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BACKGROUND

The MGH Pathology Department and Cancer Center have led the field of clinical genetic profiling for personalized cancer diagnosis. Wed developed the MGH SNaPshot assay, one of the first multi-gene cancer genotyping tests to be used in routine clinical practice (http://abcnews.go.com/video/playerIndex?id=7740568). The assay allows for molecular stratification of cancer patients, and in some cases placement of patients into trials of novel agents that target specific mutated gene products. We are now in the process of introducing next generation sequencing technologies to push patient care to the next level.

We are building a state-of-the-art system to analyze and interpret next generation sequencing data from clinical cancer samples and integrate the system with current and future hospital workflows both for production and research use. This system is central to MGH efforts in personalized diagnosis and treatment and provides a once-in-a-lifetime opportunity to impact clinical care of thousands of patients.

RESPONSIBILITIES

Interact with the various user groups to help define system specifications and use cases.
Oversight of technical design and implementation of system architecture, including data flow, NGS data storage, sample and analysis results databases, reporting and visualization.
Design and implement APIs allowing connectivity between the NGS assay system and other hospital systems
Establish pipeline version control procedures
Oversee day-to-day operation of the research and production systems
Perform project planning and report progress to the management team

REQUIREMENTS

5+ years: Development of multi-component production software systems
3+ years: Relational database design and management
Linux system administration

PREFERENCES

Experience with NoSQL databases
HPC resource management experience (e.g. LSF, SGE)
Experience with web development frameworks

LOCALE

Department: Pathology

TERMS

Hours: 40+ Hrs/week
Status: Full-time

COMPENSATION

Salary: Commensurate with level of experience

HOW TO APPLY

Please feel free to send your recent resume to stqa8350[at]gmail.com.

Discussion forums: Opportunity: Systems Architect @ Massachusetts General Hospital -- Boston, MA (US)

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