{"id":5419,"date":"2020-08-26T09:44:29","date_gmt":"2020-08-26T09:44:29","guid":{"rendered":"https:\/\/clinlabint.3wstaging.nl\/clinical-application-of-ngs-ensuring-quality\/"},"modified":"2021-01-08T11:37:10","modified_gmt":"2021-01-08T11:37:10","slug":"clinical-application-of-ngs-ensuring-quality","status":"publish","type":"post","link":"https:\/\/clinlabint.com\/clinical-application-of-ngs-ensuring-quality\/","title":{"rendered":"Clinical application of NGS \u2013 ensuring quality"},"content":{"rendered":"

Advances in Next Generation Sequencing (NGS) are bringing much higher throughput and rapidly reducing costs, whilst facilitating new mechanisms for disease prediction. Consequently, the clinical applications of NGS technologies are continuing to develop, with the potential to change the face of genetic medicine [1].<\/p>\n

by Hannah Murfet (BSc, PCQI), Product Quality Manager, Horizon Discovery<\/strong><\/p>\n

Applications of NGS in a clinical context are varied, and may include interrogation of known disease-related genes as part of targeted gene panels, exome sequencing, or genome sequencing of both coding and non-coding regions. However, as NGS moves further into the clinic, care must be taken to ensure high levels of quality assurance, rigorous validation, recording of data, quality control, and reporting are maintained. [1] [2]
Guidelines specific to NGS are beginning to emerge and to be adopted by clinical laboratories working with these technologies, in addition to those mandated by clinical accreditation and certification programmes. In this article we give an overview of the specific guidance set out by the American College of Medical Genetics and Genomics in its September 2013 report \u2018ACMG clinical laboratory standards for next-generation sequencing\u2019, and the New York State Department of Health\u2019s January 2014 document \u2018Next Generation Sequencing (NGS) guidelines for somatic genetic variant detection\u2019.<\/p>\n

Quality Assurance<\/strong>
Quality assurance (QA) in the clinical context comprises maintenance of a desired level of quality for laboratory services. Typically, quality management systems take a three tier hierarchy. At the highest level the policies define the organisation\u2019s strategy and focus. Underneath this sit the procedures, which define and document instructions for performing business\/quality management or technical activities. Underpinning both of these tiers are accurate records.
In the case of New York State Department of Health guidelines, there is clear focus on the requirement for SOPs, which can be broken down into two levels. The first level states the required flow of information, demonstrating the sequence of events, and associated responsibilities or authorities. The first level procedures are best kept at a relatively high level, and may reference more specific and detailed level two processes.
Testing sequences may be incorporated into one or more level one processes, depending on the complexity of the clinical laboratory\u2019s operations. An overview of the typical testing sequence is shown in the figure below.
Level two processes are best documented as clear \u2018how to\u2019 guides, detailing all responsibilities, materials and procedures necessary to complete the activity. For laboratory-focused activities, validation study inputs and outputs can establish clear and consistent protocols, supporting training and laboratory operation.
Accurate record keeping should include which instruments were used in each test, as well as documentation of all reagent lot numbers. Any deviations from standard procedures should be recorded, including any corrective measures [1]. Templates may be generated to ensure consistency in output records for both testing and reporting.
In addition to documented processes, implementation of predetermined checkpoints or key performance indicators should be included to permit the monitoring of QA over time. Once established, these may act as a trigger for assay drift, operator variability, or equipment issues.
In the US, compliance to the HIPAA Act (Health Insurance Portability and Accountability Act) must be implemented to ensure traceability and protection of patient data, and many authorities mandate record retention periods, including CLIA who dictate that records and test reports must be stored for at least two years [1].
Clinical laboratories may look to further certification to ensure tight QA, such as the implementation of ISO 15189, especially in countries where no formal accreditation schemes are in place. [3]<\/p>\n

Validation<\/strong>
Validation involves the in-depth assessment of protocols, tests, materials and platforms, providing confidence that critical requirements are being met. Test development and platform optimization should include factors such as determination of sample pooling parameters, and use of synthetic variants to create a strong data set, to compare tools and optimize the workflow. Validation of each entire test should be undertaken, using set conditions for sensitivity, specificity, robustness and reproducibility.  It should be noted that the first test developed may naturally carry a higher validation burden than subsequent tests developed for the same platform. Platform validation and quality management are also vital. [1,2]
Specific validation requirements for NGS as set out by the New York State Department of Health are listed below.  These guidelines may be used as a basic checklist for coverage, or to supplement more general accreditation or certification requirements, e.g. those required by CLIA or ISO 15189. [1]<\/p>\n