Case Report: Whole genome sequencing of small cell ovarian carcinomas

Small Cell Carcinoma of the Ovary (SCCO) is an extremely rare form of ovarian cancer characterised by bi-allelic mutations in the SMARCA4 gene, a member of the SWI/SNF chromatin remodelling complex. Most previous analyses have characterised SCCO using whole exome sequencing; we present the treatment plans of two SCCO patients with post-treatment analysis of whole genome sequencing and tumour RNA sequencing which include structural variant and mutational signature analysis not previously reported in the literature for this cancer type. Both patients underwent salpingo-oophorectomy followed by BEP chemotherapy and pelvic radiotherapy leading to 34 month remission in one case though one patient died 12 months post-diagnosis. Consistent with known aetiology, we identified complete SMARCA4 loss of function and probable SMARCA2 expression loss in both patients. Beyond this, both tumours present remarkably low tumour mutational burdens and were microsatellite stable though one sample also showed chromosomal instability with high levels of inversions and a ploidy level of 2.8 which has not been well characterised in SCCO patients. This report contributes towards the small number of cases of SCCO that are currently documented and have their genome characterised in the literature.