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Accelerated Gene Counting for Haplotype Frequency Estimation
Author(s) -
Thomas Alun
Publication year - 2003
Publication title -
annals of human genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.537
H-Index - 77
eISSN - 1469-1809
pISSN - 0003-4800
DOI - 10.1046/j.1529-8817.2003.00054.x
Subject(s) - haplotype , genetics , single nucleotide polymorphism , biology , haplotype estimation , genotype , allele frequency , gene
Summary Current implementations of the EM algorithm for estimating haplotype frequencies from genotypes on proximal loci require computational resources that grow as nh 2 k , where n is the number of individuals genotyped and h is the number of haplotypes possible on k loci. For diallelic loci h k = 2 k . We present an approach whose computational requirement grows as n 2 t 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.