Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling

The detection of mitochondrial DNA (mtDNA) mutations in single cells holds considerable potential to define clonal relationships at scale, coupled with information on cell state in humans. Previous methods focused on higher heteroplasmy mutations, which, while informative, are few in number and may be shaped by functional selection, providing limited lineage information and potentially introducing biases for tracing. Although more challenging to detect, intermediate- to low-heteroplasmy mtDNA mutations are valuable due to their high diversity, abundance, and lower propensity to selection. To enhance mtDNA mutation detection and facilitate fine-scale lineage tracing, we developed the single-c