Celiac Disease

Gahan, Jillian M, Byrne, Mikaela M, Hill, Matthew, Quinn, Emma M, Murphy, Ross T, Anney, Richard J L, Ryan, Anthony W, Jillian M. Gahan, Mikaela M. Byrne, Matthew Hill, Emma M. Quinn, Ross T. Murphy, Richard J. L. Anney, Anthony W. Ryan, Gahan, Jillian M., Byrne, Mikaela M., Quinn, Emma M., Murphy, Ross T., Anney, Richard J. L., Ryan, Anthony W.

Genetic variation along the length of a chromosome can influence the transcription of a gene. In a heterozygous individual, this may lead to one chromosome producing different levels of RNA, compared to its paired chromosome, for a given gene. Allelic differences in gene expression can offer insight into the role of variation in transcription, and subsequently infer a route to conferring disease risk. This phenomenon is known as allele expression imbalance or AEI, which may be assayed using a PCR-based method that includes the quantification of the relative dosage of each allele (e.g., 5' exonuclease assays, TaqMan™). Importantly, in heterozygous individuals the resolution of expression imbalance is performed within a controlled system; the comparison of the alternate allele is reported relative to the wild-type, as the experiment can be performed within a single sample, controlled for background genetic information. Alternative methods for the detection of AEI include Primer-extension MALDI-TOF (Sequenom MassARRAY(®)), Next-Generation Sequencing, and SNP genotyping arrays. Here we present the methods used for the TaqMan™ approach and include a description of the SNP identification, allele-specific PCR, and analytic methods to convert allele amplification metrics to relative allele dosage.