[Popgenlunch] Sharon Browning's talk

Joe Felsenstein joe at gs.washington.edu
Wed May 23 17:34:10 PDT 2007

Bruce Weir has forwarded me the following title and abstract for Sharon
Browning's talk next Tuesday, the 29th:

"Haplotype inference using an empirical linkage disequilibrium model."

In this talk I will address the problem of haplotype inference, with
particular reference to the large whole genome association data sets
that are currently being generated. Haplotypes are useful because they
are the natural biological unit, and inferred haplotypes are needed by
several good methods for testing for genetic association.

A person inherits one copy of each autosomal chromosome from each of
his/her parents. Genotypic data give unordered pairs of alleles
(variants) at genetic markers. The sequence of alleles along a single
chromosome copy is a ?haplotype?. Alleles that are located at
neighboring positions on a chromosome tend to be correlated (this is
known as linkage disequilibrium), thus it is possible to statistically
infer haplotypes from the genotype data.

I will review several existing methods for haplotype inference, and
present a new method based on an empirical model for linkage
disequilibrium. This new method has proved to be much faster than
competing existing methods, which is important for application to
large-scale data sets, and has accuracy comparable with the most
accurate of existing methods.

Joe Felsenstein joe at gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA

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