Archival single cell sequencing reveals persistent subclones over years to decades of DCIS progression

We developed Arc-well, the first high-throughput method that can perform single cell DNA sequencing of thousands of cells from FFPE tissues. We applied Arc-well to reconstruct copy number lineages in 10 patients with intermediate and high-grade pure DCIS and matched recurrent disease that occurred 2-16 years later with FFPE block ages 4-31 years. Our data show that in DCIS with recurrent DCIS/IDC, the dormant subclones were often missed during the initial treatment, having implications for both the clinical diagnosis and treatment of the disease.