A new statistical method for haplotype reconstruction from population data

Current routine genotyping methods typically do not provide haplotype infor mation, which is essential for many analyses of fine-scale molecular-geneti cs data. Haplotypes can be obtained, at considerable cost, experimentally o r (partially) through genotyping of additional family members. Alternativel y, a statistical method can be used to infer phase and to reconstruct haplo types. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on curren t algorithms; often, error rates are reduced by >50%, relative to its neare st competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping a dditional family members may be an inefficient use of resources.