Phantom epistasis through the lens of genealogies.

ABSTRACT: Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant with a purely additive effect on the phenotype causes the spurious inference of a significant interaction between two single-nucleotide polymorphisms (SNPs). This is more likely to arise when the two SNPs are in relatively close proximity, so while true epistasis between nearby variants could be commonplace, in practice there is no reliable way of telling apart true epistatic signals from false positives. By considering the causes of phantom epistasis from a genealogy-based perspective, we leverage the rich information contained within reconstructed genealogies (in the form of ancestral recombination graphs) to address this problem. We propose a novel method for explicitl

SUBMITTER: Ignatieva A 

PROVIDER: S-EPMC12774852 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature