scAbsolute: measuring single-cell ploidy and replication status.
Michael P SchneiderAmy E CullenJustina PangonyteJason SkeltonHarvey MajorElke Van OudenhoveMaria J GarciaBlas Chaves UrbanoAnna M PiskorzJames D BrentonGeoff MacintyreFlorian MarkowetzPublished in: Genome biology (2024)
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.
Keyphrases
- single cell
- rna seq
- copy number
- cell cycle
- high throughput
- circulating tumor
- mitochondrial dna
- cell free
- single molecule
- cell proliferation
- poor prognosis
- genome wide
- dna methylation
- gene expression
- mesenchymal stem cells
- bone marrow
- mass spectrometry
- long non coding rna
- social media
- health information
- climate change
- data analysis