A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity

By David J. Balding, R. Nichols. Genetica, 2005

441 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6f3f049353d97a8b46890b19a3b6e0957f354963

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In Genetics

Citations in the corpus

Identifying adaptive genetic divergence among populations from genome scans (2004, background): “This likelihood arises in a wide range of neutral population genetics models, in particular the infinite-island model of Wright (1943); for assumptions and derivations, see Balding and Nichols (1995), Rannala and Hartigan (1996), and Balding (2003).”
Population Structure and Cryptic Relatedness in Genetic Association Studies (2009, methodology): “For each SNP, we drew subpopulation allele fractions from the beta-binomial model described in Balding and Nichols (1995).”
Population Structure and Eigenanalysis (2006, methodology): “We note that Nicholson et al. use the same normalization, and motivate it similarly [18].”
Estimating and interpreting FST: The impact of rare variants (2013, background): “For example, selection can result in dif- ferences between FST estimated on genic and nongenic SNPs (Clark et al. 2005; Barreiro et al. 2008; Hernandez et al. 2011); complex demography can cause FST to vary with SNP allele frequency (Schaffner et al. 2005) (see below).”
The effects of human population structure on large genetic association studies (2004, methodology): “Using Bayesian methodology, we fitted a statistical model of population structure that is natural for SNP loc”
Implicit Causal Models for Genome-wide Association Studies (2017, positive): “[6], we use the Balding-Nichols model based on the HapMap dataset [2, 5]; PCA based on the 1000 Genomes Project (TGP) [3]; PCA based on the Human Genome Diversity project (HGDP) [20]; four variations of the PritchardStephens-Donelly model (PSD) based on HGDP [18]; and four variations of a configurat”
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective (2008, methodology): “Bayesian model for estimation of locus–populationspecific FST coefficients: The model for genetic differentiation used is based on ideas first introduced by Balding and Nichols (1995) and that Beaumont and Balding (2004) later used to detect loci under natural selection.”
The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits (2012, methodology): “The same subset of SNPs can be used for pairwise IBD estimation using the maximum-likelihood method of Milligan [38] implemented in PLINK [39] or the variance-components method of Balding and Nichols [40] implemented in EMMAX [41].”
Detecting loci under selection in a hierarchically structured population (2009, background): “Recent Bayesian approaches (Beaumont and Balding, 2004; Foll and Gaggiotti, 2008) assume that allele frequencies within population follow a multinomial Dirichlet distribution (Balding and Nichols, 1995; Rannala and Hartigan, 1996; Balding, 2003) with FST parameters that are a function of population-”