PCR Protocols

Volume 687 of the series Methods in Molecular Biology pp 165-175


Linking Emulsion PCR Haplotype Analysis

  • James G. WetmurAffiliated withDepartment of Microbiology, Mount Sinai School of Medicine
  • , Jia ChenAffiliated withDepartment of Preventive Medicine, Mount Sinai School of Medicine

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The experimental measurement of haplotype requires the determination of two or more genotypes on the same DNA molecule. Because such measurements are much more complicated than measurements of genotypes, haplotypes are typically inferred using population data for linkage disequilibrium between the markers of interest. We have developed a method for molecular haplotyping, linking emulsion PCR (LE-PCR), and have demonstrated that the method is sufficiently robust to determine haplotypes for multiple markers in a population setting. LE-PCR uses emulsion PCR to isolate single template molecules for simultaneous PCR of widely spaced markers and uses linking PCR to fuse these amplicons into one short amplicon, which maintains the phase of the markers. LE-PCR is illustrated for polymorphisms in human paraoxonase 1 (PON1) that have been shown to affect transcriptional activity and substrate specificity in the detoxification of organophosphates.

Key words

Linking PCR Emulsion PCR Genotype Phenotype Haplotype Paraoxonase-1