biostudies-literatureKuipers JSwiss National Science FoundationEuropean Research Councilbtaf072https://www.ebi.ac.uk/biostudies/studies/S-EPMC11897432biostudies-literatureUnknown41(3)<h4>Motivation</h4>Copy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the processing of hundreds of cells through shallow whole-genome DNA sequencing. The resulting low read-depth data poses substantial statistical and computational challenges to the identification of copy number alterations.<h4>Results</h4>We developed SCICoNE, a statistical model and MCMC algorithm tailored to single-cell copy number profiling frBioinformatics (Oxford, England)Single-cell copy number calling and event history reconstruction.PMC11897432609883179518310030Ferreira PFJahn KKuipers JTuncel MABeerenwinkel NfalseSingle-cell copy number calling and event history reconstruction.<h4>Motivation</h4>Copy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the processing of hundreds of cells through shallow whole-genome DNA sequencing. The resulting low read-depth data poses substantial statistical and computational challenges to the identification of copy number alterations.<h4>Results</h4>We developed SCICoNE, a statistical model and MCMC algorithm tailored to single-cell copy number profiling fr2025-01-01T00:00:00Z2025 Mar2025-04-04T09:07:56.344Z2025-04-04T09:07:56.344ZS-EPMC118974323994609410.1093/bioinformatics/btaf072