Allelic imbalance assays to quantify allele-specific gene expression and transcription factor binding.

A growing number of noncoding variants are found to influence the susceptibility to common diseases and interindividual variation in drug response. However, the mechanisms by which noncoding variation affects cellular and clinical phenotypes remain to be elucidated. Allele-specific assays allow testing directly the differential properties of the alleles at a regulatory variant, which are detected as an allelic imbalance. Two widely used allelic imbalance assays target cDNA and DNA from chromatin immunoprecipitation (ChIP) experiments, and therefore revealing allele-specific gene expression and transcription factor binding, respectively. The throughput of allelic imbalance assays ranges from single variant to the genome scale, which are made possible by the recent advances in genotyping and sequencing technologies (e.g., genome-wide quantitative cDNA genotyping, ChIP-seq).