Next-Gen GWAS: Full 2D Epistatic Interaction Maps Retrieve Part of Missing Heritability and Improve Phenotypic Prediction

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2024 Mar 25

PMID 38523316

Authors

Clement Carre

Jean Baptiste Carluer

Christian Chaux

Chad Estoup-Streiff

Nicolas Roche

Eric Hosy

Andre Mas

Gabriel Krouk

Affiliations

Soon will be listed here.

Abstract

The problem of missing heritability requires the consideration of genetic interactions among different loci, called epistasis. Current GWAS statistical models require years to assess the entire combinatorial epistatic space for a single phenotype. We propose Next-Gen GWAS (NGG) that evaluates over 60 billion single nucleotide polymorphism combinatorial first-order interactions within hours. We apply NGG to Arabidopsis thaliana providing two-dimensional epistatic maps at gene resolution. We demonstrate on several phenotypes that a large proportion of the missing heritability can be retrieved, that it indeed lies in epistatic interactions, and that it can be used to improve phenotype prediction.

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