A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase.

By Paul Scheet, Matthew Stephens. American Journal of Human Genetics, 2006

1,992 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b5622ba24a8a2f5ed1e67c5f294476db0423ad35

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In Genetics

Citations in the corpus

Fast and flexible simulation of DNA sequence data. (2008, methodology): “We first inferred phase in the YRI data using a hidden Markov model-based algorithm implemented in the program fastPHASE (Scheet and Stephens 2006).”
Genotype Imputation with Thousands of Genomes (2011, methodology): “Similar state-reduction techniques are used by GERBIL (Kimmel and Shamir 2005), fastPHASE (Scheet and Stephens 2006), GEDI (Kennedy et al. 2008), and other related methods.”
MaCH: Using Sequence and Genotype Data to Estimate Haplotypes and Unobserved Genotypes (2010, methodology): “, 2001] and fastPHASE [Scheet and Stephens, 2006], two state of the art haplotyping algorithms [Marchini et al.”
Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population (2010, positive): “Missinggenotypeswere imputedusing fastPHASE (Scheet and Stephens 2006).”
STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement (2009, positive): “It is common in such studies to use statistical methods to estimate haplotypes (Stephens et al. 2001; Qin et al. 2002; Scheet and Stephens 2006; Browning 2008), and their accuracy and efficiency have been discussed (Huang et al.”
Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes) (2009, methodology): “To reconstruct haplotypes from unphased genotypes we used the software FASTPHASE under default settings (Scheet & Stephens, 2006).”
Genotype imputation for genome-wide association studies (2010, background): “k = 0 (8) and θ denotes the regression parameters.”
Genomewide Prediction Accuracy within 969 Maize Biparental Populations (2014, methodology): “When the set of markers (31 to 119 SNP loci) used for each population did not have data for some lines, the missing marker data were imputed with fastPHASE (Scheet and Stephens, 2006); imputation with the full set of 2911 parental markers was not done.”
A Map of Recent Positive Selection in the Human Genome (2006, methodology): “This algorithm uses a similar model and achieves nearly the same accuracy as Phase 2, which was used to phase the HapMap data [54].”
A modern maximum-likelihood theory for high-dimensional logistic regression (2018, methodology): “In particular, we use the HMM implemented in the fastPHASE [87] fitting algorithm, which is parametrized by three vectors (r,α,θ), and we denote the corresponding distributions by HMM(r,α,θ).”
Fast and accurate genotype imputation in genome-wide association studies through pre-phasing (2012, methodology): “Some methods, such as fastPHASE 23 and Beagle 25 , reduce H by grouping similar haplotypes into clusters.”