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Koptagel H, Jun SH, Hård J, Lagergren J
PLoS Comput Biol 20 (5) e1012094 [2024-05-00; online 2024-05-09]
Cell lineage tree reconstruction methods are developed for various tasks, such as investigating the development, differentiation, and cancer progression. Single-cell sequencing technologies enable more thorough analysis with higher resolution. We present Scuphr, a distance-based cell lineage tree reconstruction method using bulk and single-cell DNA sequencing data from healthy tissues. Common challenges of single-cell DNA sequencing, such as allelic dropouts and amplification errors, are included in Scuphr. Scuphr computes the distance between cell pairs and reconstructs the lineage tree using the neighbor-joining algorithm. With its embarrassingly parallel design, Scuphr can do faster analysis than the state-of-the-art methods while obtaining better accuracy. The method's robustness is investigated using various synthetic datasets and a biological dataset of 18 cells.
PubMed 38723024
DOI 10.1371/journal.pcbi.1012094
Crossref 10.1371/journal.pcbi.1012094
pmc: PMC11125557
pii: PCOMPBIOL-D-22-01820