San Diego Supercomputer Center · 4 hours ago
Sequencing Research Associate - 137577
San Diego, CA
Contract
Onsite
Mid Level
$70K/yr - $112K/yrThe San Diego Supercomputer Center is part of the UC San Diego School of Medicine, focusing on research and clinical missions. The Sequencing Research Associate will optimize and execute a targeted next-generation sequencing workflow for Mycobacterium tuberculosis drug-resistance profiling, involving lab procedures and quality control.
Big DataDatabaseInformation Technology
Responsibilities
Optimize and execute a proprietary targeted next-generation sequencing (tNGS) workflow for culture-free Mycobacterium tuberculosis (Mtb) drug-resistance profiling using novel low complexity chemistry
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)
Complete basic run-level QC with handoff to the bioinformatics team
Meticulous written documentation
Reagent/primer inventory management
Routine equipment maintenance and calibration
Contributions to SOPs and training materials
Interface with clinical and data teams to ensure collaboration, turnaround time, and data integrity for a multi-site domestic study
Qualification
Required
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
Preferred
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
Company
San Diego Supercomputer Center
SDSC enables science and engineering discoveries through advances in computational science and data-intensive, high-performance computing.
Founded in 1985
201-500 employees
Funding
Current Stage
Growth StageTotal Funding
unknownKey Investors
National Science Foundation
2024-12-05Grant
Leadership Team
Ilkay Altintas
Division Director, Cyberinfrastructure and Convergence Research and Education
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