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.

Applicants must be currently authorized to work in the United States on a full-time basis; no visa sponsorship is available for this position.

• PhD in molecular biology, genomics, bioengineering, or related field, OR equivalent industry experience defined as 8+ years in NGS assay development with at least one shipped IVD, LDT, or commercially deployed assay.
• Demonstrated hands-on experience developing Illumina NGS assays through to production or clinical use.
• Track record of leading end-to-end root-cause investigations of complex assay failures.
• Hands-on experience developing or troubleshooting assays on liquid handling automation (Hamilton or equivalent).
• Experience working under ISO 13485, FDA design controls, or a comparable regulated quality system.
• Working proficiency in R, Python, JMP, or equivalent for sequencing data analysis and statistical experimental design (DOE, ANOVA, regression, variance decomposition).

Preferred Experience

• IVD or LDT assay development for oncology, infectious disease, or similar clinical indications.
• Hands-on experience with FFPE and/or cfDNA sample types.
• Experience with hybrid capture target enrichment and/or amplicon-based panel design.
• Named contribution to a 510(k), De Novo, PMA, or equivalent regulatory submission.
• Experience integrating assays with downstream bioinformatics pipelines.

What Success Looks Like in the First 12 Months

How We Will Evaluate Candidates

• Technical depth interview: walk through a real NGS assay failure you debugged end-to-end, including the data you used to localize the root cause.
• Experimental design exercise: design a study to characterize a defined source of variability under stated constraints.
• Cross-functional simulation: navigate a tradeoff between assay performance, automation feasibility, and regulatory impact.

• Salary range: $120,000–$150,000
• Medical, dental, and vision insurance
• Employer-Sponsored Basic Life/AD&D, Long Term Disability
• Employee Assistance Program (EAP)
• Flexible Time Off
• Stock Option Plan
• Lunch stipend for days at headquarters

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.