A comparison of bayesian methods for haplotype reconstruction from population genotype data.

By Matthew Stephens, Peter Donnelly. American Journal of Human Genetics, 2003

3,672 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Pulmonary and Respiratory Medicine

View Paper: https://www.semanticscholar.org/paper/855f6c0887f09700453f082f9ceec8fd89e89fee

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Citations in the corpus

Detection of sharing by descent, long-range phasing and haplotype imputation (2008, background): “In general, consider a SNP that is heterozygous (1,2) in A and all of his”
Species delimitation, patterns of diversification and historical biogeography of the Neotropical frog genus Adenomera (Anura, Leptodactylidae) (2014, methodology): “To determine the most probable alleles for individuals heterozygous for nDNA sequences we used phase (Stephens et al., 2001; Stephens & Donnelly, 2003) implemented in DnaSP 5 (Librado & Rozas, 2009).”
Association of Rad51 polymorphism with DNA repair in BRCA1 mutation carriers and sporadic breast cancer risk (2011, neutral): “1, Department of Statistics, University of Washington, Seattle, WA) [61,62].”
Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists (2013, methodology): “We used a Bayesian approach implemented in phase 2.0 (Stephens et al., 2001; Stephens & Donnelly, 2003) to identify heterozygous haplotypes of Fib7.”
Selecting additional tag SNPs for tolerating missing data in genotyping (2005, positive): “Numerous methods have been developed to infer haplotypes from genotype data [12,14,15].”
The evolution of molecular markers — just a matter of fashion? (2004, background): “Technical improvements that provide information about the phase of mutations (that is, the assignment of alleles to the two homologous chromosomes), are highly desirabl”
Genetic signatures of strong recent positive selection at the lactase gene. (2004, methodology): “We used two phasing programs: PHASE, a Bayesian method for phasing diploid genotype data (Stephens and Donnelly 2003; PHASE Web site), and also a similar program (wphase) that we developed for this purpose.”
DNA sequence polymorphism analysis using DnaSP. (2009, methodology): “, haplotype-based analyses such as linkage disequilibrium or haplotype diversity) also require knowledge of the haplotype phase (16).”
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. (2005, positive): “As noted by Stephens and Donnelly (2003), Bayesian approaches seem to have an advantage here, since the Bayesian framework provides a natural way of assessing uncertainty , via the conditional distribution of the haplotypes, given the genotype data.”
Cryptic species in Iphisa elegans Gray, 1851 (Squamata: Gymnophthalmidae) revealed by hemipenial morphology and molecular data (2012, methodology): “To determine the most probable alleles for individuals recovered as heterozygous on the C-MOS fragment we used PHASE (Stephens, Smith & Donnelly, 2001; Stephens & Donnelly, 2003) implemented in DnaSP 5 (Librado & Rozas, 2009).”
A comparison of phasing algorithms for trios and unrelated individuals. (2006, methodology): “The PHASE algorithm (Stephens et al. 2001; Stephens and Donnelly 2003; Stephens and Scheet 2005) is a Bayesian approach to haplotype inference that uses ideas from population genetics—in particular, coalescent-based models—to improve accuracy of haplotype estimates for unrelated individuals sampled…”
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness (2014, methodology): “We then calculated the switch error (SE) [34] of the haplotype estimates for the pedigree founders, treating the Merlin haplotypes as the truth.”
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data (2009, methodology): “DnaSP reconstructs the phase by applying various algorithms (PHASE v2.”
A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. (2006, methodology): “Another model that also aims to flexibly capture patterns of LD is the PAC model of Li and Stephens (2003), which partially underlies the PHASE software for haplotype inference and estimation of recombination rates (Stephens et al. 2001; Stephens and Donnelly 2003; Stephens and Scheet 2005).”