Lab Matters Fall 2023 | Page 29


The Next Generation Sequencing Quality Initiative : Creation of Tools to Improve Sequencing Quality Management

By Shannon Mahoney , MS , senior specialist , Advanced Molecular Detection
As sequencing platforms and capabilities have largely advanced over the past decade , public health laboratories have been faced with the hurdle of adapting quality management systems to meet the unique challenges for next generation sequencing ( NGS ) workflows .
The US Centers for Disease Control and Prevention ’ s ( CDC ) Office of Advanced Molecular Detection ( OAMD ) funded APHL and its Division of Laboratory Systems to launch the Next Generation Sequencing ( NGS ) Quality Initiative in 2019 . It endeavors to develop tools and resources to aid public health laboratories in creating a robust quality management system ( QMS ) in their sequencing and bioinformatics workflows . To ensure the initiative created a comprehensive set of resources for quality management , it utilized the 12 quality system essentials ( QSEs ) established by the Clinical Laboratory Systems Institute ( CLSI ).
This year , the NGS Quality Initiative is celebrating a major milestone in its drive to supply tools and products focused at improving the quality of NGS workflows . With over 100 published products , it is celebrating the successful development of resources that address all 12 QSEs . Customizable , ready-to-use resources that encompass the entire sequencing workflow from the wet lab protocols through bioinformatics analysis and internal assessments are now available for all public health laboratories . These resources are created for a variety of different audiences , including bench laboratorians , bioinformaticians , quality managers and laboratory managers , since they are all involved in NGS quality management and have unique needs .
By providing tools and templates that can easily be redesigned and reimagined to fit the needs of individual laboratories , the QMS can be useful for laboratories just beginning sequencing as well as for those with well-established sequencing programs . Recognizing the diversity and expansiveness of laboratory ’ s sequencing programs , the initiative also has resources for all of the major sequencing
QMS Assessment Tool : The interactive assessment tool serves as a guidance document to assist laboratories in establishing and curating their own internal quality management system with sequencing activities in mind .
Identifying and Monitoring NGS Key Performance Indicators SOP : This guidance document assists laboratories in identifying and applying quality metrics to maintain high-quality NGS testing .
NGS Method Validation Plan : This template document provides laboratories new to sequencing with the insight to generate their own method validation plan by providing near step-by-step guidance for identifying assay type , determining acceptance criteria , permitting sample requirements and more .
instruments , with over 60 published instrument-specific documents , ranging from pre-installation checklists to maintenance logs to instrument SOPs .
Of the over 100 products hosted on the QMS , two of the most downloaded products include the QMS Assessment Tool and NGS Method Validation Plan , which serve critical roles in allowing laboratories to both onboard new NGS platforms and assays , as well as ensure high quality testing is being maintained through the facilitation of their own internal QMS . The products provide users with a fundamental , yet comprehensive , process for building out sequencing operations through interactive , step-bystep templates .
As sequencing operations in public health laboratories grow alongside the NGS Quality Initiative , APHL looks to ensure that resources continue to evolve with the advent of new sequencing and
Bioinformatics Training SOP : This guidance document helps direct laboratories in the development and implementation of training courses using a “ Tell , Show , Do , Apply ” learning methodology , aimed at developing the skills and knowledge necessary to perform bioinformatic analysis .
bioinformatics tools . With products focused on all 12 CLSI QSEs , laboratories can expect resources to support almost every facet of testing , regardless of their sequencing experience . The NGS Quality Initiative hopes to continue to develop and revise the resources to ensure their products stay relevant and up to date with the current sequencing workflows . Looking ahead , the Initiative hopes to continue to expand the development of its resources to best serve the public health community , including more customized tools to aid in clinical accreditation standards for sequencing and greater resources for quality management in bioinformatics analysis . If you have any questions about this work or suggestions for resources , please contact ngsquality @ cdc . gov . g
APHL . org
Fall 2023 LAB MATTERS 27