The diversity and clinical relevance of germline DNA damage repair gene variants in 3005 patients with metastatic prostate cancer.

Abstract

227 Background: Inherited genetic variants in genes linked to DNA damage repair (DDR) can increase the risk of developing aggressive prostate cancer but the full spectrum of relevant genes and deleterious variants is unknown. We sought to determine the landscape of inherited DDR genetic variants and their clinical implications in 3005 patients with metastatic prostate cancer (mPCa). Methods: We performed targeted sequencing on peripheral blood leukocyte DNA from a meta-cohort of 3005 patients with mPCa enrolled for genetic testing between 2014 to 2025, and searched for small variants and large structural variants (SVs) across 32 DDR-associated genes. Only variants annotated as (likely) pathogenic in ClinVar or those predicted to truncate the protein were included. Clinical data for correlative analysis was available for 81%. Additional targeted sequencing on tumor DNA was selectively performed to determine somatic DDR gene status. Results: Germline DDR gene variants were detected in 269/3005 (9%) patients, six had >1 variant, half had evaluable tumor testing available. Germline variants were most common observed in BRCA2 (2.8%), ATM (1.2%), and CHEK2 (1.1%), for which second somatic allele inactivation was detected in 93%, 100%, and 20%, respectively. Rare germline variants were observed in ERCC2 (0.5%), PALB2 (0.4%), BRCA1 (0.4%), and MSH2/6 (0.3%), PMS2 (0.3%), FANCD2 (0.3%), FANCA (0.2%), RAD51B (0.2%) and CDK12 (0.1%), for which second allele inactivation was not observed for ERCC2 , PMS2 and RAD51B (n=13 with evaluable tumor testing). Somatic allele inactivation mechanisms differed per gene; some predominantly inactivated by (partial) loss of heterozygosity ( BRCA2 , CHEK2 , FANCA ) and others by secondary mutations ( ATM , PALB2 ). Novel gene-truncating germline SVs (size 38bp-29.4kb) were identified in 11 patients, making up 3/10 (30%) MSH6 / MSH2 and 2/85 (2%) BRCA2 germline variants. Patients with germline BRCA2 variants had a higher proportion of ≥4 ISUP Grade Group pathology at diagnosis (85% vs 70%, p=0.04) and more progressed to castration-resistance within 1 year (56% vs 40%, p=0.03) compared to patients without germline DDR variants, but synchronous metastatic disease was observed at similar frequencies (59% vs 58%, p=1). Germline BRCA2 variants were associated with a shorter overall survival from initial diagnosis (median 5.0 vs 10.2 years for wildtype BRCA2 , p<0.01), including in a multivariable analysis with age, synchronous metastatic disease and pathology grade group (HR 2.79, 95%CI 1.93-4.04, p<0.01). Conclusions: This large mPCa cohort enabled frequency assessment of common and rare germline variants in DDR genes. BRCA2 was prominently linked to biallelic gene loss in the tumor and disease aggression. Clinical grade tests should account for large germline SVs and consider the different mechanisms of somatic gene inactivation.