Allegheny Health Network
Job Description :
This job provides oversight, maintains and troubleshoots all automated micro-fluidics robots in the Genomics Facility in collaboration with the instrument manufacturers. Maintains and troubleshoots all QA/QC instrumentation in the Genomics Facility, analyzes complex NGS datasets to interpret variants and synthesize interpretive reports, and will work directly with faculty in the Genomics and Molecular Pathology Division to assist with data analysis.
- Maintains and troubleshoots all automated instrumentation in the Genomics Facility including the Biomek i5, Covaris and the Hamilton NGS STAR. This includes modification of scripting when needed in consultation with the manufacturer. (15%)
- Maintains and troubleshoots the performance of all QA/QC instruments in the facility including the BioAnalyzer Tape Station, Qubit fluorometer, Quant Studio 5, Nanodrop Spectrophotometer and Fragment Analyzer. (15%)
- Generates sequencing data from the Illumina NextSeq 550 Dx and MiSeq Dx and is responsible for quality review and interpretation of genomic test results under direction of clinical laboratory directors. (15%)
- Transfers raw genomics data to our AHN server for subsequent transfer to our AHN AWS site for eventual analysis by Genosity and/or our Data Enterprise Warehouse under Highmark Health. (15%)
- Provides genomic analysis for physicians and scientists in other departments as needed to guide development, implementation and interpretation of genomic test services. This includes processing files from raw BCL status through mapping and alignment and variant calling for SNV, INDELs, CNV and structural variation. This also includes the ability to run gene expression analysis beginning with raw RNA expression files through differential expression analysis. (15%)
- Performs tertiary analysis of vcf data for correlation analysis with established databases (gnomAD, TCGA, COSMIC) as well as carry out pathway analysis using available tools (KEGG Pathway Database, Ingenuity). (15%)
- Develops relationships and independently consult experts in the field to assist with interpretation of challenging variants. (5%)
- Responsible to generate, develop, and provide data at client meetings and conferences, when required. (5%)
- Other related duties as required.
- Master's Degree in Computer Science, Informatics, Bioinformatics, Genomics, Molecular Biology or related discipline
- 1 year of related work experience
- An equivalent combination of education and experience with next-generation sequencing methods and data analysis may substitute for stated requirements including where post baccalaureate training has been obtained in dedicated Bioinformatics and Genomics Studies
- 1 year of processing sequencing data from sequencer through a genomics analysis pipeline
- 1 year using R or Python to generate analytic programs for data analysis
- 1 year of performed bulk and single cell RNA sequencing analysis
- 1 year of previously working with tumor sequencing datasets
- Experience in molecular biology methods and data analysis.
- R Programming Language, Python, C++, MatLab, SQL and Cell Ranger for single cell sequencing
- Strong teamwork, interpersonal, and managerial skills.
- Strong organizational and documentation skills suitable to a clinical laboratory environment. Demonstrates ability to rapidly distill concise and succinct summaries from complex and potentially contradictory literature sources.
- Ability to work independently. Ability to prioritize and work under tight deadlines.
- Excellent verbal and written communication and organizational skills.
Disclaimer: The job description has been designed to indicate the general nature and essential duties and responsibilities of work performed by employees within this job title. It may not contain a comprehensive inventory of all duties, responsibilities, and qualifications required of employees to do this job.
Compliance Requirement: This job adheres to the ethical and legal standards and behavioral expectations as set forth in the code of business conduct and company policies.
As a component of job responsibilities, employees may have access to covered information, cardholder data, or other confidential customer information that must be protected at all times. In connection with this, all employees must comply with both the Health Insurance Portability Accountability Act of 1996 (HIPAA) as described in the Notice of Privacy Practices and Privacy Policies and Procedures as well as all data security guidelines established within the Company’s Handbook of Privacy Policies and Practices and Information Security Policy.
Furthermore, it is every employee’s responsibility to comply with the company’s Code of Business Conduct. This includes but is not limited to adherence to applicable federal and state laws, rules, and regulations as well as company policies and training requirements.
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