Multivariate Functional Regression Models for Epistasis Analysis

TL;DR

This paper introduces a multivariate functional regression model for joint epistasis analysis across multiple traits, significantly improving detection power over traditional single-trait methods.

Contribution

It formulates a novel multiple functional regression approach for detecting gene-gene interactions in multiple phenotypes, filling a key gap in genetic analysis methods.

Findings

Higher power in detecting epistasis with joint analysis

Identification of 136 gene pairs with significant epistasis

Demonstrated effectiveness on real exome sequencing data

Abstract

To date, most genetic analyses of phenotypes have focused on analyzing single traits or, analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power, and hold the key to understanding the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two gens in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large scale simulations to calculate its type I error rates for testing interaction between two genes with multiple phenotypes and to compare its power with multivariate pair-wise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate its performance, the MFRG for epistasis analysis is applied to five phenotypes and exome sequence data from the NHLBI Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 136 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has much higher power to detect interaction than the interaction analysis of single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.