Discussion

We have shown the range of genomic diversity at nucleotide, copy number and gene expression scales present in six patients with HGSC. These samples were resected prior to treatment, revealing intratumoural diversity in the tumours’ natural evolutionary state. Our results were consistent with recent reports 39 that considerable genomic diversity is measurable in HGSCs at the level of copy number. However, in some cases (cases 3 and 5) we observed large-scale copy number differences in spatially separated samples that were not evident at the level of mutational profiling, indicative of different mutational mechanisms operating independently in different parts of a tumour. Together, copy number and mutational profiling identified well-characterized mutations in genes such as PIK3CA, CTNNB1 and PDGFRB, as well as homozygous deletions in NF1, that were not present in all samples of the same case. With the exception of TP53, our data suggest that well-known, actionable driver mutations may only be partially represented if only a single sample is considered per patient. Our results establish that embedded within the context of extreme intra- and intertumour heterogeneity, TP53 mutation remains the most stable genomic feature in HGSC. However, as efforts towards precision medicine informed by mutational landscapes of tumours reach maturity, it will be imprudent to ignore the degree to which regional genomic variation is present in primary samples prior to any treatment-related selective pressures. Moreover, studies of evolution in cancer through analysis of serial biopsies (eg through pre- and post-treatment samples, or comparisons of primary and metastatic samples), will need to account for evidence of divergent profiles simply due to regional sampling bias.

Mutational profiling revealed for the first time that mutations beyond TP53 are present in FT lesions. In case 4, we used the full spectrum of mutations to establish that evolutionary trajectories of two histologically and karyotypically distinct tumours within a single patient arose from a common aetiology, with 26.2% of all mutations (including TP53) conserved in the tubal lesion. Our results indicate how histologically distinct cell populations in the same patient can be linked by common aetiology in the FT. In contrast to HGSC, endometrioid tumours are thought to develop from atypical ovarian endometriosis, with the FT merely acting as a conduit for endometrial epithelium to spread to the ovary (reviewed in 40). The possibility of the FT playing a causative role in rare cases of endometrioid carcinoma, or mixed endometrioid–serous carcinoma, has not yet been explored. Mutations in case 5 revealed the FT lesion to be a metastatic implant more closely related to a lymph node metastasis than to the ovarian samples. Thus, future investigations into aetiological underpinnings of HGSC will likely benefit from mutational comparison to extra-tubal sites to definitively establish the evolutionary origin of FT lesions.

We noted an extreme case of unexpected genomic conservation. In case 6, samples were obtained at primary surgery and after 42 months, with 21 cycles of multi-agent chemotherapy in between. The two samples exhibited near-identical genomic landscapes. Coupled with the long survivorship of this patient, this observation represents an intriguing anecdote. Larger studies will be needed to establish if stable clonal population structure is a feature of long survivorship.

Finally, as proof of concept, examination of plasma ctDNA suggested that representative mutations in the ancestral clone and mutations present in subclones could be detected in ctDNA, although sensitivity to detect mutations varied from patient to patient. This implies that clinical sensitivity analyses will need to be undertaken to establish the generalizability of ctDNA analysis to clonally diverse tumours.

In summary, our study unveils the extensive genomic diversity in primary, untreated, high-grade serous cancers of the ovary prior to treatment-related selection pressures, and illuminates highly individualized evolutionary trajectories that will require detailed consideration if curative therapeutic strategies are to be achieved.