MuVEH and mitoMuVEH improve discovery of genetic variation from single cells.

Understanding the genetic underpinnings and clonal structure of malignancies at single-cell resolution is critical to accurately predicting drug response and understanding mechanisms of drug resistance and disease evolution in heterogeneous populations of cells. Here, we introduce an accessible, multiplexable, targeted mutation enrichment approach and end-to-end analysis pipeline called MuVEH (Multiplexed Variant Enrichment by Hybridization) that increases the resolution of variant detection in scRNA-seq analysis. When applied specifically to the mitochondrial chromosome ("mitoMuVEH"), this technique can also be used to reconstruct and trace clonal relationships between individual cells. We applied both approaches to two pairs of primary bone marrow specimens from acute myelogenous leukemia (AML) patients collected at diagnosis and after relapse following Venetoclax+Azacitidine (Ven/Aza) therapy. Used together, MuVEH and mitoMuVEH reveal clonal evolution and changing mutational burden in response to treatment at single-cell resolution in these patients. Ultimately, these approaches have the potential to extract additional biological insights from precious patient samples and provide insight into the contributions clonality and genotype have during disease progression.