{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T20:29:34Z","timestamp":1788294574497,"version":"build-2803163510"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,2,26]],"date-time":"2025-02-26T00:00:00Z","timestamp":1740528000000},"content-version":"vor","delay-in-days":96,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Institut Th\u00e9matique Multi-Organismes Cancer of Aviesan"},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC StG 758170-Microbar"],"award-info":[{"award-number":["ERC StG 758170-Microbar"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Tracing cell lineages has become a valuable tool for studying biological processes. Among the available tools for human data, mitochondrial DNA (mtDNA) has a high potential due to its ability to be used in conjunction with single-cell chromatin accessibility data, giving access to the cell phenotype. Nonetheless, the existing mutation calling tools are ill-equipped to deal with the polyploid nature of the mtDNA and lack a robust statistical framework. Here we introduce scMitoMut, an innovative R package that leverages statistical methodologies to accurately identify mitochondrial lineage-related mutations at the single-cell level. scMitoMut assigns a mutation quality q-value based on beta-binomial distribution to each mutation at each locus within individual cells, ensuring higher sensitivity and precision of lineage-related mutation calling in comparison to current methodologies. We tested scMitoMut using single-cell DNA sequencing, single-cell transposase-accessible chromatin (scATAC) sequencing, and 10\u00d7 Genomics single-cell multiome datasets. Using a single-cell DNA sequencing dataset from a mixed population of cell lines, scMitoMut demonstrated superior sensitivity in identifying a small proportion of cancer cell line compared to existing methods. In a human colorectal cancer scATAC dataset, scMitoMut identified more mutations than state-of-the-art methods. Applied to 10\u00d7 Genomics multiome datasets, scMitoMut effectively measured the lineage distance in cells from blood or brain tissues. Thus, the scMitoMut is a freely available, and well-engineered toolkit (https:\/\/www.bioconductor.org\/packages\/devel\/bioc\/html\/scMitoMut.html) for mtDNA mutation calling with high memory and computational efficiency. Consequently, it will significantly advance the application of single-cell sequencing, facilitating the precise delineation of mitochondrial mutations for lineage-tracing purposes in development, tumour, and stem cell biology.<\/jats:p>","DOI":"10.1093\/bib\/bbaf072","type":"journal-article","created":{"date-parts":[[2025,2,13]],"date-time":"2025-02-13T07:16:37Z","timestamp":1739430997000},"source":"Crossref","is-referenced-by-count":7,"title":["scMitoMut for calling mitochondrial lineage-related mutations in single cells"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3100-2346","authenticated-orcid":false,"given":"Wenjie","family":"Sun","sequence":"first","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL, Sorbonne Universit\u00e9, CNRS UMR168, Physique des Cellules et Cancer , 16 rue Pierre et Marie Curie, 75005 Paris ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5893-7096","authenticated-orcid":false,"given":"Daphne","family":"van Ginneken","sequence":"additional","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL, Sorbonne Universit\u00e9, CNRS UMR168, Physique des Cellules et Cancer , 16 rue Pierre et Marie Curie, 75005 Paris ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Le\u00efla","family":"Peri\u00e9","sequence":"additional","affiliation":[{"name":"Institut Curie, Universit\u00e9 PSL, Sorbonne Universit\u00e9, CNRS UMR168, Physique des Cellules et Cancer , 16 rue Pierre et Marie Curie, 75005 Paris 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