Oncotarget

Research Papers:

The reliable assurance of detecting somatic mutations in cancer-related genes by next-generation sequencing: the results of external quality assessment in China

Rui Zhang, Jiansheng Ding, Yanxi Han, Lang Yi, Jiehong Xie, Xin Yang, Gaowei Fan, Guojing Wang, Mingju Hao, Dong Zhang, Kuo Zhang, Guigao Lin and Jinming Li _

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Oncotarget. 2016; 7:58500-58515. https://doi.org/10.18632/oncotarget.11306

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Abstract

Rui Zhang1,3,*, Jiansheng Ding1,2,3,*, Yanxi Han1,3, Lang Yi1,2,3, Jiehong Xie1,3, Xin Yang1,2,3, Gaowei Fan1,2,3, Guojing Wang1,2,3, Mingju Hao1,2,3, Dong Zhang1,2,3, Kuo Zhang1,3, Guigao Lin1,3, Jinming Li1,2,3

1National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People’s Republic of China

2Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China

3Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China

*These authors have contributed equally to this work

Correspondence to:

Jinming Li, email: [email protected]

Keywords: next-generation sequencing, reliable assurance, cancer-related genes, somatic mutations, external quality assessment

Received: April 16, 2016    Accepted: July 27, 2016    Published: August 16, 2016

ABSTRACT

To evaluate the proficiencies of laboratories utilizing next-generation sequencing (NGS) to detect somatic mutations in cancer-related genes, an external quality assessment (EQA) was implemented by the National Center for Clinical Laboratories of China in 2015. We prepared a panel of samples that comprised eight samples made by mixing synthetic mutated DNA fragments with normal human genomic DNA and one reference sample containing only genomic DNA. We validated our sample panel, and then distributed it to laboratories across China. We received complete results from 64 laboratories. The performances of 51.6 % (33/64) respondent labs were acceptable and 26.6 % (17/64) of the labs returned perfect results. In total, 449 mistakes were reported, including 201 false-negatives (201/449, 44.8 %) and 222 false-positives (222/449, 49.4 %) and 26 slightly discordant results (26/449, 5.8 %). We believe these unsatisfactory results and varied performances are mainly due to the enrichment methods used, the diverse sequencing chemistries of the different NGS platforms, and other errors within the sequencing process. The results indicate that our sample panel is suitable for use in EQA studies, and that further laboratory training in targeted NGS testing is urgently required. To address this, we propose a targeted NGS workflow with details on quality assurance procedures according to the current guidelines.


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