| Title: | Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses |
| Journal: | Nature Communications |
| Published: | 20 Mar 2025 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/40113767/ |
| DOI: | https://doi.org/10.1038/s41467-025-57601-3 |
Publication 15553
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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.</p>
12 Keywords
- Algorithms
- Genetics, Population
- Genome, Human
- Genome-Wide Association Study
- Haplotypes
- Humans
- Immunity
- Linkage Disequilibrium
- Models, Genetic
- Polymorphism, Single Nucleotide
- Selection, Genetic
- United Kingdom
4 Authors
- Yaoling Yang
- Richard Durbin
- Astrid K. N. Iversen
- Daniel J. Lawson
1 Application
| Application ID | Title |
|---|---|
| 81499 | Using human genetics to develop insight into putative causal relationships between modifiable exposures and disease endpoints |
Enabling scientific discoveries that improve human health