Understanding the allele-specific expression effects helps determine how inherited mutations may impact carriers and their offspring. Existing allele expression diagnostics, such as bacterial artificial chromosome (BAC) probes, only work on cultured cells, which increases the time required for testing.
The proposed invention uses in situ hybridization probes to detect allele specific expression in cells and tissues. Nuclear whole transcriptome RNA sequencing is used to provide an intron retention score from samples to resolve expression of target alleles. These tools can resolve epigenetic allelic effects, genomic imprinting and random X-inactivation to monitor health and disease progression, and detect disorders by profiling RNASeq data.