ArticleAmerican journal of human genetics1999
Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping.
Article in American journal of human genetics, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers.
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Who cites it
80 citing papers in PubMed.
- Sephardic origins revealed for rare skin disorder, recessive dystrophic epidermolysis bullosa, in individuals carrying the unique c.6527insC mutation.Journal of medical genetics · 2025Article
- Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data.NAR genomics and bioinformatics · 2025Article
- Tree-based QTL mapping with expected local genetic relatedness matrices.American journal of human genetics · 2023Article
- Tree-based QTL mapping with expected local genetic relatedness matrices.bioRxiv : the preprint server for biology · 2023Article
- Review
- TheCancers · 2021Article
- Estimating Time to the Common Ancestor for a Beneficial Allele.Molecular biology and evolution · 2018Article
- Testing association and maternally mediated genetic effects with the principal component analysis in case-parents studies.BMC genetics · 2016Article
- A hidden Markov model for investigating recent positive selection through haplotype structure.Theoretical population biology · 2015Article
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- A founder mutation in PET100 causes isolated complex IV deficiency in Lebanese individuals with Leigh syndrome.American journal of human genetics · 2014Article
- Review
- A fast expectation-maximum algorithm for fine-scale QTL mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Article
- An ancient founder mutation in PROKR2 impairs human reproduction.Human molecular genetics · 2012Article
- High-resolution genetic mapping with pooled sequencing.BMC bioinformatics · 2012Article
- Article
- A mutation in the Golgi Qb-SNARE gene GOSR2 causes progressive myoclonus epilepsy with early ataxia.American journal of human genetics · 2011Article
- A novel approach for haplotype-based association analysis using family data.BMC bioinformatics · 2010Article
- A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity.Annals of human genetics · 2009Article
20 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Linkage disequilibrium (LD) is of great interest for gene mapping and the study of population history. We propose a multilocus model for LD, based on the decay of haplotype sharing (DHS). The DHS model is most appropriate when the LD in which one is interested is due to the introduction of a variant on an ancestral haplotype, with recombinations in succeeding generations resulting in preservation of only a small region of the ancestral haplotype around the variant. This is generally the scenario of interest for gene mapping by LD. The DHS parameter is a measure of LD that can be interpreted as the expected genetic distance to which the ancestral haplotype is preserved, or, equivalently, 1/(time in generations to the ancestral haplotype). The method allows for multiple origins of alleles and for mutations, and it takes into account missing observations and ambiguities in haplotype determination, via a hidden Markov model. Whereas most commonly used measures of LD apply to pairs of loci, the DHS measure is designed for application to the densely mapped haplotype data that are increasingly available. The DHS method explicitly models the dependence among multiple tightly linked loci on a chromosome. When the assumptions about population structure are sufficiently tractable, the estimate of LD is obtained by maximum likelihood. For more-complicated models of population history, we find means and covariances based on the model and solve a quasi-score estimating equation. Simulations show that this approach works extremely well both for estimation of LD and for fine mapping. We apply the DHS method to published data sets for cystic fibrosis and progressive myoclonus epilepsy.
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