Relatedness coefficients and their applications for triplets and quartets of genes

Abstract

Relatedness coefficients which seek the identity-by-descent of genetic markers are described. The markers are in groups of two, three or four, and if four, can consist of two pairs. It is essential to use cumulants (not moments) for four-marker-gene probabilities, as the covariance of homozygosity, used in 4-marker applications, can only be described with cumulants. A covariance of homozygosity between pairs of markers arises when populations follow a mixture distribution. Also, the probability of four markers all identical-by-descent equals the normalized fourth cumulant. In this paper, a "genetic marker" generally represents either a gene locus or an allele at a locus. Applications of three marker coefficients mainly involve conditional regression, and applications of four marker coefficients can involve identity disequilibrium. Estimation of relatedness using genetic marker data is discussed. However, three- and four-marker estimators suffer from statistical and numerical problems, including higher statistical variance, complexity of estimation formula, and singularity at some intermediate allele frequencies.