PCR Protocols pp 165-175 | Cite as

Linking Emulsion PCR Haplotype Analysis

  • James G. Wetmur
  • Jia Chen
Part of the Methods in Molecular Biology book series (MIMB, volume 687)


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 



This work was supported by grants R21 ES011634 and P01 ES09584 from the National Institute of Environmental Health Sciences and RD831-711 from the Environmental Protection Administration.


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Copyright information

© Humana Press 2011

Authors and Affiliations

  • James G. Wetmur
    • 1
  • Jia Chen
    • 2
  1. 1.Department of MicrobiologyMount Sinai School of MedicineNew YorkUSA
  2. 2.Department of Preventive MedicineMount Sinai School of MedicineNew YorkUSA

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