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Lead Automation Engineer

  • 400 Summer Street, Boston, Massachusetts, United States
  • Full Time

About the Job

The Lead Automation Engineer works as part of a new product team, focused on improving blood-based cancer diagnostic capabilities in areas such as cancer detection, minimum residual disease, and other related applications. This team is comprised of talent from across the Roche ecosystem, including Roche Diagnostics, Roche Pharma and Foundation Medicine, operating as a single unit.

The Lead Automation Engineer is responsible for automating and scaling complex workflows and implementing processes for deployment of automated systems in clinical laboratories at multiple sites. This position is involved in all aspects of assay automation development and instrument integration. From concept to requirements definition, method development, optimization, troubleshooting and validation, the Automation Engineer identifies problem areas and develops solutions to reduce Turn-Around-Time (TAT), increase sample processing capacity and reduce cost of goods sold. 

The incumbent leverages advanced knowledge and skills of automation to work collaboratively on cross-functional teams on a variety of projects to explore, develop, optimize, test, and implement robust, scalable solutions for FMI’s sample processing workflows. Additionally, this position partners with outside vendors to develop integrated robotic solutions and ensures all automated solutions fully address business and user requirements. 

The Lead Automation Engineer position requires working in a lab environment in the presence of chemicals and reagents. 

This is a regulated position and additional information may be available from QA on the qualifications for this role pertaining to regulatory guidelines.


Key Responsibilities

  • Participate in and lead cross-functional teams focused on the development, qualification and deployment of robust and scalable integrated automation solutions.
  • Lead project planning and process updates and contribute to experimental design.
  • Review and critique presentations for others and present complex technical data to large and diverse groups.
  • Lead or contribute to innovation of current and new assays workflows, technologies and processes.
  • Collaborate with stakeholders in support of manufacturing and process workflow to establish user requirements associated with new equipment purchases and/or modifications.
  • Partner with stakeholders, team members, equipment design vendors and various internal resources in support of sustaining and growing the business model. This includes product, facilities, equipment, supply chain, services, staffing, operating procedures, policies and standards.
  • Establish user requirements associated with the design of new production lines including individual pieces of laboratory equipment and process workflow equipment.
  • Lead or contribute to the design, development, optimization, and implementation of automated liquid handling processes, systems, and streamlined workflows using DOE methodologies.
  • Drive collection of process requirements from cross-functional stakeholders.
  • Execute work with adherence to all applicable regulations.
  • Develop and improve robust automated solutions utilizing Hamilton liquid handlers and other laboratory automation equipment designed to remove bottlenecks, increase capacity and reduce TAT in FMI’s high throughput (24/7) Next Generation Sequencing laboratory.
  • Program, optimize, verify and implement new and/or improved methods on Hamilton robotic liquid handling workstations and integrated robotic systems.
  • Perform the exploration into workflows for process optimization.
  • Analyze workflows, identify bottlenecks, develop solutions and lead teams in solution implementation that improves efficiency, throughput, cost, and quality.
  • Generate and maintain requirements and test plan documentation.
  • Integrate instrument components and perform unit testing.
  • Execute guard-banding, response surface and optimization studies to optimize and characterize automated methods to improve robustness.
  • Provide on-site technical support of automation platforms.
  • Contribute to protocol generation, report writing, and presentation preparation related to automation as needed.
  • Install, test and control new versions of automated protocols on applicable instrumentation across labs and possibly across sites.
  • Provide training and documentation for new or modified workflows to end users.
  • Partner with outside vendors to design, develop and qualify integrated robotic solutions to enable high throughput processing.
  • Provide advanced technical guidance to Automation Engineers.
  • Other projects as assigned.



Basic Qualifications:

  • Bachelor’s Degree Degree in the Bioengineering, Biotechnology or the life sciences and 7 years of related experience with high-throughput laboratory instrumentation; OR,
  • Master’s Degree in fields specified above and 5 years of relevant experience; OR
  • PhD in a relevant field
  • Experience with operating and programming automated liquid handling robotics platforms and complex laboratory systems

Preferred Qualifications:

  • Experience with robotic liquid handlers from Hamilton, TECAN, Agilent Technologies, or Beckman Coulter
  • Experience with FMEA, MTBF and test case development
  • Experience with standard molecular biology techniques such as nucleic acid isolation, purification and quantitation, bioanalyzer, DNA/RNA quantitation, qPCR or Next Generation Sequencing
  • Experience with statistical data analysis using R or JMP, monitoring data quality and troubleshooting technical problems
  • Experience working in a regulated environment (e.g. CLIA, CAP, GxP, ISO)
  • Experience with developing and implementing integrated robotic systems for use in a high throughput environment
  • Experience with agile project management
  • Experience with developing, optimizing, and validating assays for use in a high throughput environment
  • Experience communicating and collaborating with internal and external colleagues and customers from diverse scientific, engineering, operational, and regulatory disciplines
  • Previous teaching or technical training experience
  • Familiarity with JIRA/Confluence, Solidworks, VBscript, Python, PERL and/or JavaScript, relational databases, SQL, LIMS or other relevant enterprise software packages
  • Familiarity with streamlining workflows and developing automated laboratory processes and instrumentation systems, including collecting and documenting requirements, developing concepts, design, testing/validation, implementing, and training
  • Knowledge of safety protocols in workshop, factory or laboratory setting
  • Ability to document and report troubleshooting procedures and resolutions
  • Ability to work as an individual as well as in a team environment
  • Strong written and oral communication skills
  • Detail oriented and well organized
  • Understanding of HIPAA and importance of privacy of patient data
  • Commitment to FMI values: patients, innovation, collaboration, and passion


About Foundation Medicine

Foundation Medicine began with an idea—to simplify the complex nature of cancer genomics, bringing cutting-edge science and technology to everyday cancer care. Our approach generates insights that help doctors match patients to more treatment options and helps accelerate the development of new therapies. Foundation Medicine is the culmination of talented people coming together to realize an important vision, and the work we do every day impacts real lives.

Confidence, or the belief that we need to check every box before applying for a job, can sometimes hold us back from going after a role that inspires us. At Foundation Medicine there's no such thing as the 'perfect' applicant, and our company is a place where every employee can make an impact and continue to grow whatever background they may have or path they may have taken. So, as long as you meet the basic qualifications for a role, please apply if you see a position that would make you excited to come into Foundation Medicine every day and help us transform cancer care.

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