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Methods Mol Biol DOI:10.1007/978-1-4939-7778-9_23

Using Droplet Digital PCR to Analyze Allele-Specific RNA Expression.

Publication TypeJournal Article
Year of Publication2018
AuthorsKamitaki, N, Usher, CL, McCarroll, SA
JournalMethods Mol Biol
Date Published2018
KeywordsAlleles, Allelic Imbalance, Genetic Markers, Humans, Polymorphism, Single Nucleotide, Regulatory Sequences, Nucleic Acid, Reverse Transcriptase Polymerase Chain Reaction, RNA

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.


Alternate JournalMethods Mol Biol
PubMed ID29717456
Grant ListR01 HG006855 / HG / NHGRI NIH HHS / United States