A Recursive Algorithm For Long Range Phasing Of SNP Genotype

Abstract

High density genotyping of individuals does not by itself yield information on phase: linkage of alleles between loci in the contributing gametes. This additional information is important, because it helps to determine which segments of chromosome are identical by descent across the population, and thereby improve inference about segregation of quantitative trait loci (QTL). This paper presents a recursive algorithm to give efficient implementation of long range phasing, a recently-published strategy that infers IBD between distant relatives from long strings of SNP genotypes that show no opposing homozygotes (i.e. no evidence of lack of IBS). These relatives can be both distant and unknown to the analysis. Successful implementation of this strategy gives opportunity to use haplotype and/or combined linkage-linkage disequilibrium analysis for QTL mapping or genomic selection.