Lab Matters Fall 2020 - Page 50

Preparedness and Response
Developing a Bioinformatics Program : The Texas Experience
S . Marcellus and R . Lee , Texas Department of State Health Services Laboratory , Austin , TX
Problem / Objective : As gene therapy , genetic research , and molecular technology have expanded , newborn screening methodologies have attempted to keep pace , resulting in the need for streamlined molecular data analysis and interpretation . The Texas Newborn Screening Program has begun development of a bioinformatics program to efficiently analyze and interpret Next Generation and Sanger sequencing data to screen newborns for SCID ( severe combined immunodeficiency ) and other conditions . Most states with newborn screening ( NBS ) bioinformatics capabilities have adapted their existing infectious disease ( ID ) informatics infrastructure for use in newborn screening . The Texas DSHS Laboratory is building infrastructure for NBS and ID concurrently , from the ground up .
Methods : The Texas Laboratory started the information gathering process by seeking input and expertise from numerous partners , including local laboratory information technologists ( IT ) and departmental IT , the University of Texas Bioinformatics Consulting Group ( UT-BCG ), and other state public health laboratories such as the Virginia Division of Consolidated Laboratory Services ( DCLS ). We are collaborating with local and departmental IT to determine the options of hardware and software that are permitted by our governing bodies and are compatible with existing systems . UT-BCG and Virginia DCLS provided training , feedback on their informatics implementation processes , and will be great resources throughout our development process . Numerous pipelines and DNA analysis tools created by public health bioinformaticians are available for review and we will select code that will best fit Texas ’ needs . To improve the workforce , the Texas Laboratory applied and was awarded a fellowship and additional training was provided to the bioinformatics fellow and other laboratory technologists .
Results and Conclusions : The Bioinformatics Program for the Texas NBS Program and ID Program is currently in development . The needs of both the NBS and ID programs are being weighed during platform selection . During platform selection and program development , IT has had several concerns including security , access , network bandwidth , and hesitancy to implement a new system . Open and frequent communication is reducing the issues with IT . The creation and implementation of a joint NBS and ID bioinformatics pipeline will facilitate faster test times , higher accuracy and precision in results , quicker result reporting and will allow for administration by a single bioinformatician . Without a bioinformatics program , critical NBS referrals could be slowed , likely causing delays to diagnosis and treatment of time-critical diseases . Laboratory test results could also be delayed for ID patients , likely causing a delay in outbreak detection and reporting . A bioinformatics program is necessary for the timely reporting of ID and NBS .
Presenter : Samantha Marcellus , Texas Department of State Health Services Laboratory , Austin , TX , smarcellus @ live . com
Providing Resources to Enhance Collaboration in the Detection of Public Health Threats and Effective Response
E . Bowles 1 , S . Escott , S . Abrams 2 , R . Nickla 3 ; 1 Wisconsin State Laboratory of Hygiene , Madison , WI , 2 Association of Public Health Laboratories , Silver Spring , MD , 3 Oregon State Public Health Laboratory , Hillsboro , ORT
The Association of Public Health Laboratories ( APHL ) provides key resources to public health laboratories ( PHLs ) through the Sentinel Laboratory Partnerships and Outreach Subcommittee ( SLPOS ) to assist in their ability to effectively communicate with and provide guidance to sentinel clinical laboratories . In fiscal year 2020 , along with input from the American Society for Microbiology ( ASM ) and the Centers for Disease Control and Prevention ( CDC ), SLPOS developed and updated essential resources that focus on enhancing the relationships between public and private laboratories .
SLPOS members began the process of updating the ASM Laboratory Response Network ( LRN ) Sentinel Level Clinical Laboratory Guidelines , which provide standardized , practical methods and techniques to rule-out or refer suspected bioterrorism agents . These guidelines provide clinical laboratorians with information on safety , testing materials , specimen collection and processing , rule-out testing flowcharts , etc . They are a critical resource utilized by both clinical and public health laboratorians .
Due to changes in the ASM guidelines and to ensure harmonization of reference materials , SLPOS is also updating the Clinical Laboratory Preparedness and Response Guide , a companion critical resource for clinical laboratorians . Other resources , such as the APHL Biothreat Agents Identification Bench Cards and poster , will also be updated as necessary , to ensure resource materials remain consistent .
SLPOS has developed other valuable resources for both clinical and public health laboratorians . The Biothreat Organism Evaluation tool assists PHLs to evaluate the ability of their Sentinel Clinical Laboratories to use the rule-out procedures according to the ASM Guidelines . The Clinical Laboratory Exposure Assessment and Monitoring tool assists PHLs with assessing whether or not there have been any exposures within the clinical laboratory to a bioterrorism agent during culture work-up and rule-out testing . It also provides guidance on follow-up prophylaxis and treatment if exposures are identified . Another resource , the Packaging and Shipping Evaluation Tool , provides a standardized resource for PHLs to assess the proper packaging and shipping of biological threat agent rule-out samples sent to them by clinical sentinel laboratories .
The resources developed by the members of SLPOS are vital tools that support the mission of collaboration within the LRN to enable a quick and accurate detection of public health threats and provide a timely , effective response .
Presenter : Samuel Abrams , Association of Public Health Laboratories , Silver Spring , MD , samuel . adams @ aphl . org