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.