Next Generation Sequencing Gets New Quality Management Tools
Laboratory professionals who perform next generation sequencing in clinical and public health settings can find new, free tools to enhance quality and safety throughout the testing process.
A quality management solution suited for a high-tech environment can be as simple as a checklist on a clipboard or a standard operating procedure (SOP). The Next Generation Sequencing (NGS) Quality Initiative, a collaboration between CDC, the Association of Public Health Laboratoriesexternal icon (APHL), and state laboratory partners offers these tools and more sophisticated resources to laboratory professionals who conduct NGS.
NGS Technology in Brief
NGS Quality Initiative products support bioinformaticians in the analysis and management of whole genome sequence data.
Next Generation Sequencing (NGS) allows for analysis of genetic material from people, plants, animals, viruses, bacteria, and other organisms. Medical technicians sequence genes from patients to help healthcare providers determine a risk of genetic diseases or identify the source of an infection. This knowledge can help patients get diagnoses for treatment specific to their illness. NGS data from healthcare systems can also help epidemiologists detect disease outbreaks in our communities quickly. Clinical and public health laboratory professionals can rely on the NGS Quality Initiative for free, customizable, downloadable tools and resources.
A Focus on Quality Management for High Quality Results
A powerful diagnostic and surveillance tool like NGS demands an equally powerful quality management system (QMS) to ensure consistent, reliable data at any scale. The equipment, material, personnel, and training required to derive and maintain high-quality information from NGS can amount to a significant investment of time and resources. Clinical and public health laboratory leaders can download free tools and resources found on CDC’s website at QMS Tools and Resources, that were produced collaboratively by the Initiative. Staff can use the products to introduce or strengthen quality management in their workflows. Download products you and your colleagues can start using today to get ready for what tomorrow brings to your laboratory.
CDC’s NGS Quality Initiative Expands Catalogue of Resources
A laboratory staff member searching for NGS QI tools.
CDC and APHL have added to a growing catalogue of tools and resources for laboratory professionals performing NGS. The Initiative develops and publishes customizable, ready-to-implement guidance documents, standard operating procedures, forms, and tools. Highlighting the release of a new selection of tools and resources, Co-Principal Investigator of the Initiative, Heather Stang, notes that “Laboratory staff can use these products as a foundational management system or to support their existing QMS. These products help laboratory staff ensure accurate, consistent sequencing results that conform to regulatory requirements, when applicable. All products are available at no cost and can be downloaded from CDC’s website.”
Laboratories can adapt these ready-to-implement tools to meet needs for training their personnel, choosing and using appropriate protocols and analyses options, and putting effective management and process controls in place. These tools are especially beneficial to laboratories performing NGS-based tests because they are ready-to-use and adaptable to meet the quality needs of any laboratory.
Serving Public Health Departments and their Laboratory Staff
The Initiative delivers products through a website managed by CDC’s Division of Laboratory Systems (DLS), the organizational home to this effort. NGS Quality Initiative subject matter expert Diego Arambula, who helps lead the project for DLS, says, “Website visits and interactions show ongoing positive engagement with our key audience members, public health departments and their laboratory staff. We’ve seen thousands of downloads from our Tools and Resources page from website visitors across the United States and around the world., This indicates there is a need for the products we’re developing and publishing that our Initiative can fulfill.” The Initiative will add more resources to this page, expanding product offerings in other Quality Systems Essentials (QSEs). So, if you’re working in NGS, bookmark the page and check it periodically.
Laboratory staff working with platforms* such as the Illumina NextSeq, MiniSeq, MiSeq, iSeq 100, the Ion PGM, and the Oxford Nanopore MinION can find resources to assist with pre-installation requirements, the physical requirements of the work environment, and considerations for ensuring safety in the workplace. CDC updated and expanded three documents outlining biosafety precautions and practices for NGS waste disposal. These and future resources can be found under the Facilities and Safety Quality System Essential (QSE).
DLS Division Director, Ren Salerno, says that, “Safety and quality go hand in hand, and you can see that in the growing collection of tools and resources we post on the NGS Quality Initiative site. Not only do we have SOPs that explicitly cover facilities and safety, but products like our pre-installation, waste management, and training guides can be used to achieve high quality results while protecting laboratory staff.”
Professionals conducting NGS can also find resources on how information and data from internal and external sources are managed throughout the laboratory’s workflow, as well as how laboratory processes are managed throughout the entire testing lifecycle. CDC recently published resources for NGS data retention and storage, a document that introduces and describes common practices for containerization, and a containerization software-specific implementation guide. In addition, you can get our resource describing the use of SanitizeMe*, a tool for filtering contaminant reads from NGS data files.
These resources support how laboratories use bioinformatic software and storage resources, organize and manage their NGS-associated data, and facilitate adoption of technologies that allow for easier pipeline sharing, while taking into account security compliance considerations and applicable regulatory requirements.
Look Forward to More Resources
The NGS Quality Initiative is completing development of tools for the remaining QSEs to provide a foundational NGS-focused QMS. The Initiative will continue to support the evolving needs of laboratories by updating existing resources as well as developing and publishing additional tools for all twelve QSEs. Consider bookmarking the Initiative’s QMS Tools and Resources page and checking it periodically for updates and new products.
Catch Up with the Initiative’s Origins
In 2019, CDC and APHL in conjunction with state and local public health laboratory partners launched the NGS Quality Initiative. Together, they sought to address challenges public health laboratories encounter when they develop and implement NGS-based tests. The NGS Quality Initiative supports laboratories as they deploy an NGS-focused QMS to validate protocols, pass audits, achieve accreditation, and to ensure the synthesis of high quality, reliable data that is useful for diagnostic or reference testing and relevant to disease surveillance systems.
The project is funded by CDC’s Office of Advanced Molecular Detection, and is co-led by the Division of Laboratory Systems, the Office of the Deputy Director for Infectious Diseases, and APHL. Additional funding was provided by CDC’s Center for Surveillance, Epidemiology, and Laboratory Services and the Clinical Laboratory Improvement Amendments (CLIA) program.
*Use of trade names and commercial sources is for identification only and does not imply endorsement by the Centers for Disease Control and Prevention, the Public Health Service, or the U.S. Department of Health and Human Services.