Analyzing Copy Number Variation with Droplet Digital PCR

Methods Mol Biol. 2018:1768:143-160. doi: 10.1007/978-1-4939-7778-9_9.


Many genomic segments vary in copy number among individuals of the same species, or between cancer and normal cells within the same person. Correctly measuring this copy number variation is critical for studying its genetic properties, its distribution in populations and its relationship to phenotypes. Droplet digital PCR (ddPCR) enables accurate measurement of copy number by partitioning a PCR reaction into thousands of nanoliter-scale droplets, so that a genomic sequence of interest-whose presence or absence in a droplet is determined by end-point fluorescence-can be digitally counted. Here, we describe how we analyze copy number variants using ddPCR and review the design of effective assays, the performance of ddPCR with those assays, the optimization of reactions, and the interpretation of data.

Keywords: Copy number variants; Digital PCR; Droplet digital PCR; Genomic structural variation; Genotyping; Genotyping assay design.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biological Variation, Individual
  • Biological Variation, Population / genetics
  • DNA / isolation & purification*
  • DNA Copy Number Variations / genetics*
  • Gene Dosage / genetics
  • Humans
  • Polymerase Chain Reaction / instrumentation
  • Polymerase Chain Reaction / methods*


  • DNA