Development of the NOGGO GIS v1 Assay, a Comprehensive Hybrid-Capture-Based NGS Assay for Therapeutic Stratification of Homologous Repair Deficiency Driven Tumors and Clinical Validation

SIMPLE SUMMARY: Genomic instability (GI) caused by homologous repair deficiency (HRD) is a novel highly clinically relevant biomarker that cannot only identify patients suffering from high-grade serous ovarian cancer that may benefit from poly-ADP ribose polymerase (PARP) inhibitors but also helps in functionally annotating mutations found within genes of the homologous repair pathway. Tumors in which GI plays a role in therapeutic considerations currently include ovarian, breast, prostate, and pancreatic cancer. Therefore, we developed, implemented, and clinically validated a comprehensive custom Agilent XT HS2 hybrid capture next-generation sequencing (NGS) assay that allows in addition to the analysis of homologous recombination repair (HRR) pathway and relevant cancer genes, complex BRCA1 and BRCA2 alterations including large deletions and the evaluation of the GI-Score (GIS) status on one single tumor sample. The NOGGO (Northeastern German Society for Gynecologic Oncology) GIS v1 assay was validated as part of the European Network for Gynaecological Oncological Trial groups (ENGOT) HRD European Initiative on a subset of the ENGOT PAOLA-1 clinical trial samples. Patients identified as HRD-positive using the NOGGO GIS v1 assay showed a benefit of progression-free survival (PFS) and overall survival (OS) with comparable hazard ratios to the Myriad MyChoice assay. ABSTRACT: The worldwide approval of the combination maintenance therapy of olaparib and bevacizumab in advanced high-grade serous ovarian cancer requires complex molecular diagnostic assays that are sufficiently robust for the routine detection of driver mutations in homologous recombination repair (HRR) genes and genomic instability (GI), employing formalin-fixed (FFPE) paraffin-embedded tumor samples without matched normal tissue. We therefore established a DNA-based hybrid capture NGS assay and an associated bioinformatic pipeline that fulfils our institution’s specific needs. The assay´s target regions cover the full exonic territory of relevant cancer-related genes and HRR genes and more than 20,000 evenly distributed single nucleotide polymorphism (SNP) loci to allow for the detection of genome-wide allele specific copy number alterations (CNA). To determine GI status, we implemented an %CNA score that is robust across a broad range of tumor cell content (25–85%) often found in routine FFPE samples. The assay was established using high-grade serous ovarian cancer samples for which BRCA1 and BRCA2 mutation status as well as Myriad MyChoice homologous repair deficiency (HRD) status was known. The NOGGO (Northeastern German Society for Gynecologic Oncology) GIS (GI-Score) v1 assay was clinically validated on more than 400 samples of the ENGOT PAOLA-1 clinical trial as part of the European Network for Gynaecological Oncological Trial groups (ENGOT) HRD European Initiative. The “NOGGO GIS v1 assay” performed using highly robust hazard ratios for progression-free survival (PFS) and overall survival (OS), as well a significantly lower dropout rate than the Myriad MyChoice clinical trial assay supporting the clinical utility of the assay. We also provide proof of a modular and scalable routine diagnostic method, that can be flexibly adapted and adjusted to meet future clinical needs, emerging biomarkers, and further tumor entities.