Efficient Estimation of Realized Kinship from Single Nucleotide Polymorphism Genotypes. Issue 3 (1st March 2017)

• Record Type: Journal Article
• Authors: Wang, Bowen; Sverdlov, Serge; Thompson, Elizabeth
• Is Part Of: Genetics. Volume 205:Issue 3(2017)
• Page Start: 1063
• Page End: 1078
• Publication Date: 2017-03-01
• Subjects: realized kinship -- genomic relationship matrix (GRM) -- local identity by descent (IBD) -- linkage disequilibrium -- locus weighting; Genetics -- Periodicals; 576.5
• DOI: 10.1534/genetics.116.197004
• Languages: English
• ISSNs: 0016-6731

Abstract

Abstract: Realized kinship is a key statistic in analyses of genetic data involving relatedness of individuals or structure of populations. There are several... 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.