Measuring ongoing chromosomal instability in single-cell DNA sequencing data

Chromosomal instability is a characteristic hallmark of cancer. It is providing part of the genomic variation that makes cancer so heterogeneous and difficult to treat. Consequently, better insights into the mechanism and dynamics of chromosomal instability are fundamental to understanding and treating cancer. First, we introduce scAbsolute – a computational tool to correctly estimate single-cell ploidy and replication status. Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy as a consequence. Correct estimation of the ploidy of single cell genomes is crucial for many aspects of downstream analysis, such as copy number calling and inference of cell phylogenies. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome doublings. 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 for various downstream analyses. Second, we introduce scUnique and the notion of recent copy number aberrations – a way to measure ongoing chromosomal instability using single-cell whole-genome DNA sequencing. We demonstrate scUnique’s effectiveness in a number of simulations and investigate the read depth required to reliably call copy number aberrations at the level of individual cells. scUnique detects differences in the activity of mutational processes in cell lines derived from treatment naive and relapse tumour samples. By measuring chromosomal instability at the level of individual cells, we provide quantitative, scalable and whole-genome level information about the dynamics of chromosomal instability, not available in previous studies relying on bulk DNA sequencing or single-cell imaging. The temporal and whole-genome resolution of scUnique offers the opportunity to gain novel insights into the generative process underlying chromosomal instability. Ultimately, this thesis contributes to a better understanding of the dynamics and fundamental mechanisms of chromosomal instability, and has the potential to improve treatment decisions in the future.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2023

Author dc:creator

• Schneider, Michael

Advisor dc:contributor.advisor

• Markowetz, Florian

• Cell cycle stage
• Chromosomal instability
• Copy number aberration
• Copy number calling
• Ongoing chromosomal instability
• Ploidy estimation
• recent copy number aberration
• Signatures of mutational processes
• Singe-cell genomics
• Single-cell copy number
• Single-cell DNA sequencing
• Whole-genome doubling
• Whole-genome duplication

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/ce52c642-54e8-4676-9f4c-173784cd99b1/download
• http://purl.org/NET/rdflicense/allrightsreserved

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.108660

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/368476