Background: Genome-wide analysis was conducted on tumors obtained from patients enrolled in the NOVA study, a Phase 3 clinical trial evaluating the PARP inhibitor niraparib as a maintenance treatment in patients with platinum-sensitive ovarian cancer. Homologous recombination deficiency (HRD) and mutations in DNA damage repair genes were evaluated.
Material and methods: DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor tissue and used to create libraries that were hybridized to a custom Agilent SureSelect capture array carrying probes for 54,091 single nucleotide polymorphism sites distributed across the human genome, as well as probes targeting 43 genes involved in DNA repair, including BRCA1 and BRCA2. The captured and enriched DNA was sequenced on an Illumina HiSeq 2500 sequencer. Sequences covering SNP positions were used to generate allelic imbalance profiles. Measures of genomic instability, including determination of an HRD score (integer value of 0-100), were calculated using allelic imbalance profiles and determination of loss of heterozygosity (LOH) by allele-specific copy number (ASCN). A previously identified HRD threshold score of 42 was used to define HRD positivity in the absence of a BRCA mutation.
Results: The NOVA study is a Phase 3, multicenter, randomized, double-blind, placebo-controlled study of niraparib as maintenance therapy in ovarian cancer patients who have either gBRCAmut or a tumor with high-grade serous histology and who have responded to their most recent chemotherapy containing a platinum agent. Tumor BRCA mutational status, HRD score and genomic sequencing of 43 DNA repair genes were obtained from tumor samples from both gBRCAmut and non-gBRCAmut cohorts. In the gBRCAmut cohort, HRD analysis of the tumor confirmed the presence of a deleterious or suspected deleterious mutation in all cases. In addition, an HRD score ≥ 42 and the presence of a deleterious mutation in TP53 with loss of heterozygosity (LOH) were observed in nearly all tumors. In the non-gBRCA cohort, somatic BRCA mutations were observed in approximately 13% of tumors, and approximately half of tumors with no evidence of a BRCA mutation had a high HRD score. In both cohorts, the use of three scoring algorithms (LOH, telomeric allelic imbalance [TAI], large-scale state transitions [LST]), was more predictive of BRCA mutational status than LOH alone. Additional genomic sequencing identified deleterious mutations with LOH in DNA repair genes, such as BRIP1, CDK12, RAD51C, PTEN, and RAD51D, with many tumors exhibiting multiple deleterious mutations.
Conclusions: High grade serous ovarian cancer is characterized by a high degree of genomic instability. Genomic analysis in the clinical setting is able to identify patients with both germline and somatic BRCA mutations, in addition to BRCAwt tumors with other genetic defects that may be sensitive to agents exploiting deficiencies in HR.
Citation Format: Keith Wilcoxen, Christopher Neff, Victor Abkevich, Joshua Timothy Jones, Kathryn Kolquist, Michael Mirza, Jerry Lanchbury, Keith Mikule, Shefali Agarwal, Anne-Renee Hartman, Alexander Gutin, Kirsten Timms. Homologous recombination deficiency (HRD) of high grade serous ovarian tumors from the NOVA Phase III clinical study. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C53.
