TAILIEUCHUNG - Báo cáo sinh học: "A rapid conditional enumeration haplotyping method in pedigrees"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học thế giới đề tài: A rapid conditional enumeration haplotyping method in pedigrees | Genet. Sel. Evol. 40 2008 25-36 INRA EDP Sciences 2008 DOI gse 2007033 Available online at Original article A rapid conditional enumeration haplotyping method in pedigrees Guimin Gao1 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 Abstract - Haplotyping in pedigrees provides valuable information for genetic studies . 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 individualmarker 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 haplotyp-ing 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. haplotyping pedigree conditional probability likelihood 1. INTRODUCTION Haplotyping in a pedigree involves the consideration of the Space of All Consistent Haplotype Configurations SACHC for the pedigree based on all observed data genotype data and pedigree structure . For a larger pedigree with a larger number of linked loci the size of SACHC is too large for an exact method to be .

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