The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.

There is a need for transplantable murine models of ovarian high-grade serous carcinoma (HGSC) with regard to mutations in the human disease to assist investigations of the relationships between tumor genotype, chemotherapy response, and immune microenvironment. In addressing this need, we performed wholeexome sequencing of ID8, the most widely used transplantable model of ovarian cancer, covering 194,000 exomes at a mean depth of 400Â with 90% exons sequenced >50Â. We found no functional mutations in genes characteristic of HGSC (Trp53, Brca1, Brca2, Nf1, and Rb1), and p53 remained transcriptionally active. Homologous recombination in ID8 remained intact in functional assays. Further, we found no mutations typical of clear cell carcinoma (Arid1a, Pik3ca), low-grade serous carcinoma (Braf), endometrioid (Ctnnb1) validates new CRISPR-generated models of HGSC to investigate its biology and promote mechanism-based therapeutics discovery.

Genomic complexity from profound copynumber aberration has prevented effective molecular stratification of ovarian and other cancers. Here we present a method for copynumber signature identification that decodes this complexity. We derived eight signatures using 117 shallow wholegenome sequenced highgrade serous ovarian cancer cases, which were validated on a further 497 cases. Mutational processes underlying the copynumber signatures were identified, including breakagefusionbridge cycles, homologous recombination deficiency and wholegenome duplication. We show that most tumours are heterogeneous and harbour multiple signature exposures. We also demonstrate that copy number signatures predict overall survival and changes in signature exposure observed in response to chemotherapy suggest potential treatment strategies. 2. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was . http://dx.doi.org/10.1101/174201 doi: bioRxiv preprint first posted online Aug. 9, 2017;The discrete mutational processes that drive copynumber change in human cancers are not readily identifiable from genomewide sequence data. This presents a major challenge for the development of precision medicine for cancers that are strongly dominated by copynumber changes, including highgrade serous ovarian (HGSOC), oesophageal, nonsmallcell lung and triple negative breast cancers 1 . These tumours have low frequency of recurrent oncogenic mutations, few recurrent copy number alterations and highly complex genomic profiles 2 .HGSOCs are poor prognosis carcinomas with ubiquitous TP53 mutation 3 . Despite efforts to discover new molecular subtypes and targeted therapies, overall survival has not improved over two decades 4 . Current genomic stratification is limited to defining homologous recombinationdeficient (HRD) tumours 57 , and classification using gene expression does not currently have clinical utility 8,9 . Detailed genomic analysis using whole genome sequencing has shown frequent loss of RB1, NF1 and PTEN by gene breakage events 10 and enrichment of amplification associated foldback inversions in nonHRD tumours 11 . However, none of these approaches has provided a broad mechanistic understanding of HGSOC, reflecting the challenges of detecting classifiers in extreme genomic complexity.Recent algorithmic advances have enabled interpretation of complex genomic changes by identifying mutational signatures genomic patterns that are the imprint of mutagenic processes accumulated over the lifetime of a cancer cell . Importantly, these studies show that tumours typically harbour multiple mutational processes requiring computational approaches that can robustly identify coexistent mutational signatures. Quantification of the exposure of a tumour to specific mutational signatures provides a rational framework to personalise therapy 14 but currently is not readily applicable to copynumber driven tumours. We hypothesized that specific feat...

Transplantable murine models of ovarian high grade serous carcinoma (HGSC) remain an important research tool. We previously showed that ID8, a widely-used syngeneic model of ovarian cancer, lacked any of the frequent mutations in HGSC, and used CRISPR/Cas9 gene editing to generate derivatives with deletions in Trp53 and Brca2. Here we have used one ID8 Trp53 −/− clone to generate further mutants, with additional mutations in Brca1, Pten and Nf1, all of which are frequently mutated or deleted in HGSC. We have also generated clones with triple deletions in Trp53, Brca2 and Pten. We show that ID8 Trp53 −/−;Brca1 −/− and Trp53 −/−;Brca2 −/− cells have defective homologous recombination and increased sensitivity to both platinum and PARP inhibitor chemotherapy compared to Trp53 −/−. By contrast, loss of Pten or Nf1 increases growth rate in vivo, and reduces survival following cisplatin chemotherapy in vivo. Finally, we have also targeted Trp53 in cells isolated from a previous transgenic murine fallopian tube carcinoma model, and confirmed that loss of p53 expression in this second model accelerates intraperitoneal growth. Together, these CRISPR-generated models represent a new and simple tool to investigate the biology of HGSC, and the ID8 cell lines are freely available to researchers.

We sought to identify the genomic abnormalities in squamous cell carcinomas (SCC) arising in ovarian mature cystic teratoma (MCT), a rare gynecological malignancy of poor prognosis. We performed copy number, mutational state, and zygosity analysis of 151 genes in SCC arising in MCT ( = 25) using next-generation sequencing. The presence of high-/intermediate-risk HPV genotypes was assessed by quantitative PCR. Genomic events were correlated with clinical features and outcome. MCT had a low mutation burden with a mean of only one mutation per case. Zygosity analyses of MCT indicated four separate patterns, suggesting that MCT can arise from errors at various stages of oogenesis. A total of 244 abnormalities were identified in 79 genes in MCT-associated SCC, and the overall mutational burden was high (mean 10.2 mutations per megabase). No SCC was positive for HPV. The most frequently altered genes in SCC were (20/25 cases, 80%), (13/25 cases, 52%), and (11/25 cases, 44%). Mutation in was associated with improved overall survival. In 8 of 20 cases with mutations, two or more variants were identified, which were bi-allelic. Ovarian SCC arising in MCT has a high mutational burden, with mutation the most common abnormality. The presence of mutation is a good prognostic factor. SCC arising in MCT share similar mutation profiles to other SCC. Given their rarity, they should be included in basket studies that recruit patients with SCC of other organs. .