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Every patient sample is a story.

That's why our Lab Ops team is focused on providing physicians with comprehensive genomic information about each person's cancer. Information that's as unique as the patients are. The insights discovered in our labs may help change their story.


Application Scientist

  • Cambridge, Massachusetts, United States
  • Full Time

About the Job

The Application Scientist is a key member of the Laboratory Operations Team at Foundation Medicine and provides onsite assay optimization and technical support for Next Generation Sequencing (NGS) based clinical assays. This position requires working in a lab environment around the presence of chemicals and regents. The position requires the ability to travel nationally (10%). 

Key Responsibilities

• Assists with the effective transfer of NGS and other molecular-based assays and processes to the CLIA/CAP/FDA regulated laboratory facility.

• Performs molecular techniques including but not limited to, nucleic acid extractions, PCR, RealTime qPCR, next-generation library preparation and next-generation sequencing.

• Collaborates with the Product Development, Process Engineering, Technology, Development Operations, Laboratory Operations, Bioinformatics, Quality Assurance and Regulatory teams to assist with assay and process development.

• Provides technical support on Next Generation Sequencing (NGS) based clinical assays that are escalated from support functions, most typically Client Services.

• Contribute to onsite assay optimization by generating detailed reports summarizing assay and process performance.

• Leads assay qualification and validation efforts for new products and product updates.

• Provides hands-on training and education-focused presentations to Laboratory Operations staff.

• Presents data, proposals and progress to internal team members.

• Generates experimental plans for assay troubleshooting and to support the Product Development and Process Engineering teams.

• Leads the development of IQ/OQ/PQ and Standard Operating Procedure documents.

• Liaises with Product Care team to assist in troubleshooting assay technical problems.

• Deliver timely and innovative solutions to address customer needs in inter-departmental collaboration with Research and Development, Commercial, Clinical, Quality Assurance, Business Development, and other teams as needed.


Basic Qualifications

• Masters Degree in Molecular Biology, Biochemistry, Genetics, Biomedical Engineering, or a scientific field of study

• 3+ years working in industry and/or academia

• 2+ years Hands-on experience with next generation sequencing and associated methodologies to analyze solid and liquid oncology specimens, including DNA and RNA sequencing protocols.

Preferred Qualifications

• Strong experience with target-enrichment approaches such as multiplex-polymerase chain reaction and hybrid selection

• Experience driving the systematic optimization and troubleshooting of complex molecular diagnostic and NGS-based assays through integration of information related to the input sample, lab processes and data analysis pipeline

• Excellent time management, organizational capabilities and attention to detail

• Demonstrated history of work in a fast-paced environment with changing and competing priorities

• Strong communication skills, demonstrated by a history of complex technical information sharing to internal and external stakeholders in various formats including reports, presentations and publications

• Expertise creating and optimizing robust protocols for use in high throughput laboratory automation systems

• Formal training and experience operating in a Laboratory Information Management Systems (LIMS)

• Experience with NGS analysis of solid and liquid biopsies

• Experience with common NGS data management and analysis tools (e.g. SAMtools, IGV/Picard, Python/Perl)

• Experience using Business Intelligence (BI) tools such as Power BI, Tableau, and Tibco Spotfire to drive information gathering and decision making

• Prior experience working in an environment adherent to regulations established by Food and Drug Administration or Certified Laboratory Improvement Amendments

• Understanding of HIPAA and importance of privacy of patient data

• Ability to work well under pressure while maintaining a professional demeanor

• Ability to travel up to 10%

• Commitment to reflect FMI's values: passion, patients, innovation, and collaboration

• Experience handling and purifying nucleic acid from typical oncology specimens (e.g. formalin-fixed paraffin-embedded, blood, bone marrow).


Please be aware that Foundation Medicine mandates COVID-19 vaccination of all employees regardless of work location. Accommodations may be made in accordance with applicable law.


About Foundation Medicine

Foundation Medicine, Inc. (FMI) 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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Internal applicants, please use your FMI email address.

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Foundation Medicine is proud to be an Equal Opportunity and Affirmative Action employer and considers all qualified applicants for employment without regard to race, color, religion, sex, gender, sexual orientation, gender identity, ancestry, age, or national origin. Further, qualified applicants will not be discriminated against on the basis of disability or protected veteran status. We also consider qualified applicants regardless of criminal histories, consistent with legal requirements. See also FMI’s EEO Statement and EEO is the Law and Supplement. If you have a disability or special need that requires accommodation, please let us know by completing this form.  (EOE/AAP Employer)

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