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Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice



Justin M. Zook, Amy Gargis, Lisa Kalman, Ira Lubin, Marc L. Salit


We direct your readers' attention to the principles and guidelines (see Supplementary Guidelines) developed by the Next-generation Sequencing: Standardization of Clinical Testing II (Nex-StoCT II) informatics workgroup, which was convened by the Centers for Disease Control and Prevention (CDC). This work represents the first effort to systematically review current practices and present consensus recommendations for the implementation of a clinical next-generation sequencing (NGS) informatics pipeline in compliance with existing regulatory and professional quality standards 1. Workgroup participants included informatics experts, clinical and research laboratory professionals, physicians with NGS experience, NGS test platform and software developers, and participants from US government agencies and professional organizations. The primary focus was the use of NGS for the detection of germline sequence variants; however, the workgroup also discussed some aspects for the use of NGS for cancer and infectious disease testing. The typical NGS analytical process and selected workgroup recommendations are summarized in Table 1, Supplementary Fig. 1 and the Supplementary Guidelines.
Nature Biotechnology


genomics, bioinformatics, Reference Materials


Zook, J. , Gargis, A. , Kalman, L. , Lubin, I. and Salit, M. (2015), Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice, Nature Biotechnology, [online], (Accessed May 30, 2024)


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Created July 8, 2015, Updated November 10, 2018