Digital PCR pp 489-512 | Cite as

Phasing DNA Markers Using Digital PCR

  • John Regan
  • George Karlin-NeumannEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1768)


Besides quantifying the absolute number of copies of known DNA targets, digital PCR can also be used to assess whether two nonpolymorphic gene sequences or two heterozygous markers reside on the same DNA molecule (i.e., are physically linked). Some useful linkage applications include: phasing variants to define a haplotype; genotyping of inversions; determining the presence of multimarker pathogenic bacteria in a metagenomic sample; and assessing DNA integrity. This chapter describes an efficient and cost-effective method for analyzing linkage of any two genetic sequences up to at least 200 Kb apart, including phasing of heterozygous markers such as that which occur abundantly in the cystic fibrosis transmembrane conductance regulator (CFTR) gene.

Key words

Phasing Linkage Haplotype Compound heterozygote Complex alleles Co-localization Genotyping inversions DNA integrity DNA sizing Large DNA isolation Digital PCR Droplet Digital PCR 



Steven McCarroll, Nolan Kamitaki, Tina Legler, Samuel Maars, Mario Caceres, and Svilen Tzonev, Niels Klitgord, and Samantha Cooper contributed to the knowledge presented in these protocols.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Digital Biology Center, Bio-Rad LaboratoriesPleasantonUSA

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