Estimation of individual admixture: Analytical and study design considerations

By Hua Tang, Jie Peng, Pei Wang, N. Risch. Genetic Epidemiology, 2005

645 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/9d855b02b829ad72eeb65302e5901c5ffdfc538d

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

Citations in the corpus

Fast model-based estimation of ancestry in unrelated individuals. (2009, methodology): “As noted by Tang et al. (2005), the admixture model tends to have difficulty identifying ancestral populations when the data set contains no individuals of unmixed ancestry.”
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets (2014, methodology): “To provide faster estimation, FRAPPE and ADMIXTURE both use a maximum-likelihood approach.”
Clumpak: a program for identifying clustering modes and packaging population structure inferences across K (2015, background): “…cluster analysis (Pritchard et al. 2000; Dawson & Belkhir 2001; Corander et al. 2003, 2004, 2008a,b; Falush et al. 2003, 2007; Guillot et al. 2005; Tang et al. 2005; Franc (cid:1) ois et al. 2006; Pella & Masuda 2006; Chen et al. 2007; Gao et al. 2007; Huelsen-beck & Andolfatto 2007; Guillot…”
Learning about human population history from ancient and modern genomes (2011, background): “or ancestry components (for example, STRUCTURE or frappe”
PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations (2007, background): “At the same time, it is sensitive to the choice of prior distributions of model parameters and relies heavily on explicit assumptions about the data that may not always hold, making the method unstable when these assumptions are violated [19,21].”
Estimating Individual Admixture Proportions from Next Generation Sequencing Data (2013, methodology): “The genotype likelihoods are the likelihood of observing the sequencing data for a single individual given the unobserved genotype, defined as L Xij G ¼ fA1;A2g } p Xij G ¼ fA1;A2g ; A1;A2 2 fA;C;G;Tg: Several methods for calculating the genotype likelihoods exist.”
Inference of Population Structure using Dense Haplotype Data (2012, background): “Methods to explore admixture have been developed that aim to be robust to the presence of LD [14,32,33], or directly model LD patterns [34] to identify ancestry segments.”
Genetic differentiation and secondary contact zone in the seagrass Cymodocea nodosa across the Mediterranean–Atlantic transition region (2008, methodology): “The methods implemented by psmix are described by Tang et al. (2005).”
Fast and Efficient Estimation of Individual Ancestry Coefficients (2014, methodology): “Inference of population structure from multi-locus genotype data is commonly performed using likelihood methods implemented in the computer programs STRUCTURE , FRAPPE or ADMIXTURE (Pritchard et al. 2000a, Tang et al. 2005, Alexander et al. 2009).”