ArticleGenetics2004
Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 5 of them syntheses that pooled it.
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Who cites it
29 citing papers in PubMed, 5 syntheses or guidelines pooled it.
- Identification of a novel susceptibility locus at 13q34 and refinement of the 20p12.2 region as a multi-signal locus associated with bladder cancer risk in individuals of European ancestry.Human molecular genetics · 2016Pooled it
- Genome-wide association study identifies multiple susceptibility loci for diffuse large B cell lymphoma.Nature genetics · 2014Pooled it
- Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.Nature genetics · 2014Pooled it
- Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.Nature genetics · 2013Pooled it
- A genome-wide association study of bladder cancer identifies a new susceptibility locus within SLC14A1, a urea transporter gene on chromosome 18q12.3.Human molecular genetics · 2011Pooled it
- Personalized genome structure via single gamete sequencing.Genome biology · 2021Review
- Two-Locus Likelihoods Under Variable Population Size and Fine-Scale Recombination Rate Estimation.Genetics · 2016Article
- The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations.Genome biology and evolution · 2014Article
- Genome-wide association study identifies multiple loci associated with bladder cancer risk.Human molecular genetics · 2014Article
- Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia.Nature genetics · 2012Article
- Fixation probability in a two-locus model by the ancestral recombination-selection graph.Genetics · 2012Article
- Fine-scale population recombination rates, hotspots, and correlates of recombination in the Medicago truncatula genome.Genome biology and evolution · 2012Article
- A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.Nature genetics · 2010Article
- Human population differentiation is strongly correlated with local recombination rate.PLoS genetics · 2010Article
- Contrasting methods of quantifying fine structure of human recombination.Annual review of genomics and human genetics · 2010Review
- The dynamic genetic repertoire of microbial communities.FEMS microbiology reviews · 2009Review
- Confounding between recombination and selection, and the Ped/Pop method for detecting selection.Genome research · 2008Article
- Phylogenetic detection of recombination with a Bayesian prior on the distance between trees.PloS one · 2008Article
- Fraction of informative recombinations: a heuristic approach to analyze recombination rates.Genetics · 2008Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There has been considerable recent interest in understanding the way in which recombination rates vary over small physical distances, and the extent of recombination hotspots, in various genomes. Here we adapt, apply, and assess the power of recently developed coalescent-based approaches to estimating recombination rates from sequence polymorphism data. We apply full-likelihood estimation to study rate variation in and around a well-characterized recombination hotspot in humans, in the beta-globin gene cluster, and show that it provides similar estimates, consistent with those from sperm studies, from two populations deliberately chosen to have different demographic and selectional histories. We also demonstrate how approximate-likelihood methods can be used to detect local recombination hotspots from genomic-scale SNP data. In a simulation study based on 80 100-kb regions, these methods detect 43 out of 60 hotspots (ranging from 1 to 2 kb in size), with only two false positives out of 2000 subregions that were tested for the presence of a hotspot. Our study suggests that new computational tools for sophisticated analysis of population diversity data are valuable for hotspot detection and fine-scale mapping of local recombination rates.
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