Biodesix, Inc. leverages Bio-Rad Droplet Digital PCR technology for oncology research and beyond What features or capabilities do you value most highly when selecting molecular detection tools? • Sensitive and specific reagents that also allow for multiplexed detection of targets in a single specimen • Ability to deliver precise, reproducible results under defined conditions for specimen collection • A workflow that can be integrated into our secure systems, such as laboratory information management systems (LIMS) and behind firewalls • Support systems and field support • Ease of use by our trained clinical laboratory staff Ultra-Sensitive, Multiplexed Molecular Detection for Biomarker Research Gary Pestano, PhD, is the chief development officer at Biodesix, Inc., a solutions-based diagnostics company. Biodesix has lever-aged Droplet Digital™ PCR (ddPCR™) for molecular biomarker research and clinical sample testing for years, taking advantage of the technology’s sensitivity, precision, accuracy, and absolute quantification of nucleic acids for non-invasive translational applications. Pestano and his scientific teams recently had the opportunity to act as beta users for Bio-Rad Laboratories’ QX600™ ddPCR System. The sensitivity and robustness that comes with the inherent specificity of ddPCR technology for counting molecules is a significant advantage in multiple clinical areas where it is important to define quantitative measures. For example, ddPCR technology is ideal for establishing thresholds for response, or for recurrence, determining the amount of a gene or cell therapy in circulation, or identifying genetic imbalances. We view this as a requirement, especially in blood-based diagnostic testing. We compared multiple partition technologies and Next-Gen-eration Sequencing (NGS) approaches when we were initially looking to add blood-based rare variant detection to our cancer testing portfolio. Bio-Rad had (and continues to have) the most comprehensive in-silico validated and ready-to-go menu of PCR targets, as well as sensitive and clinical lab user-friendly software and instruments. Cost per reaction was also a factor that favored ddPCR technology. Advances that have kept ddPCR technology relevant to labs like ours include a continually expanding menu, applications across multiple fields, such as cell and gene therapy, the ability to create our own assay designs, as well as improved ancillaries and software upgrades for workflow management and data analysis. Having a responsive service team with local technicians is also tremendously important, as this is critical in a clinical laboratory for maintaining our ability to deliver timely and quality results. Amidst COVID-19 pandemic-related supply shortages, having What led Biodesix to select ddPCR technology as a core research tool? What do you view as especially important or promising applications of sensitive molecular detection and monitoring? The current areas of promise in blood-based nucleic acid testing, e.g., with GeneStrat ddPCR, include drug therapeutic monitoring in oncology and disease detection. For example, molecular monitoring tools can detect resistance and response markers in metastatic disease, minimal residual disease (MRD) following cancer treatment, and early-stage disease as part of broad genetic screening. Of course, these applications will need to meet robust regulatory requirements to advance into routine clinical practice, but promising data exists using available technologies, including Droplet Digital PCR. 1 46 OCTOBER 2022 • INSIDE PRECISION MEDICINE • WWW.INSIDEPRECISIONMEDICINE.COM
Inside Precision Medicine October 2022: Page 46
