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

Gargis, Amy S., Kalman, Lisa, Bick, David P., Silva, Cristina da, Dimmock, David P., Funke, Birgit H., Gowrisankar, Sivakumar, Hegde, Madhuri R., Kulkarni, Shashikant, Mason, Christopher E., Nagarajan, Rakesh, Voelkerding, Karl V., Worthey, Elizabeth A., Aziz, Nazneen, Barnes, John, Bennett, Sarah F., Bisht, Himani, Church, Deanna M., Dimitrova, Zoya, Gargis, Shaw R., Hafez, Nabil, Hambuch, Tina, Hyland, Fiona C.L., Luna, Ruth Ann, Manion, Megan, MacCannell, Duncan, Mann, Tobias, McDaniel, Timothy K., Ganova-Raeva, Lilia M., Rehm, Heidi L., Reid, Jeffrey, Campo Rendon, David S., Resnick, Richard B., Ridge, Perry G., Salit, Marc L., Skums, Pavel, Ajay, Subramanian Shankar, Wong, Lee-Jun C., Zehnbauer, Barbara A., 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.


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


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