Using Droplet Digital PCR to Analyze Allele-Specific RNA Expression

Methods Mol Biol. 2018:1768:401-422. doi: 10.1007/978-1-4939-7778-9_23.


Genome-wide association studies have discovered thousands of common alleles that associate with human phenotypes and disease. Many of these variants are in non-protein-coding (regulatory) regions and are believed to affect phenotypes by modifying gene expression. In any organism with a diploid genome, such as humans, measuring the expression of each allele of a gene provides a well-controlled way to identify allelic influences on that gene's expression. Here, we describe a protocol for precisely measuring the allele-specific expression of individual genes. This method targets the nucleotide differences between the two alleles of a gene within an individual and measures the "allelic skew," the extent to which one allele is expressed more than the other. We cover the design of effective assays, the optimization of reactions, and the interpretation of the resulting data.

Keywords: Allele-specific expression; Allelic imbalance; Allelic skew; Assay design; Digital PCR; Droplet digital PCR; mRNA expression.

Publication types

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

MeSH terms

  • Alleles*
  • Allelic Imbalance / genetics*
  • Genetic Markers / genetics
  • Humans
  • Polymorphism, Single Nucleotide / genetics
  • RNA / genetics
  • RNA / isolation & purification*
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction / instrumentation
  • Reverse Transcriptase Polymerase Chain Reaction / methods*


  • Genetic Markers
  • RNA