Detection of germline alterations in homologous recombination repair genes by adaptive sampling

Abstract Germline mutations in homologous recombination repair (HRR) pathway genes, such as BRCA1/2, PALB2 and RAD51C, can lead to oncogenic transformation and cancer. Poly-ADP ribose polymerase (PARP) inhibitor therapies have been developed to selectively target HRR-deficient cancer cells in multiple cancer types, and therefore it is critical to identify germline HRR mutations in patients to inform the most effective treatment options. Current diagnostic techniques for HRR mutation detection utilize short-read next generation approaches, like the MSK-IMPACT capture-based sequencing assay, which can be time-consuming and technically complex to run and analyse. We investigated the feasibility of using nanopore sequencing with adaptive sampling to detect the full spectrum of germline mutations relevant to HRR deficiency. Blood collected from solid tumor patients previously profiled using MSK-IMPACT and known to harbor germline HRR mutations were used to benchmark adaptive sampling against capture-based short-read data, in terms of accuracy and turnaround time. We demonstrate the concordance of HRR variant calls for pathogenic mutations between the two approaches, meaning that adaptive sampling has the potential to detect clinically relevant alterations in a time-effective and highly customizable way. Further refinement of this workflow is needed to determine multiplexing capacity to reduce cost, and to establish the minimum coverage required for robust variant detection to reduce sequencing time. Also, processing more samples will further validate the accuracy and sensitivity of this methodology, enabling its adoption as a rapid low-cost diagnostic tool in clinical oncology. Biography Stephanie Chrysanthou leads the R&D team in the Integrated Genomics Operation facility at Memorial Sloan Kettering Cancer Center, USA. Her goal is to adopt and optimize new genomic technologies to enable basic, clinical and translational projects across the Cancer Center. One of her research interests includes optimizing nanopore sequencing methodologies for bulk and single-cell analysis to detect structural variants and transcript isoforms in cancer patient samples. Previously, during her doctoral and post-doctoral studies at the University of Cambridge, UK and Albert Einstein College of Medicine, New York, she worked on the epigenetic mechanisms of early mammalian embryonic development.