A comparison of phasing algorithms for trios and unrelated individuals.

By Jonathan Marchini, David J. Cutler, Nick Patterson, Matthew Stephens, Eleazar Eskin, Eran Halperin, Shin Lin, Zhaohui S. Qin, Heather M. Munro, Gonçalo R. Abecasis and 1 more. American Journal of Human Genetics, 2006

345 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/6b9c55f95cc8f4106bb62d00de560cc5d9f17fbe

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Citations in the corpus

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies (2009, methodology): “The multinomial haplotype frequency model that PLINK uses for imputation has fared poorly in recent comparisons of phasing methods [21]; its role in this analysis was to see if any accuracy is lost by using a simpler method to speed up imputation in a large and complex dataset.”
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. (2007, methodology): “The localized haplotype-cluster model clusters haplotypes at each marker to improve prediction of alleles at markers , t (cid:1) 1 , , given alleles at markers t, , on a hap-t (cid:1) 2 t (cid:1) 3,… t (cid:2) 1 t (cid:2) 2,… lotype.”
Whole population, genome-wide mapping of hidden relatedness. (2009, background): “pattern may be explained by phasing inconsistency, which results in incorrectly oriented haplotypes at heterozygous sites, commonly referred to as ‘‘switch error’’ (Lin et al. 2002; Marchini et al. 2006).”
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing (2012, result): “…comparing the results of population-and trio-based phasing in Finnish samples from the Finland–United States Investigation of Non-Insulin–Dependent Diabetes Mellitus Genetics (FUSION) study of type 2 diabetes 2,15 , we estimated that population phasing produces 1 switch error 16 per 5.5 Mb of DNA.”
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness (2014, background): “Some of these methods can also handle mother-father-child trios and parent-child duos [2–6], for more complex pedigrees there are several general pedigree analysis software packages [7–10].”
Haplotype phasing: Existing methods and new developments (2011, background): “was for some time considered a gold standard for accuracy among population-based haplotyping algorithm”
MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes (2010, methodology): “…PHASE [Stephens and Scheet, 2005b; Stephens et al., 2001] and fastPHASE [Scheet and Stephens, 2006], two state of the art haplotyping algorithms [Marchini et al., 2006], and for BEAGLE [Browning, 2006] and PL-EM [Qin et al., 2002], two alternative haplotyping algorithms that are very…”