Accelerated gene counting for haplotype frequency estimation.
Current implementations of the EM algorithm for estimating haplotype frequencies from genotypes on proximal loci require computational resources that grow as nh2k, where n is the number of individuals genotyped and h is the number of haplotypes possible on k loci. For diallelic loci hk=2k. We present an approach whose computational requirement grows as n2t where t is the largest number of loci at which an individual in the sample is heterozygous. The method is illustrated by haplotype frequency estimation from a sample of 45 individuals genotyped at 26 single nucleotide polymorphisms in the PIK3R1 gene.
Thomas
Alun
A
Department of Medical Informatics and the Center for High Performance Computing, University of Utah, 391 Chipeta Way, Suite D, Salt Lake City, UT 84108, USA. alun@genepi.med.utah.edu
D019870:1-Phosphatidylinositol 4-Kinase / Q000235:genetics; D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D011110:Polymorphism, Genetic; D044465:White People
D005819:Genetic Markers; D019870:1-Phosphatidylinositol 4-Kinase