title: Efficient Estimation of Realized Kinship from Single Nucleotide Polymorphism Genotypes.
abstract: Realized kinship is a key statistic in analyses of genetic data involving relatedness of individuals or structure of populations. There are several estimators of kinship that make use of dense SNP genotypes. We introduce a class of estimators, of which some existing estimators are special cases. Within this class, we derive properties of the estimators and determine an optimal estimator. Additionally, we introduce an alternative marker weighting that takes allelic associations [linkage disequilibrium (LD)] into account, and apply this weighting to several estimators. In a simulation study, we show that improved estimators are obtained (1) by optimal weighting of markers, (2) by taking physical contiguity of genome into account, and (3) by weighting on the basis of LD.
authors.affiliation: Department of Statistics, University of Washington, Seattle, Washington 98195-4322.
authors.forename: Bowen
authors.initials: B
authors.lastname: Wang
authors.affiliation: Department of Statistics, University of Washington, Seattle, Washington 98195-4322.
authors.forename: Serge
authors.initials: S
authors.lastname: Sverdlov
authors.affiliation: Department of Statistics, University of Washington, Seattle, Washington 98195-4322 eathomp@uw.edu.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Thompson
mesh_terms: D000465:Algorithms; D000818:Animals; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide
keywords: genomic relationship matrix (GRM); linkage disequilibrium; local identity by descent (IBD); locus weighting; realized kinship