Background: High-grade serous ovarian carcinoma (HGSOC) has a significant hereditary component, only half of which is explained by known genes. Previously, we performed germline exome sequencing on BRCA1 and BRCA2-negative HGSOC patients and identified 43 novel and 3 three previously proposed predisposition genes (PALB2, ATM, MRE11A) enriched for loss-of-function (LoF) variants compared to population controls. Due to the small number of cases per gene, additional orthogonal validation studies were implemented using an integrated germline and tumour sequencing approach.

Methods: Germline case-control analyses were performed using genomic data from 496 BRCA1 and BRCA2-negative HGSOC cases and 4273 local disease-free controls. Whole exome or whole genome Sequencing of 111 HGSOC tumours from carriers of germline LoF variants in 49 candidate and proposed genes was performed seeking evidence of biallelic inactivation.

Results: Case-control analyses confirmed enrichment for 47/49 previously identified genes. Proposed genes PALB2 and ATM validated as moderate-risk HGSOC predisposition genes, with 6/8 germline carrier tumours exhibiting biallelic inactivation accompanied by characteristic signatures. Among candidate genes, nineteen were excluded based on loss of the variant allele in one or more tumours. Twenty-four genes showed loss of the wild-type allele in one or more tumours, although only LLGL2 consistently showed biallelic inactivation in all carriers, supporting its potential as a novel HGSOC susceptibility gene.

Conclusion: This study provides corroborating evidence of a role for PALB2 and ATM in HGSOC predisposition. A putative HGSOC predisposition role for LLGL2 is supported by the observation of consistent biallelic inactivation and case-control epidemiological data. Tumour sequencing is an efficient strategy for triaging candidate cancer predisposition genes and is crucial for reproducible gene discovery in familial cancer studies that solely use case-control data.