Marc Williams, Ignacio Vázquez-Garćıa, Grittney Tam, Michelle Wu, Nancy Varice, Eliyahu Havasov, Hongyu Shi, Duaa H. Al-Rawi, Gryte Satas, Hannah Lees, Jake June-Koo Lee, Matthew Myers, Matthew Zatzman, Nicole Rusk, Emily Ali, Ronak Shah, Michael F. Berger, Neeman Mohibullah, Yulia Lakhman, S Dennis, Nadeem R. Abu‐Rustum, Carol Aghajanian, Andrew McPherson, Dmitriy Zamarin, Brian Houck‐Loomis, Britta Weigelt, Claire F. Friedman, Sohrab P. Shah
Emergence of drug resistance is the main cause of therapeutic failure in patients with high-grade serous ovarian cancer (HGSOC)1. To study drug resistance in patients, we developed CloneSeq-SV, which combines single-cell whole-genome sequencing2 with targeted deep sequencing of clone-specific genomic structural variants in time-series cell-free DNA. CloneSeq-SV exploits tumour clone-specific structural variants as highly sensitive endogenous cell-free DNA markers, enabling the relative abundance measurements and evolutionary analysis of co-existing clonal populations over the therapeutic time course. Here, using this approach, we studied 18 patients with HGSOC over a multi-year period from diagnosis to recurrence and showed that drug resistance typically arose from selective expansion of a single or small subset of clones present at diagnosis. Drug-resistant clones frequently showed interpretable and distinctive genomic features, including chromothripsis, whole-genome doubling, and high-level amplifications of oncogenes such as CCNE1, RAB25, MYC and NOTCH3. Phenotypic analysis of matched single-cell RNA sequencing data3 indicated pre-existing and clone-specific transcriptional states such as upregulation of epithelial-to-mesenchymal transition and VEGF pathways, linked to drug resistance. In one notable case, clone-specific ERBB2 amplification affected the efficacy of a secondary targeted therapy with a positive patient outcome. Together, our findings indicate that drug-resistant states in HGSOC pre-exist at diagnosis, leading to positive selection and reduced clonal complexity at relapse. We suggest these findings motivate investigation of evolution-informed adaptive treatment regimens to ablate drug resistance in future HGSOC studies. A combined sequencing technique assesses 18 patients with high-grade serous ovarian cancer over a multi-year period from diagnosis to recurrence and shows drug resistance typically arises from selective expansion of one or a few clones present at diagnosis.