APHL-CDC Newborn Screening Bioinformatics and Data Analytics Fellowship (Richmond, VA)
Fellowship Description:
The Association of Public Health Laboratories (APHL) is seeking either a post-masters or post-doc level bioinformatics fellow to assist with the Division of Consolidated Laboratory Services’ newborn screening (NBS) laboratory operations and research under the mentorship of the principle bioinformatics scientist at Division of Consolidated Laboratory Services in Richmond, VA. This fellowship will be for a minimum of 1 year, but may be up to two years based on funding availability and agreement of both laboratory and fellow to continue fellowship for a second year.
The fellow will participate in the following project:
In January 2019, the Virginia Division of Consolidated Laboratory Services (DCLS) began second tier Sanger sequencing for two Lysosomal Storage Disorders (LSD). At that time, DCLS also launched the Newborn Screening Variant Interpretation tool (NBSVI), a web based application developed by DCLS that deploys and stores the results of a series of data collection, management and annotation pipelines and provides comprehensive reports for efficient variant interpretation and improved communication between the laboratory and genetic specialists. Thus far, NBSVI has only been applied to the analysis of Sanger Sequencing results, but is applicable to variant results identified through Next-Generation Sequencing (NGS) with additional minor modifications. As DCLS plans to transition from Sanger to NGS for existing and future anticipated assays, the bioinformatics group would like to begin the investigation, build-out and validation of the dry-lab analytics in preparation for this transition. This includes additions to the information provided and the decision made by NBSVI, as well as, the addition of a NGS variant analysis pipeline. The main project will involve learning about variant interpretation, investigating available variant analysis pipelines and if deemed necessary, developing a custom scalable variant analysis pipeline for NGS data that can be applied to both single and multi-gene sequencing. Additionally, the fellow will assist the NBS bioinformatician with the ongoing version controlled development of NBSVI and other bioinformatics solutions using python programming language.
The fellow will gain the following skills:
- · Understanding of newborn screening phases and processes: pre-analytic (involving specimen collection, transport and accessioning), analytic (testing of specimens and interpretation of newborn screening results), and post-analytic (follow-up of abnormal results, confirmatory testing, medical intervention on affected newborns)
- · Competency with interpreting and reporting results as part of a Newborn Screening System
- · Submit abstracts to the Newborn Screening and Genetic Testing Symposium and other relevant meetings
- · Participate in collaboration, webinars, and training outside DCLS
- · Participation and presentation in Newborn Screening Bioinformatics informal calls with Newborn Screening Community
Eligibility:
- · Applicants must be US citizens or permanent residents. Applicants to the program must have completed a masters or doctorate degree in bioinformatics, genomics, public health, molecular biology, population health, or another related discipline by the program start date. The degree must have been received within the last five years.
- · The fellow must be competent in python or other programming languages.
- · Applicants are required to have demonstrated education and/or experience in bioinformatics
Program benefits:
Fellows receive a stipend, allowances for medical insurance and professional development, vacation, medical leave, and complimentary membership to APHL. The 2020 fellowship post-masters level stipend is $54,095/year and the post-doc level stipend is $65,448/year.