Estimation of population parameters and recombination rates from single nucleotide polymorphisms

Authors
Citation
R. Nielsen, Estimation of population parameters and recombination rates from single nucleotide polymorphisms, GENETICS, 154(2), 2000, pp. 931-942
Citations number
25
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biology,"Molecular Biology & Genetics
Journal title
GENETICS
ISSN journal
0016-6731 → ACNP
Volume
154
Issue
2
Year of publication
2000
Pages
931 - 942
Database
ISI
SICI code
0016-6731(200002)154:2<931:EOPPAR>2.0.ZU;2-W
Abstract
Some general likelihood and Bayesian methods for analyzing single nucleotid e polymorphisms (SNPs) are presented. First, an efficient method for estima ting demographic parameters from SNPs in linkage equilibrium is derived. Th e method is applied in the estimation of growth rates of a human population based on 37 SNP loci. It is demonstrated how ascertainment biases, due to biased sampling of loci, can be avoided, at least in some cases, by appropr iate conditioning: when calculating the likelihood function. Second, a Mark ov chain Monte Carl (MCMC) method for analyzing linked SNPs is del eloped. This method call be used for Bayesian and likelihood inference on linked SN Ps. The utility of the method is illustrated by estimating recombination ra tes in a human data set containing 17 SNPs and 60 individuals. Both methods are based on assumptions of low mutation rates.