Using Digital Polymerase Chain Reaction to Detect Single-Nucleotide Substitutions Induced by Genome Editing

Cold Spring Harb Protoc. 2016 Aug 1;2016(8). doi: 10.1101/pdb.prot086801.


This protocol is designed to detect single-nucleotide substitutions generated by genome editing in a highly sensitive and quantitative manner. It uses a combination of allele-specific hydrolysis probes and a new digital polymerase chain reaction (dPCR) technology called droplet digital PCR (ddPCR). ddPCR partitions a reaction into more than 10,000 nanoliter-scale water-in-oil droplets. As a result, each droplet contains only a few copies of the genome so that ddPCR is able to detect rare genome-editing events without missing them.

MeSH terms

  • DNA / chemistry*
  • DNA / genetics*
  • Gene Editing*
  • Nucleotides / analysis*
  • Nucleotides / genetics*
  • Polymerase Chain Reaction / methods*


  • Nucleotides
  • DNA