Lead Bioinformatician (cfDNA Algorithms and Pipelines)

About the role

Natera is seeking a Lead Bioinformatician to advance the algorithmic foundations of our diagnostic assays supporting Women’s and Organ health. This is an individual contributor role focused on genomics expertise to extract reliable signals from ambiguous sequencing data, particularly in low fraction (fetal, donor cfDNA) samples. You will build methodological foundations and implement algorithms for detecting challenging variants (SNVs, Indels, CNVs, SVs).

Responsibilities

• Panel and Assay Science: Provide genomics algorithm insights for our expanded panel roadmap, including gene selection rationale. Collaborate with Product, Laboratory Directors, and Research to define approaches for analytically difficult genes and assay edge cases, balancing scientific defensibility with technical feasibility.
• Caller Strategy and Method Development: Define computational strategies for new targeted and special-purpose callers. Decide when to develop new callers versus extending existing methods. Prototype and benchmark new methods, and work with engineering teams to productionize them.
• Scientific Investigation and Escalation: Serve as a genomics consultant for complex production escalations, distinguishing biological causes from analytical or pipeline issues. Turn one-off investigations into durable rules and design changes to reduce repeat work.
• Data Quality and Cross-functional Partnership: Act as the bioinformatics liaison with Variant Management, Reporting, and Laboratory Operations on data quality, variant representation, and system integration. Provide scientific rationale for Quality and Laboratory functions to assess method readiness for deployment.
• Ways of Working: Help define standards for AI-assisted scientific investigation, including guidelines for human oversight of agent-driven conclusions.

What Success Looks Like After a Year

• Contributed to the scientific and bioinformatics rationale of product roadmaps.
• Established and utilized deployment-readiness criteria for new analysis methods, with personal contributions to at least one new or extended caller.
• Proactively addressed bioinformatics aspects of complex production investigations.
• Recognized as a go-to resource for genomics questions about Natera’s assays across teams.

Requirements

• Degree in Bioinformatics, Computational Biology, Human Genetics, or a related field. Equivalent work experience is fully considered; no advanced degree required.
• 4+ years of experience analyzing short-read sequencing data for screening or diagnostic applications, preferably in a regulated, accredited, or production-adjacent setting. Relevant experience counts from the point your work became substantially independent.
• Experience contributing to bioinformatics workflows behind a sequencing assay or panel.
• Experience resolving complex investigations across biological, analytical, and systems-level causes.

Skills

• Experience developing, validating, or benchmarking bioinformatics methods (e.g., SNVs, CNVs, SVs), particularly for analytically difficult regions.
• Proficiency in Python with demonstrated experience prototyping bioinformatics tools or callers.
• Human genetics expertise to contribute to panel design, including variant spectrum, population frequency, and accuracy trade-offs.
• Familiarity with identifying regions where short reads cannot be confidently placed (e.g., homologous sequences, pseudogenes, low-complexity/repeat regions, copy-number-heavy regions).
• Experience contributing to study designs or performance criteria for bioinformatics analysis methods.
• Preferred: Direct experience with non-invasive prenatal, reproductive, or carrier screening; cfDNA or other low-fraction sequencing applications; algorithms for both short-read and long-read platforms (e.g., Illumina, ONT, PacBio).
• Cross-functional credibility with genetic counseling, variant management, reporting, and production-adjacent groups.
• Experience in an accredited or high-complexity laboratory, or familiarity with production support or escalation processes.

Pay

Compensation range: $144,000—$180,000 USD (base pay). Final compensation will vary based on experience, qualifications, and internal equity considerations.

Benefits

• Annual performance incentive bonus.
• Long-term equity awards.
• Comprehensive health benefits (medical, dental, vision).
• 401(k) with company match.
• Generous paid time off and company holidays.
• Additional wellness and work-life benefits.
• Free testing for employees and their immediate families, plus fertility care benefits.
• Pregnancy and baby bonding leave.
• Commuter benefits.
• Generous employee referral program.