Senior / Staff Scientist, NGS Assay Development

Clear Labs•San Carlos, CA

4d•Onsite

About The Position

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. 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.

Requirements

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

Nice To Haves

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.

Responsibilities

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.
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.
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.
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.