The mutation and clonality profile of genomically unstable high grade serous ovarian cancer is established early in tumor development and conserved throughout therapy resistance

High grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy, killing more than 9,000 women each year in the United States alone. Nearly 80% of patients with HGSOC tumors will experience recurrence within 5 years, but little is known about the mechanisms that drive this process. Intratumor heterogeneity is believed to be a key feature of recurrence and resistance in HGSOC tumors, with early studies reporting diverse and complex mechanisms of the seeding of metastatic sites, including metastasis reseeding the primary tumor. Few studies have investigated temporal changes to clonality and structural variants through disease recurrence and the development of chemoresistance as surgical debulking is not frequently performed at this later stage. We performed multi-omic profiling in paired chemo-naive and chemoresistant tumors from 32 HGSOC patients to investigate the mutational and genomic landscape of disease progression. Somatic mutation profiles were largely conserved through disease progression. Mutational burdens did not significantly differ across recurrence but were driven by homologous recombination repair deficiency status. Clonal composition and dynamics were measured through variant allele frequency alterations as tumors progressed from primary chemo-naïve to recurrent chemo-resistant tumors. A novel candidate driver gene, MDC1 , from the homologous recombination repair pathway, was significantly mutated and over-represented in patients with homologous recombination proficient tumors, with somatic mutations clustered in a single exon. Tumor evolution and phylogeny revealed that few changes in clonal abundance and complexity occur across the disease course in these patients. Taking structural variants into account, homologous recombination repair proficient (HRP) tumors tend to be polyclonal while homologous recombination repair deficient (HRD) tumors tend to be monoclonal, accompanied by a longer progression-free survival than the HRP patients. Three distinct classes of tumors were identified by structural variant signature analysis: tumors defined by DNA losses, tumors defined by DNA gains, and tumors defined by copy number neutral changes, which were largely defined by HRD status. Each class displayed distinct regions of the chromosome that were frequently affected by large scale SV events (>5Mb). Although no regions were frequently altered in recurrent tumors, GO analysis revealed that recurrent tumors have a significantly reduced immune response, which was not seen in the primary tumors. Ultra long read sequencing validated a majority of the SVs identified in short read sequencing and identified additional SVs undetected by short reads. These analyses identify that the phenotype of high grade serous ovarian tumors as defined by mutation and clonality profiles is established early in disease development and remain largely unchanged through chemotherapy and recurrence. This, when considered with the significant inter-patient heterogeneity identified in HGSOC, demonstrates the need for personalized therapies based on tumor profiling.