cfDNA & NGS Assay Automation

CellMax Life Inc; Sunnyvale (CA); On-site; USD 120,000 - 180,000; Full time

Job summary

CellMax Life Inc. seeks a hands-on Automation Engineer / Robotics Specialist to lead automated laboratory workflows for cfDNA-based cancer screening assays.

The role focuses on building a scalable automation platform for cfDNA sample processing and Illumina library preparation using established sequencing technologies. You will independently develop robotic methods, troubleshoot complex workflows, and collaborate with assay scientists to achieve reliable analytical performance.

Qualifications

• Bachelor's or master's degree in Automation Engineering, Robotics, Biomedical Engineering, Bioengineering, Mechanical Engineering, Biotechnology, Molecular Biology, or a related field.
• At least 3–5 years of hands-on experience developing and implementing laboratory automation workflows.
• Demonstrated experience programming and debugging liquid-handling robots, preferably Hamilton, Agilent Bravo, Beckman Coulter Biomek, or comparable platforms.
• Proven ability to write custom automation scripts and translate laboratory protocols into automated methods.
• Experience with NGS library preparation, molecular biology workflows, DNA purification, or related sample-preparation processes.
• Strong understanding of liquid handling, magnetic-bead purification, reaction setup, thermal cycling, and multistep plate-based workflows.
• Demonstrated troubleshooting skills and the ability to independently drive automation projects from development through implementation.

Responsibilities

• Design, implement, and optimize automated laboratory workflows for cfDNA processing and Illumina library preparation.
• Lead the selection and integration of automation platforms (Hamilton, Agilent, Beckman) and configure decks and workflows.
• Develop and maintain custom robotic scripts; ensure version control and documentation.
• Collaborate with assay development, quality, and regulatory teams to meet performance criteria.
• Provide technical support and training for workflow transfer to routine operations.

Skills

Robot scripting

Liquid handling

NGS automation

Instrument integration

Education

Bachelor's or master's in Automation Engineering / Robotics / Biomedical Engineering

Tools

Hamilton VENUS

Agilent VWorks

Beckman Biomek

Job description

We are seeking a highly skilled Automation Engineer / Robotics Specialist to lead the design, development, implementation, and optimization of automated laboratory workflows for a cell-free DNA (cfDNA)-based cancer screening assay.

The primary responsibility of this role is to establish a robust, reproducible, and scalable automation platform for cfDNA sample processing and next-generation sequencing (NGS) library preparation using Illumina sequencing technology.

The ideal candidate will have hands-on experience programming liquid-handling robots, developing custom automation scripts, integrating laboratory instruments, and optimizing low-input DNA workflows. Experience with oncology assays, liquid biopsy, or molecular diagnostics is highly desirable.

This is a hands-on technical role requiring the ability to independently develop robotic methods, troubleshoot complex workflows, and collaborate with assay development scientists to achieve reliable analytical performance.

Key Responsibilities

1. Robotic Platform Selection and Implementation

• Evaluate, configure, and implement laboratory automation platforms, including Hamilton Microlab STAR, Agilent Bravo, Beckman Coulter Biomek, or equivalent systems.
• Assess instrument capabilities against assay requirements, throughput targets, workflow complexity, and long-term scalability.
• Design robotic deck layouts, labware configurations, liquid-handling parameters, and integrated instrument workflows.
• Establish automation capacity for 48–96 samples per batch, with consideration for future scale-up.
• Coordinate instrument installation, commissioning, vendor support, and operational readiness.

2. Custom Automation Script Development

• Independently develop, debug, optimize, and maintain custom robotic scripts using vendor-specific software, such as Hamilton VENUS, Agilent VWorks, or Beckman Biomek software.
• Translate molecular biology protocols into reliable, executable robotic methods.
• Develop customized liquid-transfer routines, reagent dispensing, magnetic-bead handling, incubation, thermal cycling, plate movements, and workflow-control logic.
• Implement barcode-based sample identification, reagent tracking, error detection, operator alerts, and safe error-recovery procedures.
• Integrate laboratory instruments and software systems, including thermal cyclers, plate readers, barcode scanners, and LIMS.
• Maintain version-controlled scripts, method documentation, and change histories.
• Work directly with instrument vendors and internal teams to resolve complex programming and integration issues.

3. cfDNA and NGS Library Preparation Automation

• Automate and optimize cfDNA processing and Illumina-compatible NGS library preparation.
• Develop automated workflows for magnetic-bead purification, DNA cleanup, end repair, adapter ligation, UMI incorporation, amplification, hybrid capture, and library normalization, as applicable to the assay.
• Optimize liquid handling for low-input cfDNA, including minimizing sample loss, improving transfer consistency, and controlling contamination and carryover.
• Support automated processing of specimens with variable cfDNA concentrations and fragment-size distributions.
• Collaborate with assay development and bioinformatics teams to assess library quality, sequencing metrics, and downstream variant-detection performance.
• Troubleshoot workflow failures and implement corrective measures to improve assay robustness and reproducibility.

4. Method Development, Qualification, and Validation

• Design and execute experiments to evaluate automated workflow performance against established manual or reference methods.
• Establish acceptance criteria for pipetting accuracy and precision, sample recovery, library yield, fragment-size distribution, contamination, and reproducibility.
• Develop and execute instrument qualification, method verification, and performance-testing protocols as appropriate.
• Support analytical validation, method transfer, and process scale-up in collaboration with assay development, quality, and regulatory teams.
• Maintain detailed records of development experiments, deviations, corrective actions, and method changes.
• Ensure automation workflows are developed and maintained in accordance with applicable laboratory quality systems and regulatory requirements.

5. Workflow Optimization and Technical Support

• Identify opportunities to improve throughput, hands-on time, reagent utilization, instrument utilization, and cost per sample.
• Perform root-cause analysis of robotic errors, liquid-handling failures, assay variability, and instrument integration issues.
• Develop preventive maintenance and troubleshooting procedures in collaboration with instrument vendors.
• Train laboratory personnel on automated workflows, routine operation, and error recovery.
• Provide technical documentation and ongoing support during workflow transfer to routine laboratory operations.

Required Qualifications

• Bachelor's or master's degree in Automation Engineering, Robotics, Biomedical Engineering, Bioengineering, Mechanical Engineering, Biotechnology, Molecular Biology, or a related field.
• At least 3–5 years of hands-on experience developing and implementing laboratory automation workflows.
• Demonstrated experience programming and debugging liquid-handling robots, preferably Hamilton, Agilent Bravo, Beckman Coulter Biomek, or comparable platforms.
• Proven ability to write custom automation scripts and translate laboratory protocols into automated methods.
• Experience with NGS library preparation, molecular biology workflows, DNA purification, or related sample-preparation processes.
• Strong understanding of liquid handling, magnetic-bead purification, reaction setup, thermal cycling, and multistep plate-based workflows.
• Demonstrated troubleshooting skills and the ability to independently drive automation projects from development through implementation.

Preferred Qualifications

• Experience with cfDNA, ctDNA, liquid biopsy, or low-input DNA workflows.
• Experience with targeted sequencing panels, hybrid-capture methods, UMI-based sequencing, or oncology assays.
• Familiarity with Illumina library-preparation chemistry and sequencing workflows.
• Experience with CRC screening assays or other cancer early-detection applications.
• Programming experience with Python, SQL, APIs, or other tools used for instrument integration, data processing, and LIMS connectivity.
• Experience in clinical diagnostics, regulated laboratory environments, assay validation, or design-control processes.
• Experience with low-volume liquid handling, liquid-class optimization, contamination control, and automated sample tracking.

Deliverables and Measures of Success

The successful candidate will be expected to:

• Implement a fully documented, reproducible automated workflow for the specified cfDNA-based CRC screening assay.
• Demonstrate reliable operation at the required 48–96 sample batch size.
• Meet predefined acceptance criteria for liquid handling, cfDNA recovery, library preparation, and sequencing quality.
• Demonstrate acceptable contamination and carryover performance.
• Establish robust sample tracking, error handling, and recovery procedures.
• Reduce manual intervention and hands-on time without compromising assay performance.
• Complete method documentation, operator training, and workflow transfer.
• Provide a scalable automation architecture that supports future assay improvements and increased testing volume.

Key Working Relationships

The Automation Engineer will work closely with assay development scientists, molecular biologists, bioinformatics specialists, quality and regulatory personnel, laboratory operations, IT/LIMS teams, and external instrument vendors.

Ideal Candidate

The ideal candidate is a hands-on automation specialist who combines strong robotic scripting skills with a practical understanding of molecular biology and NGS. They can independently develop and debug complex methods, optimize workflows for low-input cfDNA, troubleshoot instrument and assay failures, and take ownership of the automation process from initial setup through successful implementation.

Application Requirements

Applicants should submit a résumé highlighting relevant automation platforms, programming environments, custom scripts developed, NGS or cfDNA workflows supported, and examples of automation projects delivered from development through operational implementation.