Senior Director, Clinical Genomics Engineering

Position Overview

The Senior Director Clinical Genomics Engineering is a pivotal leadership role within Natera's Software Engineering organization, responsible for building and scaling the software systems that transform genomic data into actionable clinical insights.

Reporting to the VP of Software Engineering, Scientific Computing, this leader owns the end-to-end strategy and execution of the Clinical Genomic Insights platform—a suite of cloud-native, distributed systems that ingest VCFs/BAMs from genomic pipelines, automate variant annotation and classification, streamline technical and clinical review, and generate clinical-grade reports used in patient care.

This is a rare opportunity to lead at the intersection of bioinformatics, software engineering, and clinical genomics, driving innovation not only in the technology stack but in the core scientific workflows—applying AI and machine learning to automate variant interpretation, improve review efficiency, accelerate time to result and ultimately impacting the millions of patients that Natera serves.

This platform supports both germline and somatic assays at clinical scale, giving this leader a uniquely broad lens across diverse genomic applications—from hereditary conditions and reproductive health to oncology and personalized cancer monitoring.

Primary Responsibilities

Technology & Scientific Innovation

• Define and evolve the architecture for a cloud-native, microservices-based platform powering Natera’s results interpretation and reporting capabilities.
  
  
• Drive innovation in both engineering and scientific domains, including:
  
  
• AI-assisted variant annotation and classification
  
  
• Automated technical review and variant curation pipelines
  
  
• Reflex assay orchestration and decision logic
  
  
• Report generation, rendering, and report delivery​
  
  
• Ensure systems meet clinical-grade SLAs for scalability, reliability, and accuracy across millions of variants per week and high-throughput pipelines.
  
  

Engineering Execution

• Lead cross-functional delivery across software, bioinformatics, and product to launch new assay capabilities, improve efficiency, and enhance quality.
  
  
• Instill engineering excellence through best practices in architecture, test automation, CI/CD, monitoring, and observability.
  
  
• Operate in compliance with regulatory standards including FDA, CLIA, CAP, and HIPAA, maintaining audit readiness and traceability.
  
  

Organizational Leadership

• Build and lead a high-performing engineering organization (~60+ people), scaling teams focused on platform development, scientific services, and system operations.
  
  
• Mentor and develop engineering managers and technical leads, fostering a culture of scientific rigor, collaboration, and ownership.
  
  
• Manage strategic planning, headcount allocation, and delivery velocity across complex, multi-assay programs.
  
  

Stakeholder and Strategic Partnership

• Collaborate closely with stakeholders across Laboratory Directors, Clinical Affairs, R&D, Regulatory, and Product to align delivery with business and clinical goals.
  
  
• Represent the Clinical Genomics Insights platform in company-wide architecture forums, regulatory audits, and key program reviews.
  
  

Qualifications

• Advanced degree (MS/PhD) in Genomics, Bioinformatics, Computer Science, or related field; or equivalent industry experience.
  
  
• 10+ years of engineering leadership experience, including 5+ years managing medium-to-large engineering organizations.
  
  
• Proven track record building bioinformatics software for clinical interpretation, including variant annotation, curation, and reporting.
  
  
• Deep understanding of genomic data (e.g., VCFs, BAMs), variant classification frameworks (e.g., ACMG), and tertiary analysis tools and databases (e.g., VEP, SnpEff, ClinVar, COSMIC, etc).
  
  
• Hands-on experience building cloud-based distributed systems at scale (AWS preferred), including event-driven architectures (e.g., Kafka).
  
  
• Familiarity with regulatory standards for software in medical diagnostics (e.g., SaMD, IEC 62304, 21 CFR Part 11).
  
  
• Experience delivering systems supporting both germline and somatic testing at production scale is strongly preferred.
  
  

Preferred Attributes

• Experience with AI/ML applications in genomics or clinical diagnostics.
  
  
• Familiarity with multi-omics data integration or longitudinal data pipelines.
  
  
• Strong cross-functional communication skills and ability to lead in a matrixed environment.

OUR OPPORTUNITY

Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.

The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other. When you join Natera, you’ll work hard and grow quickly. Working alongside the elite of the industry, you’ll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management.

WHAT WE OFFER

Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits. Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program!

For more information, visit www.natera.com.

Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.

All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws.

If you are based in California, we encourage you to read this important information for California residents. 

Link: https://www.natera.com/notice-of-data-collection-california-residents/

Please be advised that Natera will reach out to candidates with a @natera.com email domain ONLY. Email communications from all other domain names are not from Natera or its employees and are fraudulent. Natera does not request interviews via text messages and does not ask for personal information until a candidate has engaged with the company and has spoken to a recruiter and the hiring team. Natera takes cyber crimes seriously, and will collaborate with law enforcement authorities to prosecute any related cyber crimes.

For more information:
- BBB announcement on job scams 
- FBI Cyber Crime resource page