ArticleNature communications2025
Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Evaluating confounding in rare variant genome wide association studies.Nature communications · 2026Article
- Graph transformer for ancient ancestry inference.bioRxiv : the preprint server for biology · 2026Article
- KANN: estimation of genetic ancestry profiles by nearest neighbor regression.Nucleic acids research · 2026Article
- Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations.Nature communications · 2026Article
- An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data.Journal of computational biology : a journal of computational molecular cell biology · 2026Article
- From individuals to ancestries: Towards attributing trait variation to haplotypes.PLoS genetics · 2025Article
- Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.Nature communications · 2025Article
- DynamicbioRxiv : the preprint server for biology · 2025Article
- Haplotype Matching with GBWT for Pangenome Graphs.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
4 authors.
Funding
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 that haplotypes better represent ancestries than principal components, whilst linkage-disequilibrium of ancestry identifies signals of recent changes to population-specific selection for many genomic regions associated with immune responses, suggesting avenues for understanding the pathogen-immune system interplay on a historical timescale.
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Registered trials
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