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Open Access

A rapid conditional enumeration haplotyping method in pedigrees

Genetics Selection Evolution200840:25

https://doi.org/10.1186/1297-9686-40-1-25

Received: 19 February 2007

Accepted: 27 July 2007

Published: 15 January 2008

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.

Keywords

haplotypingpedigreeconditional probabilitylikelihood

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Authors’ Affiliations

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

Copyright

© INRA, EDP Sciences 2008

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