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 to drive automated development, productionalization, and validation of clinical NGS assays. This hands-on IC role translates bench chemistry into robust, auditable workflows for clinical deployment.

The role collaborates with assay development, automation, quality, and operations to design and qualify automated methods for library prep, extraction, and QC, applying DOE/SPC and aiming for scalable, compliant processes in an

Qualifications

• BS/MS in Chemical Engineering, Bioengineering, Biochemistry, Biotechnology, or a related field.
• 6+ years of 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.

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.

Skills

DOE

SPC

Gage R&R

Root cause analysis

Data-driven process development

Independent cross-stream work

Stealth-stage environment

Education

BS/MS in Chemical Engineering, Bioengineering, Biochemistry, Biotechnology, or related field

Tools

Liquid handling platforms

Job description

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 collaboration.