Senior Process Engineer, Assay Development

San Diego Stealth Startup; San Diego (CA); On-site; USD 131,000 - 140,000; Full time

Job summary

San Diego Stealth Startup is seeking a Senior Process Engineer in San Diego to drive automated NGS workflows from bench chemistry to production-ready, audited processes. You will collaborate across assay development, automation, QA/regulatory, and operations to deliver robust, scalable methods for library prep, extraction, and QC.

The role requires a builder mindset, comfort with ambiguity, and disciplined engineering in an early-stage environment where the roadmap is evolving.

Qualifications

• BS/MS in Chemical Engineering, Bioengineering, Biochemistry, Biotechnology, or related field.
• 6+ years of process engineering in clinical diagnostics or regulated labs.
• Hands-on experience with automated lab workflows and liquid handling platforms.
• Experience supporting LDT and/or FDA-regulated IVD development and design controls.
• Practical fluency with DOE, SPC, and data-driven process development methods.

Responsibilities

• Develop, optimize, and qualify automated workflows for NGS library preparation.
• Transfer bench-developed chemistry to automation platforms, resolve robustness issues.
• Apply DOE, SPC, and other statistical tools to characterize process performance.
• Contribute to reagent and consumable manufacturing, QC methods, and lot release.
• Execute IQ/OQ/PQ for automation and instrumentation in partnership with lab ops.
• Maintain process documentation, maps, BOMs, and design control alignment.
• Support tech transfer to clinical labs and assist validation during scale-up.

Skills

Process engineering

NGS automation

DOE

Statistical methods

Automation platforms

Education

BS/MS in Chemical Engineering or related field

Job description

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.

Location: San Diego, CA

Job Type: Full-Time

Compensation: $131,000 - $140,000

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 collaboration.