scUnique: Measuring Ongoing Chromosomal Instability

Chromosomal instability is a hallmark of cancer that can drive tumour heterogeneity and treatment resistance. However, scalable methods to measure the dynamics of chromosomal instability are lacking and thus historic genomic scars can be hard to distinguish from markers of currently active mutational processes. Here, we introduce scUnique, a novel approach to measure ongoing chromosomal instability from single-cell whole genome sequencing (scWGS) data. scUnique performs phylogeny-aware joint segmentation to refine single-cell copy number profiles and identifies recent copy number aberrations as statistically supported changes on the leaves of the inferred phylogenetic tree. This yields a per-cell measure of ongoing chromosomal instability at genome-wide resolution. We validate scUnique in (i) a comprehensive benchmarking study, (ii) in CRISPR-Cas-based experimental systems, and (iii) single-cell derived clones of a well-characterised ovarian model. We show that scUnique distinguishes ongoing HRD and FBI mutational processes. These results show that scUnique provides quantitative, scalable, genome-level information about ongoing chromosomal instability, not available in previous studies relying on bulk DNA-sequencing or single-cell imaging. In the future, these improved measurements could refine the understanding of mechanisms of chromosomal instability and lead to dynamic biomarkers for improved treatment decisions.