Assuring the quality of next-generation sequencing in clinical laboratory practice
By Amy S. Gargis, L. Kalman, M. Berry, D. Bick, D. Dimmock, T. Hambuch, Fei Lu, E. Lyon, Karl V. Voelkerding, B. Zehnbauer and 30 more. Nature Biotechnology, 2012
463 citations recorded by the source corpus.
To the Editor: We direct your readers’ attention to the principles and guidelines (Supplementary Guidelines) developed by the Nextgeneration Sequencing: Standardization of Clinical Testing (Nex-StoCT) workgroup. These guidelines represent initial steps to ensure that results from tests based on nextgeneration sequencing (NGS) are reliable and useful for clinical decision making. The US Centers for Disease Control and Prevention (CDC) convened this national workgroup, which collaborated to define platform-independent approaches for establishing technical process elements of a quality management system (QMS) to assure the analytical validity and compliance of NGS tests with existing regulatory and professional quality standards. The workgroup identified and addressed gaps in quality practices that could compromise the quality of both clinical laboratory services and translational efforts needed to advance the implementation and utility of NGS in clinical settings. The workgroup was composed of experts with knowledge of and experience with NGS and included clinical laboratory directors, clinicians, platform and software developers and informaticians, as well as individuals actively engaged in NGS guideline development from accreditation bodies and professional organizations. Representatives from US government agencies also participated. These guidelines address four topics that are components of quality management in a clinical environment: (i) test validation, (ii) quality control (QC) procedures to assure and maintain accurate test results, (iii) the independent assessment of test performance through proficiency testing (PT) or alternative approaches and (iv) reference materials (RMs). Discussions were limited to the analytic and informatics processes required for accurate variant calling. The workgroup did not address how variants are prioritized, interpreted or reported. The workgroup recommendations are summarized in Table 1. Although the workgroup focused on detection of DNA sequence variations associated with heritable human disorders, many of the principles and recommendations described are also relevant to the application of NGS to other areas of laboratory medicine, including the diagnosis, prognosis and treatment of cancer and infectious-disease testing. Validation is the process of establishing analytical performance specifications for a clinical test system developed in house to confirm that the system is suitable for its intended use1. During the validation process, the laboratory must demonstrate that the assay functions as expected and provides
Subfields: Cancer Research, Genetics, Pathology and Forensic Medicine
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In Genetics
Citations in the corpus
- Guidelines for diagnostic next-generation sequencing (2015, methodology): “Each of these techniques is described in Gargis et al. (2012) and Rehm et al. (2013).”
- Ultrafast one‐pass FASTQ data preprocessing, quality control, and deduplication using fastp (2023, background): “In almost all application scenarios of sequencing, the effectiveness of data preprocessing usually greatly impacts the final analysis results [1].”
- A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples (2014, methodology): “As laboratory contamination by rotavirus was noted in the previously published NGS data set (Grard et al. 2012), a subsequent NGS data set was generated from the same serum aliquot.”