Practical Guidance to Implementing Quality Management Systems in Public Health Laboratories Performing Next-Generation Sequencing: Personnel, Equipment, and Process Management (Phase 1)

Abstract

Quality standards as part of an effective quality management system (QMS) are the cornerstone for generating high-quality test results. Next-generation sequencing (NGS) has the potential to improve both clinical diagnostics and public health surveillance efforts in multiple areas, including infectious diseases. However, the laboratories adopting NGS methods face significant challenges due to the complex and modular process design. This document summarizes the first phase of quality system guidance developed by the Centers for Disease Control and Prevention (CDC) NGS Quality Workgroup. The quality system essentials of personnel, equipment, and process management (quality control and validation) were prioritized based on a risk assessment using information gathered from participating CDC laboratories. Here, we present a prioritized QMS framework, including procedures and documentation tools, to assist laboratory implementation and maintenance of quality practices for NGS workflows.

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance

“…The clinical interpretation of identified variants is not standard for all diseases. This issue is being resolved by generating standardized analysis, interpretation and reporting guidelines (Endrullat et al, 2016;Roy et al, 2016;Li et al, 2017;Lindeman et al, 2018;Roy et al, 2018;Hutchins et al, 2019). Incomparable results carry huge implications in clinical applications and should be regulated sooner rather than later (Endrullat et al, 2016).…”

Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays

“…For more general applications, Burd [9] provides an in-depth summary of validation strategies and criteria that apply to molecular assays for infectious diseases. More recently, the Centers for Disease Control and Prevention also published a practical guideline for implementing NGS-based assays in a public health setting [10]. Although progress has been made in the field, an appropriate validation and performance assessment platform for NGS-based HIVDR testing has not been developed.…”

Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework

“…Many clinical labs use software or bioinformatics pipelines to perform sequence analysis and as such, validation of the pipeline in use is necessary to ensure the test can reliably detect variation [ 6 , 7 ]. As HIVDR testing continues to become common practice for guiding ART regimes, clinical labs need to maintain both internal and external quality control measures, as well as a uniform standard of quality assurance [ 5 , 8 ]. The use of modern technologies such as NGS continues to drive massive data production, creating a need to systematically organize both clinical and quality control results, while flagging potential problems that could impact data quality.…”

“…While there is extensive coverage of quality control procedures for sample processing in NGS and specifically HIV-sequencing, the data produced by such techniques provide multiple opportunities for continued quality control of the final sequence [ 2 , 7 , 8 , 14 ]. The integration of an LIS allows for the management of samples and their associated data while automating workflows and incorporating instrument specifications, ultimately allowing the user to view all data associated with an assay as a package within a centralized program [ 15 ].…”