Gene Discovery through Germline Whole Exome Sequencing in Patients with Endometriosis-Associated Ovarian Cancer

Introduction: Endometriosis is common, effecting 5-25% of women of reproductive age. Its aetiology remains poorly understood, but is likely multifactorial, including hormonal, immunological, and genetic factors. Endometriosis shares several characteristics with malignancy, including a capacity for invasion, and is associated with an increased risk of ovarian cancer, particularly endometrioid and clear cell subtypes. Up to 60% of the underlying familial risk of ovarian cancer remains unexplained by high risk genes, particularly in endometrioid and clear cell ovarian cancers where the rate of germline BRCA1/2 mutations is low. With endometriosis’ estimated heritability of 51%, and its association with clear cell and endometrioid ovarian cancer, differing genetic predispositions must be considered in this group. Patients & Methods: Women from the Variants in Practice (ViP) research study, which enrols women with ovarian cancer and uninformative BRCA1/2 germline results for further genetic testing, were selected on the basis of clear cell or endometrioid ovarian cancer arising within an endometriotic focus. Germline whole exome sequencing (WES) was performed using next-generation platforms (Agilent SureSelect capture, Illumina HiSeq 2500). Potential loss of function variants were annotated through an established bioinformatics core; annotated data were filtered to exclude artefactual variants and likely irrelevant variants. Variant frequencies per gene were calculated and compared to control populations from publically available data (Genome Aggregation Database) to identify genes of interest with an increased ratio of loss of function germline variants. Further characterisation based on published expression and functional data identified promising gene candidates related to endometriosis associated ovarian cancer (EAOC).Results: Sixty-four ovarian cancer cases with endometriosis in the histopathology report were identified from the ViP cohort of 610 patients. On review, 25 cases of EOAC were identified, 15 endometrioid, 8 clear cell, and 2 mixed clear cell and endometrioid; 23 patients had adequate DNA for WES. A total of 344 germline loss of function variants were identified in 311 genes, after filtering for poor quality likely artefactual variants and common polymorphisms (allele frequency >0.005 in a population database), as well as excluding uncharacterised proteins, pseudogenes and highly polymorphic genes (immunoglobulins, taste and olfactory receptors). The literature on function, expression and known associations of all 311 genes was reviewed, prioritising them for further investigation. Based on variant quality and a documented function in ovarian cancer or endometriosis, a documented function in other malignancies, or a theoretical function in cancer, 30, 89 and 44 variants were prioritised in 28, 85 and 43 genes, respectively. Of those, 14 were identified as the most likely candidate genes with an increased ratio of loss of function variants in the cohort compared to control populations ranging from 4.3 to 237.9.Conclusion: The underlying genetic factors influencing EAOC risk differ from those in high grade ovarian cancer. Using this highly curated population, 14 candidate genes with an increased rate of loss of function variants per gene compared to control populations and a potentially functional relevance to endometriosis and/or ovarian cancers were identified. These genes will be discussed in further detail before characterisation in an expanded patient cohort.