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727 HRD scoring with a SNP assay
  1. T Mckee,
  2. Y Christinat,
  3. S Leboube and
  4. L Ho
  1. Hôpitaux Universitaires de Genève (HUG), Genève, Switzerland


Introduction/Background*Homologous recombination deficiency (HRD) is a well-known characteristic of BRCA-mutated tumors, an alteration present in ~30% of ovarian cancers and with different frequencies in breast, prostate and pancreatic cancers. The PAOLA-1 trial demonstrated that responders to Poly (ADP-ribose) polymerase (PARP) inhibitors do not only include BRCA-mutated tumors but also tumors that are BRCA-wildtype and display an HRD phenotype. Given its importance, many different scores and technologies have been proposed and commercialized to assess the HRD phenotype. Nonetheless many of these solutions are expensive and/or complicated to implement in practice.

Methodology We propose a novel HRD scoring algorithm based copy number alterations obtained from a clinical-grade SNP assay that works on FFPE samples (ThermoFisher Oncoscan Assay). The method has been evaluated on 400 high-grade ovarian carcinoma and 100 triple-negative breast cancer samples from the TCGA cohort. A validation was performed on an internal cohort of 50 ovarian cancers.

Result(s)*The algorithm performed better than two well-known commercial methods, the compound score from Telli et al. (LST+LOH+TAI) and the percentage of LOH bases across the genome, and classified correctly the BRCA-mutated cancers into the HRD category.

Conclusion*The high concordance with the LST+LOH+TAI score led to its inclusion into the clinical routine at the Geneva University Hospitals. The method is also being evaluated as a biomarker to predict response to Olaparib as part of phase 3 of the ENGOT HRD European Initiative (EHEI).

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