Sequencing Research Associate IV - Medicine - 138839

The Department of Medicine (DOM) is the largest department within the UCSD School of Medicine and is responsible for fulfilling the teaching, research, and clinical missions of the University of California, San Diego School of Medicine. The department employs approximately 500 salaried faculty, 168 academic appointees, 331 residents, fellow and postdocs and 479 staff personnel.

Under direction of the Principal Investigators (PI) of an NIH funded project, with a high degree of independence, the Sequencing Research Associate will optimize and execute a targeted next-generation sequencing (tNGS) workflow for culture-free Mycobacterium tuberculosis (Mtb) drug-resistance profiling using a novel assay developed in our lab. A major focus of this role is amplicon-panel optimization-including primer-pool balancing, dropout troubleshooting including primer redesign, and iterative improvements to coverage uniformity across targets-implemented through small, designed experiments and rigorous quality-control (QC) tracking.

The Sequencing Research Associate will process clinical research specimens per standard operating procedures (SOPs); prepare indexed libraries; perform bead clean-ups; run library QC (e.g., qPCR and other quantitative/QC methods; fragment analysis accessed as needed); pool libraries; operate an Illumina iSeq100; and complete basic run-level QC with handoff to the bioinformatics collaborator. Additional responsibilities include meticulous written documentation, reagent/primer inventory management, routine equipment maintenance and calibration, and contributions to SOPs and training materials. The role interfaces with clinical and data teams to ensure collaboration, turnaround time, and data integrity for the domestic study. Other duties assigned as needed.

• Experience with sequencing library preparation and quality control: electrophoresis gels and qPCR; ability to interpret yield and melt-curve results.

• Hands-on experience with multiplex polymerase chain reaction (PCR) or similar molecular assays OR Experience with primer design, primer-pool balancing and coverage-uniformity troubleshooting (identify dropouts/over-representation and adjusting primer concentrations and clean-up conditions) OR Experience with sequencing library preparation and quality control: electrophoresis gels and qPCR; ability to interpret yield and melt-curve results.

• Demonstrated ability with meticulous documentation in a lab notebook; accurate reagent/lot tracking, instrument IDs, deviations, and corrective actions.

• Demonstrated clear written and verbal communication; ability to follow standard operating procedures (SOPs), escalate anomalies promptly, and collaborate with bioinformatic, clinical, and data teams.

• Strong organizational skills to manage multiple project components on fixed timelines; ability to support occasional evening/weekend runs to meet turnaround goals.

• Demonstrated problem-solving mindset with attention to detail; ability to anticipate consumable needs, stage materials, and maintain readiness in a high-throughput environment.

• Demonstrated reagent/primer inventory management and lot-qualification workflows (receiving checks, certificates of analysis, storage logs, expiration control).

• Demonstrated ability to perform routine instrument maintenance and calibration; ability to follow service schedules, document activities, and minimize downtime.

• Demonstrated spreadsheet skills for QC tracking and per-amplicon trend logs; comfort importing/exporting run metrics and generating simple charts/tables.

• Demonstrated ability to design and execute small, structured optimization experiments (e.g., limited factorial "DoE-lite" for annealing/extension and bead ratios); ability to summarize findings with accept/reject recommendations.

• Experience with primer design and assessment tools (e.g., Primer3, BLAST, IDT OligoAnalyzer) for basic in-silico checks (specificity, dimer/hairpin risk).

• Experience with Biosafety Level-2 (BSL-2) biosafety cabinet practices with potentially infectious human materials; compliance with Environment, Health & Safety (EH&S) requirements and personal protective equipment (PPE) use.

• Proficiency operating Illumina benchtop sequencers (e.g., iSeq100): run setup, loading, basic monitoring, and shutdown.

• Experience with laboratory information systems (e.g., laboratory information management system-LIMS) or structured file/metadata handoffs; attention to data integrity.

• Experience with Mycobacterium tuberculosis diagnostic reference testing, genomics of resistance, clinical samples

• Experience with translating benchtop assays onto automation platforms.

• On-site, laboratory-based role at UC San Diego; remote work is not available for routine responsibilities.

• Occasional evening/weekend work to support fixed batch schedules.

• Employment is subject to a criminal background check.

• Must be willing to work with potentially infectious human materials under Biosafety Level-2 (BSL-2) practices, following Environment, Health & Safety (EH&S) requirements and using appropriate personal protective equipment (PPE).