Identification of Pedigree Relationship from Genome Sharing
G3 (Bethesda), (July 2013)DOI: 10.1534/g3.113.007500
Abstract
Determination of degree of relationship has traditionally been undertaken using genotypic data on individual loci, typically assumed to be independent. With dense marker data as now available it is possible to identify the regions of the genome shared identical by descent (ibd). This information can be used to determine pedigree relationship (R), e.g. cousins vs second cousins and also distinguish pedigrees which have the same Wright's relationship (R) such as half-sibs and uncle nephew. We use simulation to investigate the accuracy with which pedigree relationship can be inferred from genome sharing for uniparental relatives (a common ancestor on only one side of their pedigree), specifically the number, position (whether or not at chromosome ends) and length of shared regions ibd on each chromosome. Moments of the distribution of the likelihood ratio (including its expectation, the Kullback-Leibler distance) for alternative relationships are estimated for model human genomes, with the ratio of the mean to the standard deviation of the likelihood ratio providing a useful reference point. Two relationships differing in R can readily be distinguished provided at least one has high R, e.g. ca. 98.5% correct assignment of cousins and half cousins, but only about 75% for second cousins once removed and third cousins. Two relationships with the same R can be distinguished only if R is high, e.g. half sibs and uncle-nephew, with probability of correct assignment about 5/6.