Senior Process Engineer, Assay Development

Senior Process Engineer, Assay Development Location: San Diego, CA Job Type: Full-Time Compensation: $131,000 - $140,000 Position Overview We are seeking a Senior Process Engineer to drive the development, automation, and productionalization of clinical next-generation sequencing (NGS) assays. This is a hands-on individual contributor role focused on translating bench-developed chemistry into robust, automated, audit-ready workflows that are ready for clinical lab deployment. The Senior Process Engineer will work in close partnership with assay development scientists, automation engineers, quality/regulatory specialists, and laboratory operations to design and qualify automated methods for library preparation, nucleic acid extraction, and sample quantitation and normalization. The role requires a builder’s mindset, comfort with ambiguity, and the discipline to apply rigorous engineering practices in an early-stage environment where the process roadmap is still being defined. Key Responsibilities • Develop, optimize, and qualify automated workflows for NGS library preparation.. • Partner with assay development scientists to transfer bench-developed chemistry onto automation platforms, identifying and resolving robustness, scaling, and operability issues. • Apply DOE, SPC, and other statistical tools to characterize process performance, define operating windows, and establish in-process and release specifications. • Contribute to reagent and consumable manufacturing and qualification activities, including QC method development and lot release strategy. • Execute equipment qualification activities (IQ/OQ/PQ) for automation and ancillary instrumentation in partnership with engineering and lab operations. • Support development and maintenance of process documentation, including process maps, equipment lists, and bills of materials, in alignment with design control expectations. • Participate in tech transfer of NGS assays to the clinical laboratory, supporting validation activities and resolving process issues that surface during scale-up and deployment. • Partner cross-functionally with chemistry, automation, software, quality, and lab operations to drive sustainable process improvements. Qualifications • BS/MS in Chemical Engineering, Bioengineering, Biochemistry, Biotechnology, or a related field. • 6+ years of experience in process engineering or process development within clinical diagnostics, NGS, biotech, or other regulated laboratory environments. • Hands-on experience developing and optimizing automated laboratory workflows, including direct protocol development on liquid handling platforms. • Demonstrated experience supporting clinical or near-clinical NGS assays, including library preparation, nucleic acid extraction, methylation conversion, or sample QC workflows. • Prior experience supporting LDT and/or FDA-regulated IVD assay development. Working knowledge of design controls and regulated development frameworks (ISO 13485, IVD or LDT context), with experience operating in a quality-driven environment. • Practical fluency in data-driven process development methods — DOE, statistical process control, Gage R&R, root cause analysis. • Ability to operate independently across multiple workstreams in an early-stage environment where requirements evolve. • Comfort operating in a stealth-stage, resource-constrained environment where processes are being built from the ground up. Why Join Us • Influence the foundational technologies and strategies of a company poised to shape the future of clinical genomics and healthcare. • Work in a dynamic, collaborative environment where innovation and scientific rigor are deeply valued. • Join a seasoned and multidisciplinary team tackling high-impact problems at the intersection of science and engineering. • Competitive compensation and equity package, comprehensive benefits, and flexibility to support work-life integration. We are an equal opportunity employer. We thrive on diversity and…