Open Access
Genet. Sel. Evol.
Volume 40, Number 1, January-February 2008
Page(s) 25 - 36
Published online 21 December 2007
Genet. Sel. Evol. 40 (2008) 25-36
DOI: 10.1051/gse:2007033

A rapid conditional enumeration haplotyping method in pedigrees

Guimin Gao1 and Ina Hoeschele2

1  Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
2  Virginia Bioinformatics Institute and Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, USA

(Received 19 February 2007; accepted 27 July 2007; published online 21 December 2007)

Abstract - Haplotyping in pedigrees provides valuable information for genetic studies (e.g., linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of the conditional probability of a haplotype configuration to the largest conditional probability of all haplotype configurations in order to eliminate those configurations with relatively low conditional probabilities. The new algorithm is much more efficient than our previous method and the widely used software SimWalk2.

Key words: haplotyping / pedigree / conditional probability / likelihood

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© INRA, EDP Sciences 2008