Clinical Bioinformatician - Clinical Genomics Laboratory

When & where

• Work Location: Tarrytown, NY
• Hybrid: 4 days per week on site

Discover your role

• NGS pipeline validation & optimization: Lead or co-lead analytical validation and revalidation of NGS bioinformatics pipelines for clinical assays, including germline and future disease applications. Optimize sensitivity, specificity, limit of detection, and variant allele fraction thresholds using clinical samples and in silico data sets. Define and document pipeline configurations, filtering criteria, and QC thresholds in accordance with AMP/CAP best practice guidelines and applicable CLIA, CAP, and state regulatory requirements.
• Bioinformatics tool evaluation & selection: Benchmark and select tools for alignment, variant calling, annotation, and quality control based on assay design, specimen type, and sequencing platform. Inform build-versus-buy decisions through technical evaluation of vendor-supplied pipeline solutions.
• Production pipeline operations: Oversee daily execution of validated clinical pipelines and monitor performance across sequencing runs and patient samples through QC programs and key performance indicators. Troubleshoot pipeline failures, data quality issues, and software errors; escalate complex problems to the Laboratory Director as appropriate.
• Change management & version control: Support pipeline updates through impact assessment, revalidation planning, and change documentation. Apply version control best practices throughout development and release to maintain traceability and regulatory compliance.
• Pipeline development support: Contribute to the design and development of new or updated pipelines, incorporating selected tools, containerization, and workflow orchestration.
• Data management & regulatory compliance: Manage genomic and patient data in accordance with applicable privacy laws and federal, state, and institutional data security policies. Maintain audit-ready records of pipelines, validation studies, software versions, and standard operating procedures. Support data integrity through verification, sample identifier management, and audit logging.
• Cost monitoring & resource management: Track and report cloud compute and storage usage, software license costs, and vendor tool expenditures. Flag cost trends and anomalies, identify savings opportunities that preserve clinical performance and compliance, and provide usage data and trend summaries to support leadership's budget planning.

This role requires

• Master's degree in Bioinformatics, Computational Biology, Genomics, or a related field. A Bachelor's degree with substantial hands-on experience in a CLIA-regulated clinical genomics or molecular diagnostics laboratory is accepted in lieu of a Master's degree.
• 2–4 years of experience in a clinical molecular diagnostics or clinical genomics laboratory, with demonstrated hands-on NGS bioinformatics pipeline validation experience in a CLIA-regulated setting
• Proven experience performing or supporting NGS bioinformatics pipeline validation in a CLIA-regulated clinical laboratory, including establishing sensitivity, specificity, limit of detection, and VAF thresholds
• Experience with short-read sequencing data from high-throughput platforms, including run-level and sample-level QC, demultiplexing, and troubleshooting data quality issues
• Hands-on experience validating, configuring, and supporting commercial or vendor-supplied secondary analysis and variant interpretation platforms in a clinical setting, including managing software updates, settings, and filtering criteria
• Working knowledge of NGS file formats (FASTQ, BAM/CRAM, VCF) and standard tools for alignment, variant calling, annotation, and quality control, with the ability to benchmark vendor and open-source tools against one another
• Proficiency in Linux/Unix environments and in Python or R, including scripting for QC, data analysis, and integration or automation around vendor platforms