Sr Clinical Genomics Scientist

About City of Hope

City of Hope is an independent biomedical research and treatment organization for cancer, diabetes and other life-threatening diseases.

Founded in 1913, City of Hope is a leader in bone marrow transplantation and immunotherapy such as CAR T cell therapy. City of Hope's translational research and personalized treatment protocols advance care throughout the world. Human synthetic insulin, monoclonal antibodies and numerous breakthrough cancer drugs are based on technology developed at the institution. AccessHope™, a subsidiary launched in 2019 serves employers and their health care partners by providing access to City of Hope's specialized cancer expertise.

A National Cancer Institute-designated comprehensive cancer center and a founding member of the National Comprehensive Cancer Network, City of Hope is ranked among the nation's "Best Hospitals" in cancer by U.S. News & World Report and received Magnet Recognition from the American Nurses Credentialing Center. Its main campus is located near Los Angeles, with additional locations throughout Southern California and in Arizona.

City of Hope's commitment to Diversity, Equity and Inclusion

We believe diversity, equity and inclusion is key in serving our mission to provide compassionate patient care, drive innovative discovery, and advance vital education focused on eliminating cancer and diabetes in all of our communities. Our commitment to Diversity, Equity and Inclusion ensures we bring the full range of skills, perspectives, cultural backgrounds and experiences to our work -- and that our teams align with the people we serve in order to build trust and understanding. We are dedicated to fostering a community that embraces diversity - in ideas, backgrounds and perspectives; this is reflected in our work and represented in our people.

Position Summary

• Strong experience in analysis of NGS data (including quality metrics, mapping, variant calling, quantitation of gene expression and biological interpretation)
• Experience in analysis of large genomic data sets including integration with data available from public or private sources.
• Experience in algorithm development for NGS data analysis.

The position provides oversight to maintaining and curating the City of Hope knowledge databases and ensures accurate identification and precise classification of variants/mutations detected through standard molecular genetic testing. The position assists in developing and maintaining bioinformatics pipelines for the Next Generation Sequencing (NGS) applications, performs NGS data analysis, assists in the integration of digital pathology, and keeps the data analysis software up to date. This role requires a broad knowledge of molecular biology with strong scientific understanding of genomics paired with working knowledge of bioinformatics and statistics to provide technical support including development of somatic/germline variant calling workflows, rapid prototyping of existing and novel bioinformatics algorithms, validation of the algorithms, maintaining the internal databases.

Key Responsibilities include:

Use comprehensive knowledge of scientific theory and departmental policies andprocedures to assist the variant curator team in curating genetic variants/mutationsdetected through standard molecular genetic testing using information from existing

databases and from literature.

Develop protocols for classifying genetic variation according to ACMG/AMPguidelines, curation in internal databases, submission to ClinVar, and forpublication.

Select, design, and implement scalable workflows for curation, variant analysisand interpretation.

Review clinical sequencing data output and assist in classifying variants todifferent pathogenicity levels using public databases and in-silico tools todetermine impact of the variant on the protein function.

Maintain detailed records of all analyses and curation work.

Read scientific literature to identify and curate the functional outcomes ofvariants in population level.

Establish and manage data infrastructure and analytics tool to facilitate molecularanalysis of the large datasets generated from NGS applications.

• Develop and manage workflows to process molecular data generated from NGS.
• Develop, validate and incorporate new pipelines and databases into the existingclinical analysis pipelines.
• Assist the integration of digital pathology into the bioinformatics pipeline.
• Enhance and troubleshoot existing bioinformatics methods and data analysissoftwares improving their assay capabilities as well as their technical robustness.
• Maintain the internal databases updated.
• Validate the upgrades of data analysis softwares.
• Train department personnel in the use of specialized and custom softwarepackages and databases.

Contribute and assist with preparation and submission of abstracts and scientific papers.

• Generate, organize and manage the large genomic datasets throughout manuscriptpublication process from draft through submission.
• Enhance professional growth and development by reviewing current literature andby participation in educational programs, workshops, conferences, and meetings.
• Prepare and deliver presentations based on scientific and technical progress andachievements.

Follow policies/procedures/regulatory requirements and perform other work assignments.

• Comply with all departmental and organizational policies and procedures andparticipate in corporate/departmental safety and quality activities.
• Perform other work assignments as required to maintainsustain and improvequality care and patient's outcomes.

Basic education, experience and skills required for consideration:

Minimum Education:

• Ph.D. in Biological Sciences

Minimum Experience:

• 5 years of experience in a related scientific discipline.

Preferred Experience:

• Knowledge of elementary statistics, interpretation of graphs and quickgrasp of scientific data.
• Experience using advanced database management system software, suchas Microsoft SQL Server, desirable.
• Proficiency in scripting languages (python, perl) and proficiency withR/Bioconductor.
• Proficiency with Linux and bash scripting.

Additional Information:

• As a condition of employment, City of Hope requires staff to comply with all state and federal vaccination mandates.
• Full Time

City of Hope is committed to creating a diverse environment and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, religion, color, national origin, sex, sexual orientation, gender identity, age, status as a protected veteran, or status as a qualified individual with disability. #LI-LK