Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data.

By D. Fallin, N. Schork. American Journal of Human Genetics, 2000

436 citations recorded by the source corpus.

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In Genetics

Citations in the corpus

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. (2006, background): “This model (11) is reminiscent of the “linkage” model of Falush et al. (2003), who modeled genotype data at loosely linked markers in structured populations.”
A new statistical method for haplotype reconstruction from population data. (2001, methodology): “A more technical, less substantial methodological difference between the approaches is that we assessed accuracy of haplotype sample frequency estimates using the discrepancy (effectively following Excoffier and Slatkin [1995]), whereas Fallin and Schork (2000) use the mean squared error (MSE).”
A new algorithm for haplotype‐based association analysis: the Stochastic‐EM algorithm (2004, methodology): “While simulation studies have already investigated the accuracy of ML algorithms for haplotype frequencies estimation (Chiano & Clayton, 1998; Fallin & Schork, 2000), little work has been carried out on the parameters characterizing the haplotype-phenotype association.”
Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. (2002, methodology): “Both Stephens et al. (2001b) and Fallin and Schork (2000) performed assessments of their algorithms when HWE was violated and concluded that the impact on their algorithms was not dramatic.”
Score tests for association between traits and haplotypes when linkage phase is ambiguous. (2002, background): “Some recent studies on the utility of the likelihood method (Fallin and Schork 2000; Tishkoff et al. 2000; Fallin et al. 2001) have reported the following properties: (1) it provides accurate estimates of the most frequent haplotypes but tends to be inaccurate for rare haplotypes (Tishkoff et al.…”
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects (2003, methodology): “Fallin & Schork (2000) carried out a simulation study to examine the accuracy of the EM-based procedure for estimating haplotype frequency as a function of some of the above factors.”
Chapter 11: Genome-Wide Association Studies (2012, background): “frequencies exist, and generally lead to reasonable results [18].”
Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. (2005, positive): “This is consistent with previous observations that haplotype inference methods are not especially sensitive to deviations from the assumption of Hardy-Weinberg equilibrium that underlies most of them (Fallin and Schork 2000; Stephens et al. 2001).”