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Updated: Aug 30, 2026

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Accelerated gene counting for haplotype frequency estimation
1Department 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
Abstract:
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.
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