Senior / Staff Scientist, NGS Assay Development

About Clear Labs

Clear Labs (CL) harnesses the power of next-generation sequencing (NGS) to simplify complex diagnostics for clinical and applied markets. By creating a fully automated platform that brings together DNA sequencing, robotics, and cloud-based analytics, Clear Labs democratizes genomics applications to deliver better clarity. Clear Labs' turnkey platform accelerates outcomes and improves accuracy from food-borne pathogens to infectious diseases.

Position Summary

You will own the end-to-end performance of NGS assays running on Illumina platforms, from wet lab execution through data interpretation. The work directly determines assay reliability in clinical use and is foundational to scaling our diagnostic platform.

This role is leveled Senior or Staff based on demonstrated scope, autonomy, and track record of shipping NGS assays into regulated environments. We will calibrate level during the interview process.

This is a hands-on role, not a managerial one. It is best suited for scientists who have repeatedly debugged failed NGS experiments and can trace issues across assay design, automated execution, and downstream data.

How This Role Operates

• Reports to: Director of Assay Development
• Partners daily with Automation Engineering, Bioinformatics, Manufacturing, and Regulatory / Quality.
• Owns assay performance decisions on assigned product workstreams; signs off on experimental designs, root-cause findings, and verification study conclusions within scope.
• Expected to escalate cross-functional tradeoffs and regulatory implications to the Director of Assay Development.

Location: San Carlos, CA

Primary Responsibilities

Assay Development (Core)

• Troubleshoot and optimize full NGS workflows: extraction, fragmentation, end repair, ligation, library prep, target enrichment or amplification, pooling, and sequencing.
• Identify root causes of assay failures and implement durable, documented fixes.
• Redesign assay components for robustness, scalability, and reproducibility under production conditions.
• Lead verification, characterization, and reagent qualification studies that drive assay decisions.
• Own measurable improvements in assay reliability, variability, and yield on assigned workstreams.

Data Analysis and Experimental Design

• Analyze sequencing data and run metrics to diagnose performance issues across the wet-to-dry interface.
• Design experiments using DOE, regression, and hypothesis testing; quantify variance contributions.
• Build and maintain quantitative performance metrics that characterize assay variability and stability.
• Conduct reagent stability studies and lot-to-lot qualification.

Automation Integration

• Develop and troubleshoot assays running on liquid handling automation (Hamilton or equivalent).
• Partner with automation engineers to translate manual protocols into validated automated workflows.
• Diagnose and resolve automation-related sources of variability.

Regulatory and Quality

• Execute work under design controls and a quality management system (ISO 13485 or equivalent).
• Contribute to analytical validation activities (LoD, precision, specificity, reproducibility, interference).
• Apply structured problem-solving tools (FMEA, CAPA, change control) as part of routine work.