Lab Matters Fall 2020 - Page 49

APHL 2020 POSTER ABSTRACTS reference-free pipeline ( Utah Public Health Laboratory ) and Lyve-SET ( Centers for Disease Control and Prevention ), as well as , Staphopia ( Emory University ). These pipelines utilize Singularity images created from Docker containers available on the State Public Health Bioinformatics ( StaPH-B ) Docker Hub .
SHL continues to explore new tools and analysis platforms . As SHL generates more sequence data , organizing sequence files needed for specific analysis is a growing challenge . SHL is developing a PostgreSQL database that will track the location of fastq files and pipeline outputs , as well as , pipeline versions ( for reproducibility ) and metadata . The database , hosted on SHL ’ s servers , will allow us to quickly locate files according to specific parameters such as organism name , sequence type , or collection facility . The search output will be used to automatically recover files of interest and start subsequent analysis . SHL is also utilizing the UI Interactive Data Analytics Service ( IDAS ) resource as the front end for the files tracking database and to host one of its applications for analyzing resistance and virulence genes . Finally , SHL started to develop a workflow to automatically track Carbapenem-resistant Enterobacteriaceae ( CRE ) genes and organisms based on the combined AMR data from SHL ’ s information system and WGS analysis output .
Local universities can be instrumental in providing the necessary computing resources to expand bioinformatics capacity at a public health laboratory . An overview of this partnership , as well as , the pipelines and tools used by SHL could provide a road map for other state public health laboratories .
Presenter : Alankar Kampoowale , State Hygienic Laboratory at The University of Iowa , Iowa City , IA , alankar-kampoowale @ uiowa . edu
Molecular Paradigm Shifts in Newborn Screening Systems
H . Desai , O . Akinsola and G . Zarbalian , Association of Public Health Laboratories , Silver Spring , MD
Newborn screening is known to be one of the most effective public health programs . With the rapid expansion of conditions that can be detected and the advent of next-generation sequencing ( NGS ), newborn screening systems must leverage relevance of new screening technologies to augment current methods for complex multigene disorders and coordinate the results with short- and long-term follow up . The implementation period for conditions added to the recommended uniform screening panel ( RUSP ) vary across regions , and newborn screening public health laboratories prepare by addressing the social , ethical , financial , and legal questions of adopting new methodologies . For this poster we showcase different screening methodologies and workflows for cystic fibrosis ( CF ) and severe combined immunodeficiency ( SCID ) to demonstrate the paradigm shift in adopting new technologies to complement current methods and the impact they have on follow-up procedures . We also demonstrate that there is no “ one size fits all ” or “ cookie cutter ” approach to newborn screening and each program must tailor their practices to best meet the needs of newborns in their state and detect rare disorders in a timely manner .
Presenter : Hiral Desai , Association of Public Health Laboratories , Silver Spring , MD , hiral . desai @ aphl . org
Creation of an Online Newborn Screening Educational Program Using Adaptive Learning
C . Hinton 1 , C . Cuthbert 1 , A . Gaviglio 2 ; 1 Centers for Disease Control and Prevention , Atlanta , GA , 2 G2S Corporation , St . Paul , MN
Newborn screening is a public health program that identifies conditions that can affect a child ’ s long-term health or survival . Early detection , diagnosis , and intervention can prevent death or disability and enable children to reach their full potential .
A well-trained workforce is essential to ensuring that public health laboratories have the capacity to conduct the critical activities of newborn screening to ensure timely detection of affected newborns . High turnover of staff , emerging technologies , implementation of new complex conditions , and policy changes that impact newborn screening practice all point to the need for a comprehensive educational program . Such a program should be targeted at the needs of the evolving newborn screening community to deliver consistent communication of best practices and new content .
One of the challenges in designing educational resources for a community with diverse educational and technical capabilities is how to present content that engages both the novice and the expert learner . To address these needs , CDC ’ s Newborn Screening and Molecular Biology Branch has created an online educational product . CDC has contracted with an educational vendor to develop the product . The educational product uses an adaptive learning platform that adjusts in real-time to the needs of each learner and constantly tailors the lesson content and teaching approach based on the responses of each individual learner . As such , both the novice and the expert can take the same course and have different learning experiences , with the aim of moving both learners towards greater mastery of the course material . The initial release of the educational product includes three modules that cover : 1 ) Amino Acid Disorders , 2 ) Severe Combined Immunodeficiency ( SCID ), and 3 ) Molecular Methods . These modules will provide Continuing Education credits and will be available free of cost through the CDC TRAIN Learning Network , a comprehensive catalog of online public health training opportunities .
The online newborn screening product will educate public health professionals from US newborn screening programs about the newborn screening system , current and emerging technologies , current and anticipated screened conditions , and policies and issues that impact practice . The product will be on-demand and free with material curated by the CDC . An adaptive learning platform has been shown to increase learner motivation and competency in other biomedical and clinical fields . It is anticipated that this online educational product will reinforce learning newborn screening professionals , incorporate learner self-evaluation , be responsive to variations in learner response , and provide real-time adaptive response to individual learners .
Presenter : Cynthia Hinton , Centers for Disease Control and Prevention , Atlanta , GA , ceh9 @ cdc . gov
Newborn Screening and Genetics
Fall 2020 LAB MATTERS 47