Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations

Reconstructing lineage relationships in complex tissues can reveal mechanisms underlying development and disease. Recent methods combine single-cell transcriptomics with mitochondrial DNA variant detection to establish lineage relationships in primary human cells, but are not scalable to interrogate complex tissues. To overcome this limitation, here we develop a technology for high-confidence detection of mitochondrial mutations from high-throughput single-cell RNA-sequencing. We use the new method to identify skewed immune cell expansions in primary human clonal hematopoiesis. Overall design: This project demonstrates a new technology to enrich mitochondrial DNA (mtDNA) mutations from 3' single-cell RNA-seq (scRNA-seq) libraries. The technology is termed MAESTER, or Mitochondrial Alteration Enrichment from Single-cell Transcriptomes to Establish Relatedness.