Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.

ABSTRACT: The search for the underlying genetic contributions to complex traits and diseases relies on accurate genetic data from populations of interest. Outbred populations, like the Diversity Outbred (DO), are commonly genotyped using commercial SNP arrays, such as the Giga Mouse Universal Genotyping Array (GigaMUGA). However, array genotypes are expensive to collect, subject to significant ascertainment bias, and too sparse to capture the genetic structure of highly recombined mouse crosses. We investigated the efficacy of sequencing-based genotyping by comparing genotyping results between the GigaMUGA, double-digest restriction-site associated DNA sequencing (ddRADseq), and low-coverage whole-genome sequencing (lcWGS). We aligned reads at ~ 1× coverage and imputed segregating SNPs from the eigh

SUBMITTER: Widmayer SJ 

PROVIDER: S-EPMC12365916 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature