J Cancer 2019; 10(8):1814-1824. doi:10.7150/jca.29535 This issue

Research Paper

Challenges of Providing Concordant Interpretation of Somatic Variants in Non-Small Cell Lung Cancer: A Multicenter Study

Peng Gao1,2,3, Rui Zhang1,3✉, Ziyang Li1,2,3, Jiansheng Ding1,2,3, Jiehong Xie1,3, Jinming Li1,2,3✉

1. National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China;
2. Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China;
3. Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China

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Gao P, Zhang R, Li Z, Ding J, Xie J, Li J. Challenges of Providing Concordant Interpretation of Somatic Variants in Non-Small Cell Lung Cancer: A Multicenter Study. J Cancer 2019; 10(8):1814-1824. doi:10.7150/jca.29535. Available from https://www.jcancer.org/v10p1814.htm

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Background: Success of multiple-gene mutation tests by next-generation sequencing (NGS), associated with molecular targeting therapies for cancers, depending on the accuracy and consistency of interpreting variants. Here, we summarized reports from clinical laboratories for cases with non-small cell lung cancer (NSCLC) and discussed conflicting interpretations of somatic variants.

Methods: Three mimetic DNA samples, containing six somatic mutations, were prepared based on three clinical case reports of NSCLC. Clinical reports and genetic testing questionnaires were collected from 67 laboratories enrolled in this investigation.

Results: Thirty-four laboratories with correct variant results identified two variants, based on FDA approval of targeted drugs for the same tumor, consistently, with strong clinical significance, whereas the other variants were classified with conflicting interpretations. Discordant interpretations were reported for ERBB2 with three different classifications, including strong clinical significance (53.0%, 18/34), potential clinical significance (38.2%, 13/34), and unknown significance (8.8%, 3/34). In the variant therapeutic drug recommendation section, 32.4% of the laboratories (11/34) did not recommend all the available therapeutic drugs designated by the National Comprehensive Cancer Network (NCCN). In the remaining group of 33 laboratories with incorrect variant results, less correct classifications were acquired for the variants with strong clinical significance.

Conclusions: Owing to numerous reasons, the interpretation of variants differed greatly, which might in turn lead to the inappropriate clinical care of patients with NSCLC. By analyzing the limitations of different databases used by laboratories, we integrated various types of databases with different levels of evidence to form a comprehensive and detailed variant interpretation pipeline, aiming to standardize the variant classification and provide accurate and sufficient therapeutic drug recommendation to clinicians for minimal-inappropriate therapeutic options.

Keywords: clinical significance, next-generation sequencing, non-small cell lung cancer, somatic variant