Identification of homologous recombination and repair (HRR) deficiency using circulating tumor DNA (ctDNA) in advanced prostate cancer (aPC).

Abstract

180 Background: ctDNA testing is a non-invasive means to identify genomic alterations in patients with aPC, including BRCA1/2 and other HRR gene alterations, which are targetable by PARP inhibitors (PARPi). However, classes of HRR inactivating mutations, such as copy number loss and large genomic rearrangements (LGRs) are challenging to detect by ctDNA. Here we describe a CLIA-validated plasma-based ctDNA test that identifies copy number loss and LGRs, in addition to SNV and Indels, in HRR genes. We report the landscape of HRR deficiency (HRD) in a clinical population of > 2,000 patients with aPC. Methods: 2932 samples from patients with aPC previously tested as part of clinical care using an 83-gene cfDNA NGS assay (Guardant360) within an 11-month period were reanalyzed for presence of HRD. HRD alterations were defined as copy number loss, LGR (i.e. intergenic or intragenic gene rearrangements) and deleterious SNV/Indel in 7 clinically focused HRR genes ( ATM, BRCA1, BRCA2, CDK12, CHEK2, PALB2, RAD51D). Clinical information, when available, was obtained from test requisition forms. Results: The median age of the analyzed cohort was 73 years (range: 31-100); when known, the majority of patients were tested at disease progression (81%, 2242/2750). In total, an inactivating BRCA1/2 variant was was identified in 26% (605/2932) of reanalyzed patients, comprising BRCA1/2 loss of heterozygosity (LOH) (13.4% of patients), deleterious SNV or Indels (5.5%), homozygous deletions (3.3%) and LGRs (1.1%). The prevalence of patients with any inactivating HRR alteration increased to 38.5% with the expanded 7 gene set. Overall, prevalence of loss-of-function mutations (SNV/Indel, homozygous deletion or LGR) in BRCA2 was 4.5X frequent than in BRCA1 and comparable to previously described prostate cohorts (8.4% and 1.8% compared to 8.6% and 1.1% in tissue, respectively). Conclusions: Genomic profiling by ctDNA identified an HRR alteration landscape comparable to previously characterized tissue cohorts, with enrichment in BRCA2 over BRCA1 inactivating mutations and frequent BRCA1/2 LOH. Patients with aPC may benefit from PARPi eligibility determination using rapid and reliable ctDNA assessment, particularly at progression. Future studies should assess PARPi outcomes for this population.