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Sr Clinical Genomics Scientist

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Company :
City of Hope

Location :
Duarte, California

Expiry Date :
Tue, 15 Dec 2020 23:59:59 GMT

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Description :
About_City_Of_Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6,000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope is a remarkable non-profit institution, where compassion and advanced care go hand- in-hand with excellence in clinical and scientific research. City of Hope is a National Cancer Institute designated Comprehensive Cancer Center and a founding member of the National Comprehensive Cancer Network, an alliance of the nation s leading cancer centers that develops and institutes standards of care for cancer treatment. Position_Summary 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, 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 and procedures to assist the variant curator team in curating genetic variants/ mutations detected through standard molecular genetic testing using information from existing databases and from literature. * Develop protocols for classifying genetic variation according to ACMG/AMP guidelines, curation in internal databases, submission to ClinVar, and for publication. * Select, design, and implement scalable workflows for curation, variant analysis and interpretation. * Review clinical sequencing data output and assist in classifying variants to different pathogenicity levels using public databases and in-silico tools to determine 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 of variants in population level. Establish and manage data infrastructure and analytics tool to facilitate molecular analysis 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 existing clinical analysis pipelines. * Enhance and troubleshoot existing bioinformatics methods and data analysis software improving their assay capabilities as well as their technical robustness. * Maintain the internal databases updated. * Validate the upgrades of data analysis software. * Train department personnel in the use of specialized and custom software packages and databases. Contribute and assist with preparation and submission of abstracts and scientific papers. * Generate, organize and manage the large genomic datasets throughout manuscript publication process from draft through submission. * Enhance professional growth and development by reviewing current literature and by participation in educational programs, workshops, conferences, and meetings. * Prepare and deliver presentations based on scientific and technical progress and achievements. Follow policies/procedures/regulatory requirements and perform other work assignments. * Comply with all departmental and organizational policies and procedures and participate in corporate/departmental safety and quality activities. * Perform other work assignments as required to maintainsustain and improve quality care and patients outcomes. * Qualifications Basic education, experience and skills required for consideration: * Ph.D. in Biological Sciences * 5 years of experience in a related scientific discipline. * Excellent communication, writing and computational skills as well as a track record of working in a clinical laboratory environment. * In-depth understanding of the biology, molecular mechanisms and functional studies of human genetic disease genes. * 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. * Experience in statistical analysis of complex biological data. * Cross-disciplinary and strong analytical skills as well as broad experience using computational methods, databases, software and hardware. * Preferred_Education_Experience_And_Skills * Knowledge of elementary statistics, interpretation of graphs and quick grasp of scientific data. * Experience using advanced database management system software, such as Microsoft SQL Server, desirable. * Proficiency in scripting languages (python, perl) and proficiency with R/ Bioconductor. * Proficiency with Linux and bash scripting. * 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. Show moreShow less