Efficient localization of mutations by interval haplotype analysis.

We have developed a mathematical algorithm to implement a method for localizing mutations using haplotype analysis. Our strategy infers haplotypes based on the determination of genotypes of a proximal and a distal marker for 21 chromosomal intervals distributed across the mouse genome (corresponding to two intervals for Chromosomes (Chrs) 1 and 2 and one for the remaining 17 autosomes). To simulate the analysis of mice homozygous for recessive mutations, we tested the efficacy of our method on over 200 data sets generated from two independent mapping panel data sets containing the genotypes of 46 F2 progeny of an intercross and 94 F2 progeny of a backcross. In all cases we were able to identify the chromosomal interval carrying the recessive mutation despite the fact that some of the data sets consisted of as few as 10 meioses. Our strategy proved sensitive and expedient, since the simulated genome-wide screen could be executed by genotype analysis of 40 microsatellite markers in small numbers of intercross or backcross progeny.