Assuring the quality of next-generation sequencing in clinical laboratory practice : Nature Biotechnology : Nature Publishing Group

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Assuring the quality of next-generation sequencing in clinical laboratory practice : Nature Biotechnology : Nature Publishing Group

Assuring the quality of next-generation sequencing in clinical laboratory practice

• Amy S Gargis,¹
• Lisa Kalman,¹
• Meredith W Berry,²
• David P Bick,³
• David P Dimmock,³
• Tina Hambuch,⁴
• Fei Lu,²
• Elaine Lyon,^{5, 6}
• Karl V Voelkerding,^{5, 6}
• Barbara A Zehnbauer,¹
• Richa Agarwala,⁷
• Sarah F Bennett,⁸
• Bin Chen,¹
• Ephrem L H Chin,^{9, 33}
• John G Compton,¹⁰
• Soma Das,¹¹
• Daniel H Farkas,¹²
• Matthew J Ferber,¹³
• Birgit H Funke,^{14, 15}
• Manohar R Furtado,¹⁶
• Lilia M Ganova-Raeva,¹⁷
• Ute Geigenmüller,^{18, 33}
• Sandra J Gunselman,^{19, 33}
• Madhuri R Hegde,⁹
• Philip L F Johnson,²⁰
• Andrew Kasarskis,^{21, 33}
• Shashikant Kulkarni,²²
• Thomas Lenk,²³
• C S Jonathan Liu,²⁴
• Megan Manion,²⁴
• Teri A Manolio,²⁵
• Elaine R Mardis,²⁶
• Jason D Merker,²⁷
• Mangalathu S Rajeevan,²⁸
• Martin G Reese,²⁹
• Heidi L Rehm,^{14, 15}
• Birgitte B Simen,³⁰
• Joanne M Yeakley,^{31, 33}
• Justin M Zook³²
• & Ira M Lubin¹
• et al.

• Affiliations
• Corresponding author

Journal name:

Nature Biotechnology

Volume:

30,

Pages:

1033–1036

Year published:

(2012)

DOI:

doi:10.1038/nbt.2403

Published online

08 November 2012

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To the Editor

We direct your readers' attention to the principles and guidelines (Supplementary Guidelines) developed by the Next-generation Sequencing: Standardization of Clinical Testing (Nex-StoCT) workgroup. These guidelines represent initial steps to ensure that results from tests based on next-generation 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.