Variant Analyst

The Clinical Informatics Programmer Specialist 4  applies advanced professional clinical informatics concepts and extensive knowledge of industry practices to projects of all levels of scope and complexity.

Involves the development and implementation of the organization's information systems and tools that are applied to clinical information. Works closely with clinicians across all hospital / healthcare departments to optimize effective use of systems. Coordinates analytical support for health management, including profiling, health economics, and business analytics / performance metrics. Defines systems and applications to support various functions. May provide customer service, troubleshooting and maintenance.

UCSF Health’s Genetics and Genomics Services, Clinical Cancer Genomics Lab (CCGL) and Genomics Medicine Lab (GML) aim to achieve the highest standards in patient care. The labs provides clinical genomics testing services in a wide variety of clinical areas with highly trained subspecialists who are recognized nationally and internationally for their expertise.

% 

of time

Support clinical operations of genetic testing laboratory throughgene curation, assessment of gene-disease correlation, and variant curation across the various genetic tests offered by the laboratory (e.g. hereditary cancer panel, exome, genome, and cancer gene panels).

Analyze clinical data selecting variants for curation/confirmation, variant nomenclature following HGVS guidelines.

Draft provisional medical reports for laboratory director review and sign out.

Routine assessment of quality control metrics and , assisting with troubleshooting in collaboration with lab technicians and bioinformaticians as needed.  

Track and manage the flow and analysis of patient data.

Develop and maintain databases of patient case status, human phenotype ontologies, and associated genetic analysis pipelines. 

Ensure the handling of patient data is HIPAA and CLIA compliant. 

Develop, maintain, and update local databases of clinical variant annotations relevant to human disease.

Aid the laboratory directors and staff during the test development and validation of clinical testing pipelines.

Assist in the development of procedures and rules for classifying genetic variation according to ACMG/AMP guidelines, curation in internal databases, submission to ClinVar, and for publication.

Contributes to facilitating and promoting internal and external genomic projects by providing scientific or intellectual information. 

Yes

Participate as a productive member of the work team and prepare cases for weekly team meetings.

Work with cross-functional teams, department, and providers on developing new tests, strategies to improve efficiency and accuracy for the GML/CCGL. 

Yes

Assist in the instruction of trainees and training of new laboratory personnel. 

Perform other related work as needed.

Required Qualifications:

• Broadly encompassing or highly in-depth knowledge of 1-2 areas of focus in clinical informatics specialty areas. Knowledge of controlled terminology, clinical workflows, user interface optimization, clinical decision support, rules development, data integration and mining, clinical ontologies and adoption of technology.
• In-depth knowledge of all relevant clinical informatics software and systems, and of the highly-complex concepts, principles, policies, methodologies, techniques, best practices, regulations, and standards practices involved with patient care and electronic medical data management in the UC health care system.
• Advanced interpersonal communications skills, to convey highly technical information and instructions to all levels of clinical users in a clear and concise manner, to provide technical support, and to develop and deliver training materials as needed.
• Ability to apply advanced problem-resolution skills to highly complex issues, quickly diagnose problems, and develop, test, and implement appropriate and effective solutions in a timely manner.
• Advanced ability to serve as a technical leader and information resource, and to work collaboratively with senior staff and management across departments, providing advice, counsel, and analysis on issues of policy, functionality, system efficiency, upgrades, business analytics, and industry advances and trends.

Preferred Qualifications:

• Advanced organizational and project management skills, with the ability to lead a team, prioritize tasks, and see projects through from inception to completion on schedule.
• Advanced analytical skills and expertise in documentation and reporting, with the ability to apply metrics, design and run queries, collect and analyze performance data, and produce sophisticated reports and analyses for management use.

Education, Licenses/Certifications:

• Bachelor's degree in health care information technology, computer science, or related area, and / or equivalent combination of experience / training - Required
• M.S.-Level Scientist in Medical Genetics or Genomics - Preferred