biostudies-literatureWang KCancer Research UKNCI NIH HHS3968-3982.e15https://www.ebi.ac.uk/biostudies/studies/S-EPMC11831769biostudies-literatureUnknown186(18)Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.CellArchival single-cell genomics reveals persistent subclones during DCIS progression.PMC11831769C38317/A24043P30 CA01667224043R01 CA185138R01 CA240526R01 CA236864Kumar TNavin NEGibbons DLWesseling JZhang JSawyer ELips EHThompson AMWang JWang KZhao YZurita AJBai SThennavan AKing LMMarks JRShah VMinussi DCFutreal ASei EAparicio ACasasent AKLi JChapin BYang Lvan der Borden CLXiao ZKristel PTran TMHu MGrand Challenge PRECISION ConsortiumHwang ESYe JfalseArchival single-cell genomics reveals persistent subclones during DCIS progression.Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.2023-01-01T00:00:00Z2023 Aug2026-06-02T18:23:38.528Z2025-04-07T11:27:47.04ZS-EPMC118317693758636210.1016/j.cell.2023.07.024