An Emulsion Polymerase Chain ReactionBased Method for Molecular Haplotyping

Genotypes are easily measured using a variety of experimental methods. However, experimental methods for measuring haplotypes, i.e., molecular haplotyping, are limited. Instead, haplotypes often are statistically inferred from genotype data with varying degrees of confidence, depending on the extent of linkage disequilibrium (LD) between markers. We have developed a method for molecular haplotyping, linking-emulsion polymerase chain reaction (LE-PCR), that should find application in studies where LD is limited, especially when the polymorphisms in question affect the function of a single gene product. We have illustrated this technology with the human paraoxonase 1 gene (PON1), where polymorphisms affecting transcription and enzymatic activity show incomplete LD. PON1 is an enzyme with multiple activities, including detoxification of organophosphates.