Abstract
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.
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Acknowledgments
Our understanding of allelic skew has greatly benefited from the work of Tom Mullen and Jim Nemesh in our lab. This work was supported by a grant from the National Human Genome Research Institute (R01 HG006855, to SAM).
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Kamitaki, N., Usher, C.L., McCarroll, S.A. (2018). Using Droplet Digital PCR to Analyze Allele-Specific RNA Expression. In: Karlin-Neumann, G., Bizouarn, F. (eds) Digital PCR. Methods in Molecular Biology, vol 1768. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7778-9_23
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DOI: https://doi.org/10.1007/978-1-4939-7778-9_23
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