ASEP: gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing

Allele-specific expression (ASE) quantifies the relative expression of two alleles in a diploid individual, and such expression imbalance potentially contributes to phenotypic variation and disease pathophysiology among individuals. We developed ASEP, a method that is able to detect gene-level ASE under one condition, as well as, ASE difference between two conditions (e.g., pre- vs post-treatment) across individuals. Application of ASEP to human macrophage RNA-seq dataset has illustrated its ability to uncover ASE / differential ASE genes related to cardiometabolic traits. Overall design: Human peripheral blood mononuclear cell (PBMC)-derived macrophages (HMDM) and M1-polarized HMDM were sequenced by Illumina HiSeq 2500 with poly-A selection