Junke Wang
This dissertation deciphers somatic evolution and metastatic dissemination through single-cell copy number profiling by integrating experimental and computational advances. First, to de-fine the baseline of copy number mosaicism in healthy tissues, I profiled 83,206 epithelial cells from normal breast tissues of 49 healthy women using single-cell DNA sequencing and analyzed matched single-cell DNA&ATAC co-assays from 19 women, showing that all women harbor rare aneuploid epithelial cells (median 3.19%) that increase with age and most aneuploid cells undergo clonal expansion (median 82.22%). The recurrent CNA events, including 1q gain and 10q/16q/22q losses, overlap with alterations seen in invasive breast cancers while belong mainly to luminal lin-eages in histologically normal ductal and lobular structures. Second, I developed CopyKit, a scalable end-to-end framework for single-cell DNA copy number analysis, with a method to infer absolute ploidy at single-cell resolution. Applying these methods to 11,845 cells from primary tumors and matched metastases resolved clonal substructure, reconstructed metastatic lineages, identified primary-tumor subclones that seeded distant metastasis, and revealed both spatial in-termixing and regional segregation of subclones in liver metastases. Together, these results show that high-throughput single-cell copy number profiling, coupled with scalable and robust compu-tational modeling, can resolve phylogenetic evolution from normal tissue mosaicism to malignant evolution and provide a quantitative framework for studying tumor initiation, progression and metastasis.