The New York Genome Center (‘NYGC’) 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 concentrating on informatics programming specializing in molecular diagnostics, you will be responsible for the generation of next-generation sequencing (NGS) data 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. The primary responsibilities include pipeline engineering, cloud computing, end-to-end analysis of whole genome and exome sequencing data using established pipelines, assisting in validation of new clinical assays, performing custom case-by-case bioinformatics analyses. You will be part of a clinical lab team of 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 algorithms used in clinical sequencing analyses. You will assist clinical informatics and laboratory scientists in developing and validating new NGS based clinical laboratory tests. This is an excellent opportunity for individuals with a strong computational background seeking to gain experience in clinical bioinformatics, molecular diagnostics and reporting. Note, this is not a clinical research position.

Key Responsibilities

• Implement and execute analysis pipelines and workflows using WDL and Cromwell on public cloud platforms (GCP / AWS)
• Develop executables for NGS data generation and data analysis
• Develop and query databases using SQL queries
• Process and maintain current clinical molecular diagnostic NGS data workflows for report generation
• Analyze validation experiments for laboratory developed tests (LDT)
• Benchmark new tools for sequencing data analysis and propose improvements
• Develop and apply novel analysis approaches to aid clinical sample variant prioritization
• Analyze clinical sequencing data using established workflows.
• 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
• Develop and maintain a database of variants, curation, and notes.

Requirements & Qualifications

Required

• MS degree with work experience in cancer or hereditary disease next generation sequencing (NGS) analysis required, candidates with a PhD in cancer genomics or human genetics with demonstrable biomedical NGS bioinformatics skills welcomed
• Strong programming skills in Python and shell scripting
• Database skills such as experience with SQL
• Basic understanding of human genetics
• Work experience and algorithm understanding of standard software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools
• Knowledge in the analysis of SNV, Indel, CNV and structural variants including variant annotation using standard tools like VEP or SnpEff.
• Familiarity with various NGS QC principles
• Work experience with commonly used public genomics datasets (1000 genomes, ExAC, OMIM, ClinVar, HGMD, CIViCDB, PharmGKB, OncoKB etc.)
• Details-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics
• Team oriented with excellent written and verbal communication skills

Preferred

• Prior experience working in CLIA environment is a plus
• Experience in variant calling benchmarking and clinical validation analysis (eg. concordance, limit of detection, assay reproducibility)
• Programming skills in R
• Experience of working in a Linux environment, experience with SGE
• Experience with web-development (HTML, CSS, JavaScript, TypeScript and related)

Competencies

• 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. This position is not eligible for fulltime remote work.

Salary

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 NYGC 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.