On the edge of deletion: Using natural and engineered microhomology to edit the human genome

As long read sequencing becomes more commonplace in genome analysis, the number of deletion variants associated with human traits and disease are anticipated to continue growing at a rate that may well outpace the increase in novel single nucleotide variant (SNV) discoveries. Such a paradigm shift will be met with an increased demand for gene editing technologies that enable functional analyses in a human model system such as induced pluripotent stem (iPS) cells. The outcome of gene editing is ultimately determined by cellular repair pathways and can be predicted by the surrounding DNA sequence. As multiple studies have revealed microhomology at the edges of natural deletion variants, eliciting microhomology mediated end joining (MMEJ) presents a reliable approach to create specific deletions. In this review, we discuss the shifting trends in human genome variant discovery, briefly review DNA repair processes and the associated prediction algorithms, demonstrate the utility of MMEJ in generating both loss- and gain-of-function alleles, and finally speculate on the impact these advances will have on the future of human functional genomics.