FDA-CDER Research Opportunity in Next Generation Sequencing Oncology Bioinformatics

Application Deadline

3/29/2024 3:00:00 PM Eastern Time Zone

Description

*Applications will be reviewed on a rolling-basis.

This project will be located in the Office of Oncologic Diseases (OOD), Office of New Drugs (OND).  This research project is to comprehensively evaluate and compare technologies, methods, and tools to elucidate current limitations, address fundamental technical challenges, establish reference samples and data sets, and provide a standard framework for the accurate and cost-effective profiling of immune cell repertoires from next-generation sequencing (NGS) data. Ultimately, the multi-center collaborative efforts of this research project will yield critical knowledge to inform FDA's evaluation of and reliance on immune cell receptor profiling data submitted in clinical trials to support approval of therapies for patients with hematologic malignancies. Additionally, the impact of the project may extend beyond oncology to inform the evaluation and use of immune receptor profiling data collected in clinical trials for other immunological disorders across a range of therapeutic areas. Through multiple external collaborations with academic and government partners, the participant will assess the use of NGS technology to answer critical regulatory science research questions in of immune receptor profiling, including but not limited to, performance characteristics of RNA-based, DNA-based, or single cell-based sequencing assays, data analytical tools and quality metrics. The main objective of this program is to assess critical parameters involved in the adoption of NGS technology for health care and regulatory decision making. These parameters include both wet lab and dry lab components such as sample processing, laboratory protocols, bioinformatics, data processing, and related statistical analyses.

Under the guidance of a mentor the participant will gain knowledge in the following areas:

• analyzing various bioinformatics approaches to understand best practices for NGS analysis along with novel methodologies
• examining current standard operating procedures and protocols, along with emerging tools, to understand best practices for NGS data generation, quality control, and downstream analysis
• collaborating with a multi-disciplinary team including clinicians, biologists, chemists, programmers, and regulators, and engage with multiple investigators for individual projects

The Center for Drug Evaluation and Research (CDER) performs an essential public health task by making sure that safe and effective drugs are available to improve the health of people in the United States. As part of the U.S. Food and Drug Administration (FDA), CDER regulates over-the-counter and prescription drugs, including biological therapeutics and generic drugs. This work covers more than just medicines.

This program, administered by ORAU through its contract with the U.S. Department of Energy to manage the Oak Ridge Institute for Science and Education, was established through an interagency agreement between DOE and FDA. The appointment is for 12 months. The participant will receive a monthly stipend commensurate with educational level and experience. Proof of health insurance is required for participation in this program. The appointment is full-time at FDA in the Silver Spring, Maryland area. Participants do not become employees of FDA, DOE or the program administrator, and there are no employment-related benefits.

Completion of a successful background investigation by the Office of Personnel Management is required for an applicant to be on-boarded at FDA.  OPM can complete a background investigation only for individuals, including non-US Citizens, who have resided in the US for a total of three of the past five years.

FDA Ethics Requirements

If an ORISE Fellow, to include their spouse and minor children, reports what is identified as a Significantly Regulated Organization (SRO) or prohibited investment fund financial interest in any amount, or a relationship with an SRO, except for spousal employment with an SRO, and the individual will not voluntarily divest the financial interest or terminate the relationship, then the individual is not placed at FDA.   For additional requirements, see FDA Ethics for Nonemployee Scientists. 

FDA requires ORISE participants to read and sign their FDA Education and Training Agreement within 30 days of his/her start date, setting forth the conditions and expectations for his/her educational appointment at the agency.  This agreement covers such topics as the following:

• Non-employee nature of the ORISE appointment;
• Prohibition on ORISE Fellows performing inherently governmental functions;
• Obligation of ORISE Fellows to convey all necessary rights to the FDA regarding intellectual property conceived or first reduced to practice during their fellowship;
• The fact that research materials and laboratory notebooks are the property of the FDA;
• ORISE fellow’s obligation to protect and not to further disclose or use non-public information.

Qualifications

The qualified candidate should have received a bachelor's, master's, or doctorate in one of the relevant fields.

Preferred skills/experience:

• A doctorate degree in Computer Science or Bioinformatics
• Master’s degree (or above) in Biological Science.
• Qualified masters and bachelors level degrees may also be considered provided that the candidate demonstrates strong analytical experience.
• Familiarity with next-generation sequencing technologies and data analysis, including development and application of algorithms to perform analysis of BCR/TCR sequencing, whole genome, and RNA-Seq (bulk or single cell) data
• Knowledge of scripting, development languages and cloud-based (AWS) computational environment
• Knowledge of molecular biology techniques (including nucleic acid purification and next-generation sequencing library preparation)

Eligibility Requirements

• Degree: Bachelor's Degree, Master's Degree, or Doctoral Degree.