ArticleAmerican journal of human genetics2024
Modeling recent positive selection using identity-by-descent segments.
Article in American journal of human genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Genomic insights into natural selection in recent human history.Nature reviews. Genetics · 2026Review
- Signatures of pathogen-driven selection and Austronesian gene flow of Papua New Guinea HLA alleles.American journal of human genetics · 2026Article
- 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
- No evidence for disassortative mating based on HLA in a small-scale, endogamous population.bioRxiv : the preprint server for biology · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Accessible, Realistic Genome Simulation with Selection Using stdpopsim.Molecular biology and evolution · 2025Article
- Identity-by-descent segments in large samples.Theoretical population biology · 2025Article
- Estimating gene conversion rates from population data using multi-individual identity by descent.American journal of human genetics · 2025Article
- Accessible, realistic genome simulation with selection using stdpopsim.bioRxiv : the preprint server for biology · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- Multiple-testing corrections in case-control studies using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- Fast simulation of identity-by-descent segments.Bulletin of mathematical 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
- Fast simulation of identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
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3 authors.
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Abstract
Recent positive selection can result in an excess of long identity-by-descent (IBD) haplotype segments overlapping a locus. The statistical methods that we propose here address three major objectives in studying selective sweeps: scanning for regions of interest, identifying possible sweeping alleles, and estimating a selection coefficient s. First, we implement a selection scan to locate regions with excess IBD rates. Second, we estimate the allele frequency and location of an unknown sweeping allele by aggregating over variants that are more abundant in an inferred outgroup with excess IBD rate versus the rest of the sample. Third, we propose an estimator for the selection coefficient and quantify uncertainty using the parametric bootstrap. Comparing against state-of-the-art methods in extensive simulations, we show that our methods are more precise at estimating s when s≥0.015. We also show that our 95% confidence intervals contain s in nearly 95% of our simulations. We apply these methods to study positive selection in European ancestry samples from the Trans-Omics for Precision Medicine project. We analyze eight loci where IBD rates are more than four standard deviations above the genome-wide median, including LCT where the maximum IBD rate is 35 standard deviations above the genome-wide median. Overall, we present robust and accurate approaches to study recent adaptive evolution without knowing the identity of the causal allele or using time series data.
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