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).

If employed by the University of California, you will be required to comply with our Policy on Vaccination Programs, which may be amended or revised from time to time. Federal, state, or local public health directives may impose additional requirements.

If applicable, life-support certifications (BLS, NRP, ACLS, etc.) must include hands-on practice and in-person skills assessment; online-only certification is not acceptable.

UC San Diego Health Sciences is comprised of our School of Medicine, Skaggs School of Pharmacy and Pharmaceutical Sciences, The Herbert Wertheim School of Public Health and Human Longevity Science, and our Student Health and Well-Being Department. We have long been at the forefront of translational - or "bench-to-bedside" - research, transforming patient care through discovery and innovation leading to new drugs and technologies. Translational research is carried out every day in the hundreds of clinical trials of promising new therapies offered through UC San Diego Health, and in the drive of our researchers and clinician-scientists who are committed to having a significant impact on patient care. We invite you to join our team!

Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached.

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The University of California is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected status under state or federal law.

For the University of California's Anti-Discrimination Policy, please visit: https://policy.ucop.edu/doc/1001004/Anti-Discrimination

UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information.

UC San Diego Health maintains a marijuana and drug free environment. Employees may be subject to drug screening.

Misconduct Disclosure Requirement: As a condition of employment, the final candidate who accepts an offer of employment will be required to disclose if they have been subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct; or have filed an appeal of a finding of substantiated misconduct with a previous employer.

a. "Misconduct" means any violation of the policies governing employee conduct at the applicant's previous place of employment, including, but not limited to, violations of policies prohibiting sexual harassment, sexual assault, or other forms of harassment, or discrimination, as defined by the employer. For reference, below are UC's policies addressing some forms of misconduct:

• UC Sexual Violence and Sexual Harassment Policy
• UC Anti-Discrimination Policy
• Abusive Conduct in the Workplace