Abstract 729: Landscape of homologous recombination repair (HRR) mutations in prostate cancer profiled by ctDNA next-generation sequencing
Authors: Yen Jennifer , Gnerre Sante , Barbacioru Catalin , Helman Elena , Manor Ohad , Yablonovitch Arielle , Satya Ravi Vijaya , Liu Leo , Saam Jennifer , Fairclough Stephen , Nagy Becky , Lanman Richard , Chudova Darya , Talasaz AmirAli 
Published: September 2020

Abstract
Background: PARP inhibition can cause synthetic lethality and increased therapeutic sensitivity in patients with HRR deficiency (HRD), which can be detected through the molecular profiling of HRR genes. Prostate cancer has a high prevalence of HRD (20-25%, Athie 2019). High failure rates for tissue biopsy in metastatic prostate cancer patients (25-75%) (Ross 2005, Spritzer 2013) pose challenges for HRD profiling, underscoring the need for a non-invasive, ctDNA alternative. Copy number loss, a frequent cause of HRD, is further difficult to call due to signal dilution by cell-free leukocytic DNA. We developed a pipeline that detects loss-of-function SNV/Indels, structural rearrangements, and gene deletions to identify HRD on GuardantOMNITM, a 500-gene liquid biopsy panel. We present its performance across &gt;620 prostate cancer GuardantOMNITM samples.
Methods: Samples from 627 prostate cancer patients were processed on GuardantOMNITM RUO, with median unique coverage of 4982 molecules sequenced to 20,000x read depth. Somatic and germline SNVs and small indels were called using the Guardant bioinformatics pipeline (Helman 2018). A novel HRD module was developed to annotate pathogenic SNV/Indels and identify structural rearrangements, gene-level homozygous deletions, loss-of-heterozygosity (LOH) and genome-wide LOH, comprising of a novel CNV (Barbacioru 2019) and de-novo fusion caller (Gnerre, submitted). Loss-of-function variants were analyzed in 24 HRD genes.
Results: Pathogenic alterations in HRD genes were called in 260/620 (42%) prostate cancer samples with ctDNA detected: 28% of all samples had a pathogenic somatic or germline SNV/Indel, 20% had a homozygous deletion, 3.4% had a rearrangement involving an HRD gene. The majority of SNV/Indels occurred in BRCA2 (31% of all 158 SNV/Indels) and ATM (22%), similar to tissue (Dahwan 2016), but mutations also occurred across an additional 21 genes, including CDK12 (8%), CHEK2 (5%) and NBN (3.8%). Of prostate patients with a germline BRCA1/2 SNV/Indel and sufficient tumor shedding for LOH detection (max MAF&gt;10%), 10/19 (52%) also had LOH, compared to 86% in tissue (Jonsson 2019). Homozygous deletions were enriched in BRCA2 (6.9% of all samples), ATM (4.4%) and CHEK1 (2.3%). Rearrangements, including fusions and multi-exonic deletions, accounted for 6.5% of inactivating HRD mutations detected. In total, 24% of prostate samples had a biallelic inactivation involving an SNV, Indel or deletion.
Conclusion: We demonstrate in a prostate cancer cohort that GuardantOMNITM ctDNA profiling calls all classes of mutations contributing to HRD, with relative prevalence of alterations consistent with those in tissue. CfDNA presents a potential alternative for identifying patients who may benefit from PARP or cisplatin/platinum therapies, expanding the prevalence from 28% using small variants to 42% with the complete HRD biomarker set.
Citation Format: Jennifer Yen, Sante Gnerre, Catalin Barbacioru, Elena Helman, Ohad Manor, Arielle Yablonovitch, Ravi Vijaya Satya, Leo Liu, Jennifer Saam, Stephen Fairclough, Becky Nagy, Richard Lanman, Darya Chudova, AmirAli Talasaz. Landscape of homologous recombination repair (HRR) mutations in prostate cancer profiled by ctDNA next-generation sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 729.