findings

PoDA identified pathways associated with breast and liver cancer.

The method revealed pathways with genomic differences contributing to disease susceptibility.

PoDA demonstrated improved detection of pathway-level effects over existing techniques.

Abstract

Genome-wide association studies have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However, while typical GWAS analysis techniques treat markers individually, complex diseases are unlikely to have a single causative gene. There is thus a pressing need for multi-SNP analysis methods that can reveal system-level differences in cases and controls. Here, we present a novel multi-SNP GWAS analysis method called Pathways of Distinction Analysis (PoDA). The method uses GWAS data and known pathway-gene and gene-SNP associations to identify pathways that permit, ideally, the distinction of cases from controls. The technique is based upon the hypothesis that if a pathway is related to disease risk, cases will appear more similar to other cases than to controls for the SNPs associated with that pathway. By systematically applying the method to all pathways of potential interest, we can identify those for which the hypothesis holds true, i.e., pathways containing SNPs for which the samples exhibit greater within-class similarity than across classes. Importantly, PoDA improves on existing single-SNP and SNP-set enrichment analyses in that it does not require the SNPs in a pathway to exhibit independent main effects. This permits PoDA to reveal pathways in which epistatic interactions drives risk. In this paper, we detail the PoDA method and apply it to two GWA studies: one of breast cancer, and the other of liver cancer. The results obtained strongly suggest that there exist pathway-wide genomic differences that contribute to disease susceptibility. PoDA thus provides an analytical tool that is complementary to existing techniques and has the power to enrich our understanding of disease genomics at the systems-level.