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Bioinformatics Scientist/Programmer, Clinical Cancer Genomics Laboratory

Organization
University of California, San Francisco
Job Location
1450 3rd St
San Francisco, CA 94158
United States
Job Description

UCSF is seeking a qualified candidate to serve as Bioinformatics Scientist / Programmer for the Clinical Cancer Genomics Laboratory (CCGL). In this role, this individual will be part of a team responsible for design, construction, and maintenance of a genomic analysis pipeline supporting the UCSF500 Cancer Gene Panel assay, a molecular test profiling DNA from tumor and normal tissue to identify mutations that may drive a patient’s cancer and aid in diagnosis and treatment. Our internally developed cloud-based genomic analysis pipeline detects single nucleotide variants, small and medium indels, structural rearrangements, copy number variants, and microsatellite instability, and communicates with sequencing core services, laboratory information management systems and clinical reporting software.

Under the general direction of the Associate Director of Informatics of the CCGL, the Bioinformatics Scientist / Programmer will design and develop new components for our pipeline to support new and enhanced clinical testing. New features slated for development include gene fusion detection via RNAseq and detection of mutational signatures. Other new software developed will provide support for automating aspects of sample analysis and error reporting and integration with other clinical systems. Additional responsibilities will include supporting the development of new target capture panels and test validation as well as quarterly data analysis to improve QC and support clinical annotation. In this role, the Bioinformatics Scientist / Programmer will interface with molecular pathologists, laboratory and administrative staff, medical researchers, technical teams for related clinical systems and data repositories, and research consortia.

Requirements

• PhD in Bioinformatics or related field
• Minimum five years of experience with Illumina sequencing data, genetic variant calling, variant analysis, annotation and filtering
• In-depth knowledge of genomics and cancer biology
• Proficiency with Python, R, Unix / Linux OS and shell scripting, and associated libraries
• Strong knowledge of statistics and experience working with large genomics datasets
• Familiarity with cancer variant databases and clinical ontologies
• Working knowledge of Java
• Ability to communicate technical information in a clear and concise manner

About Our Organization

The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10-campus UC system dedicated exclusively to the health sciences.

The mission of the Clinical Cancer Genomics Laboratory (CCGL) at UCSF is to develop and validate genomic testing to support cancer clinical care and research. The CCGL provides the UCSF500 Cancer Gene Panel assay, a molecular test profiling DNA from tumor and normal tissue to identify mutations that may drive a patient’s cancer and aid in diagnosis and treatment.


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