Identification of Pedigree Relationship from Genome Sharing

Abstract

Determination of degree of relationship traditionally has 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 to distinguish pedigrees that 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 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 SD of the likelihood ratio providing a useful reference point. Two relationships differing in R can be readily distinguished provided at least one has high R, e.g., approximately 98.5% correct assignment of cousins and half-cousins, but only approximately 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 being approximately 5/6.