Year: 2026
Type: preprint
Abstract: Reconstructing clonal relationships among human cells is fundamental to understanding development, aging, and disease. Somatic mitochondrial DNA (mtDNA) mutations act as endogenous single-cell barcodes measurable alongside cell-state profiles, but lineage tracing has traditionally focused on high-heteroplasmy variants, which are easier to detect but few and potentially shaped by selection. Whether the more abundant lower-heteroplasmy variants encode bona fide lineage information has not been tested against an independent clonal reference. Using lentiviral barcoding of human hematopoietic cells to establish ground-truth clone identities, we show that after stringent molecule-level error filtering, mutation calls below 10% per-cell heteroplasmy account for roughly half of all lineage-informative calls. Retaining the full heteroplasmy spectrum approximately doubled the clonal-assignment area under the precision– recall curve relative to a >10% cutoff, and single-molecule-supported calls improved recovery when retained collectively. These findings establish lower-heteroplasmy mtDNA mutations as an abundant, bona fide record of clonal history, substantially expanding the clonal resolution attainable in human tissues without genetic engineering.
Institutions: Broad Institute, Boston Children's Hospital, Howard Hughes Medical Institute, Harvard University, Dana-Farber Cancer Institute, Whitehead Institute for Biomedical Research, Koch Institute for Integrative Cancer Research At MIT, Massachusetts Institute of Technology, Harvard Stem Cell Institute
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7203872204
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