ArticleBulletin of mathematical biology2025
Fast simulation of identity-by-descent segments.
Article in Bulletin of mathematical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Multiple-testing corrections in case-control studies using identity-by-descent segments.American journal of human genetics · 2026Article
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Identity-by-descent segments in large samples.Theoretical population biology · 2025Article
- Multiple-testing corrections in case-control studies using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- Potential and pitfalls of using identity-by-descent for malaria genomic surveillance.Trends in parasitology · 2025Review
- Multiple-testing corrections in selection scans using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
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3 authors.
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Abstract
The worst-case runtime complexity to simulate haplotype segments identical by descent (IBD) is quadratic in sample size. We propose two main techniques to reduce the compute time, both of which are motivated by coalescent and recombination processes. We provide mathematical results that explain why our algorithm should outperform a naive implementation with high probability. In our experiments, we observe average compute times to simulate detectable IBD segments around a locus that scale approximately linearly in sample size and take a couple of seconds for sample sizes that are less than 10,000 diploid individuals. In contrast, we find that existing methods to simulate IBD segments take minutes to hours for sample sizes exceeding a few thousand diploid individuals. When using IBD segments to study recent positive selection around a locus, our efficient simulation algorithm makes feasible statistical inferences, e.g., parametric bootstrapping in analyses of large biobanks, that would be otherwise intractable.
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