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.

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 guard banding, 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.

• Own labware selection, qualification, and system robustness/guard banding 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.

• 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…