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Schneider MP, Cullen AE, Pangonyte J, Skelton J, Major H, Van Oudenhove E, Garcia MJ, Chaves Urbano B, Piskorz AM, Brenton JD, Macintyre G, Markowetz F. scAbsolute: measuring single-cell ploidy and replication status. Genome Biol 2024; 25:62. [PMID: 38438920 PMCID: PMC10910719 DOI: 10.1186/s13059-024-03204-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute's capabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods. scAbsolute provides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.
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Affiliation(s)
- Michael P Schneider
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Amy E Cullen
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Justina Pangonyte
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Jason Skelton
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Harvey Major
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Elke Van Oudenhove
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Maria J Garcia
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Anna M Piskorz
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - James D Brenton
- University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Geoff Macintyre
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Florian Markowetz
- University of Cambridge, Cambridge, UK.
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK.
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Ferreri C. On a hyperbinomial process. COMMUN STAT-THEOR M 1996. [DOI: 10.1080/03610929608831681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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