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PMID: 11779816 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Two-locus sampling distributions and their application.

Genetics ·Vol. 159 ·No. 4 ·2001-12-00 ·Pages 1805-17

Hudson RR

Abstract

Methods of estimating two-locus sample probabilities under a neutral model are extended in several ways. Estimation of sample probabilities is described when the ancestral or derived status of each allele is specified. In addition, probabilities for two-locus diploid samples are provided. A method for using these two-locus probabilities to test whether an observed level of linkage disequilibrium is unusually large or small is described. In addition, properties of a maximum-likelihood estimator of the recombination parameter based on independent linked pairs of sites are obtained. A composite-likelihood estimator, for more than two linked sites, is also examined and found to work as well, or better, than other available ad hoc estimators. Linkage disequilibrium in the Xq28 and Xq25 region of humans is analyzed in a sample of Europeans (CEPH). The estimated recombination parameter is about five times smaller than one would expect under an equilibrium neutral model.

MeSH Terms
Alleles Heterozygote Humans Likelihood Functions Linkage Disequilibrium Models, Genetic Models, Statistical Monte Carlo Method Polymorphism, Genetic Recombination, Genetic X Chromosome
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Hudson R R
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA. [email protected]
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1093/genetics/159.4.1805
Email
[email protected]
Published
2001-12-00
Pages
1805-17
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1461925
Subset
IM
Grants
NHGRI NIH HHS · HG01847 · United States
NHGRI NIH HHS · HG02098 · United States
NHGRI NIH HHS · HG02107 · United States
External Links
PubMed source DOI: 10.1093/genetics/159.4.1805 PMC Full Text View journal details
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