A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy

CONCLUSIONS: We demonstrate that saliva-derived canine DNA is suitable for whole-genome sequencing, highlighting the feasibility of client-based sampling. Low-pass sequencing and imputation require caution as incorrect allele assignments result when the subject possesses alleles that are absent in the reference panel. Larger panels have the capacity for greater allelic diversity, which should reduce the potential for imputation error. Although low-pass sequencing can accurately impute allele dosage, we highlight issues with phasing accuracy that impact haplotype-based analyses. Consequently, if accurately phased genotypes are required for analyses, we advocate sequencing at high depth (> 20X).PMID:38216889 | PMC:PMC10785484 | DOI:10.1186/s12711-024-00875-w

Source: Genet Sel Evol - January 12, 2024 Category: Genetics & Stem Cells Authors: David Wragg Wengang Zhang Sarah Peterson Murthy Yerramilli Richard Mellanby Jeffrey J Schoenebeck Dylan N Clements Source Type: research