Sequencing Research Associate - 137577

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 general supervision of the Principal Investigator (PI), the Staff Research Associate will optimize and execute a proprietary targeted next-generation sequencing (tNGS) workflow for culture-free Mycobacterium tuberculosis (Mtb) drug-resistance profiling using our novel low complexity chemistry. A major focus of this role is amplicon-panel optimization-including primer-pool balancing, dropout troubleshooting, and iterative improvements to coverage uniformity across targets-implemented through small, designed experiments and rigorous quality-control (QC) tracking.

The SRA will process clinical research specimens per standard operating procedures (SOPs); prepare indexed libraries; perform bead clean-ups; run library QC (qPCR); pool libraries; operate benchtop sequencers (e.g., Illumina iSeq100); and complete basic run-level QC with handoff to the bioinformatics team. 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 a multi-site domestic study.

• Hands-on experience with multiplex polymerase chain reaction (PCR).

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

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

• Experience with primer-pool balancing and coverage-uniformity troubleshooting (identify dropouts/over-representation; adjust primer concentrations, or clean-up conditions).

• Sequencing run-level quality interpretation: read per-amplicon depth tables/plots, percent reads mapped, control behavior, and basic coverage metrics; organize outputs for bioinformatics review.

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

• 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.

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

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

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

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

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

• 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

• 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; 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).

• Employment is subject to a criminal background check.