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

Gargis, Amy S. and Kalman, Lisa and Bick, David P. and Silva, Cristina da and Dimmock, David P. and Funke, Birgit H. and Gowrisankar, Sivakumar and Hegde, Madhuri R. and Kulkarni, Shashikant and Mason, Christopher E. and Nagarajan, Rakesh and Voelkerding, Karl V. and Worthey, Elizabeth A. and Aziz, Nazneen and Barnes, John and Bennett, Sarah F. and Bisht, Himani and Church, Deanna M. and Dimitrova, Zoya and Gargis, Shaw R. and Hafez, Nabil and Hambuch, Tina and Hyland, Fiona C.L. and Luna, Ruth Ann and Manion, Megan and MacCannell, Duncan and Mann, Tobias and McDaniel, Timothy K. and Ganova-Raeva, Lilia M. and Rehm, Heidi L. and Reid, Jeffrey and Campo Rendon, David S. and Resnick, Richard B. and Ridge, Perry G. and Salit, Marc L. and Skums, Pavel and Ajay, Subramanian Shankar and Wong, Lee-Jun C. and Zehnbauer, Barbara A. and Zook, Justin M. and Lubin, Ira M. (2015) Optimization of Next-Generation Sequencing Informatics Pipelines for Clinical Laboratory Practice. Nature Biotechnology, 33 (7). pp. 689-693.

Abstract

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 design, optimization, and implementation of an informatics pipeline for clinical next-generation sequencing (NGS) in compliance with existing regulatory and professional quality standards1. Workgroup participants included informatics experts, clinical and research laboratory professionals, physicians with experience in NGS results interpretation, NGS test platform and software developers, and participants from US government agencies and professional organizations. The primary focus was the design, optimization, and implementation of an NGS informatics pipeline for the detection of germline sequence variants; however, the workgroup also discussed 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.

Item Type: Article
Keywords: clinical informatics, next-generation sequencing
Date Deposited: 13 Oct 2015 13:13
Last Modified: 13 Oct 2015 13:13
URI: https://oak.novartis.com/id/eprint/21834

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