Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL

Single-cell barcoding technologies enable genome sequencing of thousands of individual cells in parallel, but with extremely low sequencing coverage (<0.05 [Formula: see text]) per cell. While the total copy number of large multi-megabase segments can be derived from such data, important allele-specific mutations – such as copy-neutral loss-of-heterozygosity (LOH) in cancer – are missed. We introduce Copy-number Haplotype Inference in Single-cells using Evolutionary Links (CHISEL), a method to infer allele- and haplotype-specific copy numbers in single cells and subpopulations of cells by aggregating sparse signal across hundreds or thousands of individual cells. We applied CHISEL to 10 single-cell sequencing datasets of [Formula: see text] cells from two breast cancer patients. We identified extensive allele-specific copy-number aberrations (CNAs) in these samples, including copy-neutral LOHs, whole-genome duplications (WGDs), and mirrored-subclonal CNAs. These allele-specific CNAs affect genomic regions containing well-known breast cancer genes. We also refined the reconstruction of tumor evolution, timing allele-specific CNAs before and after WGDs, identifying low-frequency subpopulations distinguished by unique CNAs, and uncovering evidence of convergent evolution.