A new statistical method for haplotype reconstruction from population data.

By Matthew Stephens, N. J. Smith, Peter Donnelly. American Journal of Human Genetics, 2001

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In Genetics

Citations in the corpus

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).”
MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes (2010, methodology): “For comparison, the table also includes results for 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…”
Markers, old and new, for examining Phytophthora infestans diversity (2004, methodology): “To obviate the need to derive haplotypes by expensive cloning and sequencing, accurate theoretical approaches have been developed (Clark, 1990; Stephens et al., 2001).”
Summer–Fall Distribution of Stocks of Immature Sockeye Salmon in the Bering Sea as Revealed by Single-Nucleotide Polymorphisms (2010, neutral): “Unfortunately, although phasing within populations can be inferred (Stephens et al. 2001), phasing in fish from a mixture of populations cannot since the method assumes Hardy–Weinberg equilibrium.”
Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. (2003, methodology): “A new version of the software package PHASE (Stephens et al. 2001) is under development,Markov chain to model LD, so that the probability of observing types (x1, . . . , xL) at L loci along a chromosome and it will deal with these problems by incorporating the PAC likelihood into a Markov chain Mont”
Likelihood-Based Inference on Haplotype Effects in Genetic Association Studies (2006, background): “One appealing approach is to consider the haplotypes for multiple SNPs within candidate genes (Hallman et al., 1999; International SNP Map Working Group, 2001; Patil et al., 2001; Stephens et al., 2001).”
Haplotype phasing: Existing methods and new developments (2011, methodology): “More accurate phasing can be obtained by better a priori modelling of probabilities of haplotype configurations, as is done by the coalescent-based and hidden Markov model (HMM) methods described belo”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “…separation of alleles (haplotypes) previously required laborious cloning techniques or analysis of multiple samples from the same population (e.g., Stephens et al. 2001, Browning & Browning 2011), high-throughput sequencers now produce data that allow alleles to be phased bioinformatically (given…”
A method for genome-wide genealogy estimation for thousands of samples (2019, methodology): “We combined the genome-wide significant GWAS hits (p < 5 ⇥ 10 8) of the GWAS catalogue [3] and the UK Biobank project [4].”
STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement (2009, neutral): “Acknowledgment: The authors thank Kyle Vogan and Allen Wilcox for their participation in the workshop and for their comments; Michele Cargill (Affymetrix) and Aaron del Duca (DNA Genotek) for their participation in the workshop as observers; and the Public Population Project in Genomics (P3G), hoste”
Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene (2011, background): “1 (Stephens et al. 2001), which has been shown to provide accurate estimates of haplotype frequencies from population data (Marroni et al.”
Reference-based phasing using the Haplotype Reference Consortium panel (2016, background): “Eagle2 achieves this performance via two key ideas that distinguish it from previous phasing algorithms [3–14]: a new data structure based on the positional Burrows-Wheeler transform [19] and a rapid search algorithm that explores only the most relevant phase paths through a hidden Markov model…”
A comparison of bayesian methods for haplotype reconstruction from population genotype data. (2003, methodology): “Stephens et al. (2001a) described two algorithms based on two different priors for the haplotype frequencies: the first, the " naive Gibbs sampler, " used a Dirichlet prior distribution; the second, implemented in PHASE v1.”