Opening the Black Box of Imputation Software to Study the Impact of Reference Panel Composition on Performance.

ABSTRACT: Genotype imputation is widely used to enrich genetic datasets. The operation relies on panels of known reference haplotypes, typically with whole-genome sequencing data. How to choose a reference panel has been widely studied and it is essential to have a panel that is well matched to the individuals who require missing genotype imputation. However, it is broadly accepted that such an imputation panel will have an enhanced performance with the inclusion of diversity (haplotypes from many different populations). We investigate this observation by examining, in fine detail, exactly which reference haplotypes are contributing at different regions of the genome. This is achieved using a novel method of inserting synthetic genetic variation into the reference panel in order to track the perform

SUBMITTER: Dekeyser T 

PROVIDER: S-EPMC9956390 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature