One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants

Abstract

Next-generation sequencing (NGS) is replacing other molecular techniques to become the de facto gene diagnostics approach, transforming the speed of diagnosis for patients and expanding opportunities for precision medicine. Consequently, for accredited laboratories as well as those seeking accreditation, both objective measures of quality and external review of laboratory processes are required. External quality assessment (EQA), or Proficiency Testing (PT), can assess a laboratory's service through an independent external agency, the EQA provider. The analysis of a growing number of genes and whole exome and genomes is now routine; therefore, an EQA must be delivered to enable all testing laboratories to participate. In this paper, we describe the development of a unique platform and gene target independent EQA scheme for NGS, designed to scale from current to future requirements of clinical diagnostic laboratories testing for germline and somatic variants. The EQA results from three annual rounds indicate that clinical diagnostic laboratories are providing an increasingly high-quality NGS service and variant calling abilities are improving. From an EQA provider perspective, challenges remain regarding delivery and performance criteria, as well as in analysing similar NGS approaches between cohorts with meaningful metrics, sample sourcing and data formats.

Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development

“…Such analytical validation requires the careful prospective endto-end study of appropriately justified method parameters and performance characteristics (e.g., accuracy, precision, limits of detection, specificity, robustness) from sampling through to data reporting. In order to demonstrate safety and effectiveness, developers of NGS-based tests must provide assurance of accurate and reliable detection of clinically relevant variants through careful design, development and analytical validation of such techniques [12,13,19,20,26]. NGS tests can be quite complex, involving many elements to achieve proper collection, and handling of clinical and laboratory samples, selection of adequate sampling materials, accurate laboratory analysis, and correct data processing through use of appropriate bioinformatics pipelines.…”

“…NGS tests can be quite complex, involving many elements to achieve proper collection, and handling of clinical and laboratory samples, selection of adequate sampling materials, accurate laboratory analysis, and correct data processing through use of appropriate bioinformatics pipelines. Therefore, robust validation policies, processes, controls and monitoring must be in place to ensure NGS-based tests, including individual test elements and methods, that directly impact on the reliability of data are fit for purpose throughout the data processing and testing life cycle [9,12,13,19,20,26].…”

Commentary: Cancer research quality and tumour classification

“…Documentation training, equipment maintenance, internal and external quality assurance are all pre-requisites for accreditation and improved results. 8 Good Laboratory Practice (GLP) is an attempt to achieve similar levels of accuracy within research laboratories, but many would argue that the changing nature of the research from day to day or experiment to experiment makes it impossible to meet the standards expected of clinical laboratories.…”

Application of Next Generation Sequencing in Laboratory Medicine

“…NGS has a wide spectrum of applications in laboratory medicine and has become an integrated part of precision medicine. The technology has been widely used in diagnosis, prognosis, and therapy selection for constitutional disorders, oncology, and infectious diseases [3][4][5]. Concurrently, an increasing amount of well curated clinical, genetic, and genomic data is being generated by NGS, further driving the development of precision medicine [6].…”