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Bioinformatics Analyst – Oncology, Clinical Laboratory


New York Genome Center

Job Location

101 Avenue of the Americas, 7th Floor
New York, NY 10013
United States

Job Description

Job Description
The New York Genome Center is looking for a highly motivated, detail-oriented individual to join our expanding Clinical Informatics division within the NYGC CLIA Laboratory. As a Bioinformatics Analyst specializing in molecular diagnostics, you will be responsible for the analysis of next-generation sequencing (NGS) data for cancer conformant to CLIA / CLEP guidelines. You will work as part of a team of highly experienced laboratory and informatics staff and scientists at the NYGC CLIA Laboratory. You will be asked to perform variant calling analysis from whole genome/whole exome patient sample sequencing data. You will help identify and QC NGS somatic variants for molecular diagnostic reporting purposes. You will implement and maintain variant calling pipelines. You will be part of a team of CLIA scientists and laboratory personnel taking an active part in generating, developing and reporting patient sample genomic profile reports. You will be responsible to help implement and benchmark the most up to date variant calling algorithms used in clinical sequencing. You will assist clinical informatics and laboratory scientists in developing and validating new NGS based clinical laboratory tests. Note, this is not a clinical research position.

Key Responsibilities
Analyze clinical oncology sequencing data using established workflows
Implement, execute and maintain analysis pipelines and workflows
Assist in producing final CLIA oncology molecular diagnostics reports
Develop and apply novel analysis approaches to aid clinical sample variant prioritization
Benchmark new tools for sequencing data analysis and propose improvements
Analyze validation experiments for laboratory developed tests (LDT)
Summarize results in written or oral reports for CLIA laboratory personnel at weekly internal meetings or collaborating scientists and oncologists at external tumor boards
Assist CLIA laboratory personnel in preparing data, text and figures for case analysis, LDT validation proposals, manuscripts and external presentations
Perform and evaluate appropriate sequencing QC measures
Other reasonable tasks, as requested.
Required Skills
Experience & Qualifications

MS degree and 3+ years work experience in cancer or hereditary disease next generation sequencing (NGS) analysis or PhD in cancer genomics with demonstrable biomedical NGS bioinformatics skills
Experience in oncology or disease-focused genomics
Strong programming skills in Python, shell scripting and experience using R for data analysis
Work experience with various sequence analysis tools, including BWA, GATK, Picard, samtools,
Work experience and algorithm understanding of standard variant calling tools, such as (but not limited to) MuTect, Strelka, VarScan, Pindel, Bic-Seq, Facets, Sequenza, Crest, Delly, Fusioncatcher, Haplotypecaller or equivalent
Knowledge in the analysis of SNV, Indel, CNV and structural variants
Familiarity with various NGS QC principles
Work experience with commonly used public genomics datasets (1000 genomes, ExAC, OMIM, ClinVar, HGMD, CIViCDB, PharmGKB, OncoKB etc.)
Detail-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics
Team oriented with excellent written and verbal communication skills


Experience in variant calling benchmarking and clinical validation analysis (e.g. concordance, limit of detection, assay reproducibility)
Experience working in a Linux environment, experience with SGE
Experience working in a cloud computing environment (AWS or GCP)

The requirements listed are representative of the knowledge, skill, and/or ability required for this position. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions of the role.

Don’t meet every single requirement? Studies have shown that women and minorities are less likely to apply to jobs unless they meet every single qualification. At NYGC we are dedicated to building a diverse, inclusive and authentic workplace, so if you’re excited about this role but your past experience doesn’t align perfectly with every qualification in the job description, we encourage you to apply anyway. You may be just the right candidate for this or other roles.

Required Experience
Technical and Professional Skills: Consistently demonstrates skills and knowledge relevant for current role; strives to expand the depth and breadth of technical and professional skills; works with a high level of integrity; exhibits focus and discipline; appropriately prioritizes, manages expectations and delivers on commitments.
Collaborative & Communicative: Models collaboration and teamwork; brings out the best in others; effectively works with all levels, internally and externally; respects and embraces diversity of perspective; communicates clearly and listens carefully; uses good judgment as to what to communicate and when to do so.
Adaptable & Innovative: Adaptable and embraces change; develops new insights and pursues improvements and efficiency; fosters exchange of new ideas and willing to challenge the status quo; takes initiative and is solution-oriented; engages in work with passion and curiosity.

Work Flexibility

NYGC has established a flexible work policy to give employees and other staff more ability to balance their work, personal commitments, and commuting challenges. The incumbent in this position is eligible for a flexible work schedule. We prefer a candidate who can work onsite fulltime, but we are open to a hybrid remote work arrangement for this position, with supervisory approval.


The pay range for this position is $78-90k per year; base pay offered may vary depending on job-related knowledge, skills, and experience. In addition, NYGC offers a full range of medical, financial, and other benefits as well as generous time off.

About the New York Genome Center
The New York Genome Center (NYGC) is an independent, nonprofit, academic research organization dedicated to advancing genomic research. NYGC scientists and staff are furthering new approaches to diagnosing and treating neurological diseases and cancer through their unique capabilities in whole genome sequencing, RNA sequencing, state-of-the art analytics, and the development of genomic tools. NYGC concentrates specifically on disease-based research in the following areas: neuropsychiatric disease (autism, schizophrenia, bipolar); neurodegenerative disease (ALS, Alzheimer’s, Parkinson’s, Huntington’s), and cancer.

Located in Lower Manhattan, the New York Genome Center was founded by and remains closely affiliated with twelve leading academic medical centers and research universities in the New York region and beyond, engaging in research projects with and for these institutions. Essential to our collaborative work is an outstanding faculty, whose members typically hold a joint appointment at NYGC and a partner university. They support our scientific mission by conducting independent research in areas of mutual interest to us and the wider scientific community.

Equal Opportunity
Diversity, equity, and inclusion are central to the core mission at the NYGC. We strive to create a workplace environment that is welcoming and fair to all regardless of race, ethnicity, gender, sexual orientation, physical ability, or religion. We believe that when people of various backgrounds, life experiences, and perspectives work together in an inclusive and equitable environment we gain new and valuable perspectives that otherwise would have been missed. Valuing and supporting all NYG employees as individuals while helping them realize their full potential is critical to promoting greater collaboration, innovation, and discovery – fostering a sense of belonging for our greatest strength, our people. We recognize that there is still work to be done that will require sustained commitment from the entire organization.

The New York Genome Center is a VEVRAA Federal Contractor. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, creed, color, gender, religion, national origin, sexual orientation, age, disability, genetic predisposition or carrier status, protected veteran or military status, domestic violence victim status, partnership status, caregiver status, alienage or citizenship status, marital status, or any other characteristic protected by applicable law. The New York Genome Center takes affirmative action in support of its policy to hire and advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities.

FLSA Status – Exempt

This position is eligible for visa sponsorship and relocation assistance.