A comprehensive assessment of a newly designed non-exonic SNP-based NGS panel for HRD detection

Ovarian cancer is a global problem, is typically diagnosed at a late stage, and has no effective screening strategy. Platinum-based chemotherapy or Poly(ADP-ribose) polymerase inhibitors (PARPis) treatment are most frequently applied for ovarian cancer patients who are inoperable and in the advanced stage. The recognition of homologous recombination deficiency (HRD) as a biomarker to predict the efficiency of Platinum-based or PARPis treatment. Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES) can detect tumor HRD status but have several disadvantages restricting their clinical application. My choice HRD CDx and Foundation Focus CDx have been approved by FDA for HRD detection. However, whether they apply to the Chinese population or not is still unknown. This study developed an non-exonic SNP-based Tg-NGS panel and comprehensively examined its performance. Our results showed that the panel is cost and time-saving compared with WGS but equivalent to SNP microarray on CNV and HRD detection, especially for Chinese patients. This newly developed kit is promising in clinical application to guide ovarian cancer and other cancer therapy.