ArticleAmerican journal of human genetics2006
A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data.
Article in American journal of human genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Recombination plasticity in response to temperature variation in reptiles.PLoS genetics · 2025Article
- Inferring recombination patterns in African populations.Human molecular genetics · 2021Review
- A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks.Advances in neural information processing systems · 2018Article
- Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.G3 (Bethesda, Md.) · 2016Article
- The 8p23 inversion polymorphism determines local recombination heterogeneity across human populations.Genome biology and evolution · 2014Article
- Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots.Proteome science · 2012Article
- Female-to-male breeding ratio in modern humans-an analysis based on historical recombinations.American journal of human genetics · 2010Article
- Contrasting methods of quantifying fine structure of human recombination.Annual review of genomics and human genetics · 2010Review
- Estimation of fine-scale recombination intensity variation in the white-echinus interval of D. melanogaster.Journal of molecular evolution · 2009Article
- Population genomic inference of recombination rates and hotspots.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Bioinformatics in China: a personal perspective.PLoS computational biology · 2008Review
- Fraction of informative recombinations: a heuristic approach to analyze recombination rates.Genetics · 2008Article
- FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3.Bioinformation · 2008Article
- Recombination rate estimation in the presence of hotspots.Genome research · 2007Article
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3 authors.
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Abstract
Computational detection of recombination hotspots from population polymorphism data is important both for understanding the nature of recombination and for applications such as association studies. We propose a new method for this task based on a multiple-hotspot model and an (approximate) log-likelihood ratio test. A truncated, weighted pairwise log-likelihood is introduced and applied to the calculation of the log-likelihood ratio, and a forward-selection procedure is adopted to search for the optimal hotspot predictions. The method shows a relatively high power with a low false-positive rate in detecting multiple hotspots in simulation data and has a performance comparable to the best results of leading computational methods in experimental data for which recombination hotspots have been characterized by sperm-typing experiments. The method can be applied to both phased and unphased data directly, with a very fast computational speed. We applied the method to the 10 500-kb regions of the HapMap ENCODE data and found 172 hotspots among the three populations, with average hotspot width of 2.4 kb. By comparisons with the simulation data, we found some evidence that hotspots are not all identical across populations. The correlations between detected hotspots and several genomic characteristics were examined. In particular, we observed that DNaseI-hypersensitive sites are enriched in hotspots, suggesting the existence of human beta hotspots similar to those found in yeast.
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