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DIR CLINICAL GENOMICS


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M2Gen Building, 10902 N McKinley Drive, Tampa, FL 33612

Bioinformatics

Full Time

80

Day Shift

Mon-Friday 9-5:30

M2Gen is a health informatics solution subsidiary of the H. Lee Moffitt Cancer and Research Institute in Tampa, Florida. M2Gen is the operational and coordinating center for the Oncology Research Information Exchange (ORIEN), an alliance of cancer centers across the US. We strive to be a leader in creating and delivering health informatics solutions through evidence-based approaches to predict and meet the needs of cancer patients. Be part of the cure by joining M2Gen's team and impacting the future of cancer care.

Position Highlights:

 

The Director of Clinical Genomics works internally with M2Gen's IT, Bioinformatics, Medical Informatics and product teams and externally with service and technology vendors to coordinate key operational aspects of generating and delivering clinical and research grade molecular data in support of the Avatar program and other M2Gen molecular data initiatives. ORIEN Avatar brings the nation's leading cancer centers and biopharmaceutical companies together in a first-of-its kind initiative to share and study "big data" within a cutting-edge informatics environment. The director is responsible for delivering properly processed, analyzed, filtered and annotated NGS data (WES and RNAseq) to ORIEN members and pharma sponsors. Specific duties include building a talented workforce, seeking input from ORIEN and pharma bioinformaticians, clinical labs, identifying, evaluating and selecting various NGS pipelines for processing and WES and RNAseq data, performing the corresponding pipeline analyses and sequencing related QC, and communicating the pipeline related analysis results internally and externally, interacting with ORIEN members and pharma sponsors to help them use the Avatar data and address their specific questions.

 

This position will also be responsible for evaluating databases, tools to annotate variants' functions, impacts, and design reports at various levels. 

 

The ideal candidate will demonstrate:

 

·        Solid programming skills in R, Python or another high level programming language

·        Expert in NGS (research and clinical) pipeline analyses, including BWA, GATK, Mutect, Tophat2, STAR, Cufflinks, and tools for detection of gene fusions, calling structural variations and inference of copy number variations

·        Knowledge and experience of Unix/Linux, proficient in shell command scripting

·        Deep understanding of genomic annotation databases and data formats: ANOVAR, ClinVar, PolyPhen, SIFT, dbSNP, 1000 Genome, refSeq, Ensembl gene annotations and SAM/BAM, BED, MAF, VCF, WIG, GFF/GTF file formats

·        Extensive expertise on QA/QC tools such as FASTQC, QC3, RSeQC and components of GATK

·        Capability of implementing customized scripts internally for extensive QC measurements

·        Expert knowledge on other widely used NGS data processing tools such as samtools, bedtools, bamtools etc

·        Experience working in a cloud based, high performance computing environment

·        Knowledge of public databases (e.g. TCGA, ICGC, cBioPortal) and data visualization tools (e.g., IGV, UCSC genome browser)

·        Willingness and ability to learn new skills quickly

·        Passion for science and oncology

·        Strong leadership skills coupled with the ability to lead and influence cross-functional, cross-company teams as we establish new capabilities.

·        Ability to work effectively in a team environment with research scientists, biotech/pharma, cancer center IT/informatics personnel, data managers, programmers, and statisticians

·        Excellent communication and networking skills

·        Capability to select or deselect individuals with the appropriate collaborative mindset

·        Ability to handle numerous complex internal / external relationships at a time

·        Ability to understand and appreciate needs and perspectives of the stakeholders/partnerships

·        Ability to recognize and constructively address problems and conflicts

·        Demonstrated ability to engage in effective joint problem-solving to address key working together challenges

·        Knowledge of FDA/ICH guidelines and industry standard practices regarding the management of clinical trial data standards

·        Working knowledge of global regulatory requirements regarding data standards

·        Some travel may be required

 

Experience and Credentials:

 

·        Ph.D. in Bioinformatics of related  field

·        10+ years of experience post Ph.D

·        Experience in clinical NGS pipeline analysis

 

Note: This position may be based in Tampa, FL or Boston, MA

Moffitt Cancer Center is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, or protected veteran or disabled status. We seek candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence.