Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.

ABSTRACT: Increasingly efficient methods for inferring the ancestral origin of genome regions are needed to gain insights into genetic function and history as biobanks grow in scale. Here we describe two near-linear time algorithms to learn ancestry harnessing the strengths of a Positional Burrows-Wheeler Transform. SparsePainter is a faster, sparse replacement of previous model-based 'chromosome painting' algorithms to identify recently shared haplotypes, whilst PBWTpaint uses further approximations to obtain lightning-fast estimation optimized for genome-wide relatedness estimation. The computational efficiency gains of these tools for fine-scale local ancestry inference offer the possibility to analyse large-scale genomic datasets using different approaches. Application to the UK Biobank shows th

SUBMITTER: Yang Y 

PROVIDER: S-EPMC11926123 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature