Systems Integration Lead / Process Engineer

About Clear Labs

Clear Labs builds an end-to-end, FDA-cleared next-generation sequencing (NGS) diagnostics platform. Our system, Clear Dx, combines automated sample-to-report workflows with an assay menu spanning oncology and infectious disease testing. We're a hands-on team building hardware, software, and wet-lab science together, and we're looking for senior engineers ready to take full ownership of systems, not just advise from the sidelines.

Position Summary

We're hiring a Systems Integration Lead to sit at the interface between assay science and automation engineering — taking benchtop assays and redesigning them into automation-friendly, production-compatible processes. This is a hands-on, senior role responsible for labware qualification, system robustness and guardbanding, and designing and executing acceptance criteria and verification/validation as protocols move from bench to automated production, including closing the current gap where sequencing sits outside our automated oncology workflow as a manual, off-deck step.

Reports to: COO/CSO

Location: San Carlos, CA

Travel: No travel required.

Primary Responsibilities

• Own labware selection, qualification, and system robustness/guardbanding across the automated platform, including DOE-driven robustness testing and failure-mode analysis for automated process steps.
• Take benchtop assays developed by the assay science team and redesign them into automation-friendly, production-compatible processes.
• Design and execute acceptance criteria and potentially verification/validation protocols as processes move from bench to automated production.
• Drive on-deck integration of sequencing into oncology assay workflows, closing the current gap where sequencing runs as a manual, off-deck process outside the automated system.
• Lead technical evaluation and integration of new NGS sequencing platforms (e.g., Illumina, Oxford Nanopore) and library prep chemistries onto the automated platform.
• Serve as the technical bridge between assay science and automation engineering, translating wet-lab protocols into robust, industrialized, automatable processes.
• Partner with Regulatory and Quality to ensure system and workflow changes are appropriately validated and documented for an FDA-cleared diagnostics environment.
• Lead technical diligence on new sequencer, automation, and reagent vendor partnerships, including independently assessing vendor-provided integration timelines and effort estimates.

• Senior level: 8+ years of hands-on process/automation engineering or systems integration experience in diagnostics, medical device, or another regulated laboratory environment for Senior level; 8–10+ years for Principal level — ideally including work translating early-stage or research-originated protocols into scaled automated production.

• Working knowledge of FDA design-control and 510(k) considerations as they apply to system, workflow, and labware changes.
• Prior experience in oncology diagnostics (companion diagnostics, comprehensive genomic profiling, or MRD workflows) strongly preferred.
• Strong cross-functional communicator, comfortable translating between bench scientists and automation/hardware engineers.
• A genuine preference for hands-on, at-the-bench work over slide review — you'll be building and testing systems yourself.

Technical Skills — NGS

• Hands-on experience with at least one major NGS sequencing platform (Illumina and/or Oxford Nanopore), including run setup, sequencing chemistry, and flow cell/consumable workflows.
• Working knowledge of NGS library preparation chemistries relevant to clinical panels (hybrid capture and/or amplicon-based enrichment).
• Experience integrating or supporting a secondary analysis pipeline (e.g., DRAGEN or equivalent) and understanding how upstream lab changes propagate to sequencing QC metrics and analysis output.
• Familiarity with NGS assay QC parameters and how automation or platform changes can affect them.

Technical Skills — Automation, Labware & Systems Robustness

• Hands-on experience with Hamilton STAR/STAR2 liquid handling platforms, including VENUS software, deck design, and integrating third-party modules.
• Demonstrated experience in labware selection, qualification, and DOE-based robustness testing (tolerance analysis, failure-mode analysis) for automated liquid-handling processes.
• Strong statistical skills (design of experiments, process capability analysis, hypothesis testing, tolerance stack-up) applied to robustness and verification/validation study design.
• Track record translating manual, research-originated wet-lab protocols into production-grade, automatable, robust processes suitable for a regulated environment.
• Understanding of how liquid-handling method design and labware selection affect downstream NGS library quality and sequencing performance.

• Salary range: $160,808 to $196,544
• Medical, dental, and vision insurance
• Employer-Sponsored Basic Life/AD&D, Long Term Disability
• Employee Assistance Program (EAP)
• Discretionary Time Off
• Stock Option Plan
• Lunch stipend for days at headquarters

Notice of E-Verify Participation: Clear Labs participates in the federal E-Verify program to confirm the identity and employment eligibility of all newly hired employees. For more information, please review the E-Verify Participation Poster (English/Spanish) and the Right to Work Poster (English/Spanish).

Disclaimer: The above job description is intended to describe the general nature and level of work being performed by individuals assigned to this position. It is not intended to be an exhaustive list of all duties, responsibilities, and skills required. Responsibilities and duties may change or be adjusted to meet the needs of the company, and additional duties may be assigned as necessary. The job description is subject to change at any time at the discretion of the Company.