bioRxivGenomicsPreprint
scAbsolute: Measuring single-cell ploidy and replication status
Michael P SchneideriD, Amy E CulleniD, Justina PangonyteiD, Jason Skelton, Harvey Major, Elke Van OudenhoveiD, María J. GarcíaiD, Blas Chaves-UrbanoiD, Anna PiskorziD, James D. BrentoniD, Geoff MacintyreiD, Florian M. MarkowetziD
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 scAbsolutes 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.
- organism: human
- assay: whole-genome sequencing
- research focus: variant calling
- research focus: dimensionality reduction
- approach: statistical model
- Citations
- 2
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