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pISSN 2950-9114 eISSN 2950-9122
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Report On Proficiency Testing

Lab Med Qual Assur 2021; 43(2): 65-71

Published online June 30, 2021


Copyright © Korean Association of External Quality Assessment Service.

Report of the Korean Association of External Quality Assessment Service on Next-Generation Sequencing Analysis for Somatic Variants (2018–2020)

Hongkyung Kim , Dongju Won , Saeam Shin , Seung-Tae Lee , and Jong Rak Choi

Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea

Correspondence to:Saeam Shin
Department of Laboratory Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
Tel +82-2-2228-2453
E-mail saeam0304@yuhs.ac

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Next-generation sequencing is widely used to detect a variety of genetic defects in many disorders. The detection of somatic variants in patients with cancer, including hematologic malignancy, is important for diagnosis, treatment, and prognosis. However, due to the complicated process, accurate and reliable detection of somatic variants by next-generation sequencing remains challenging. We investigated the proficiency tests conducted by the Korean Association of External Quality Assessment Service from 2018 to 2020 and their effects on the analytical performance of clinical laboratories. During the 3-year study period, six rounds of proficiency tests were conducted. In each round, the participating laboratories were required to report Tier I/II somatic variants detected from electronic data and a DNA specimen. The analytical performance was evaluated by calculating the acceptance rate for each genomic position investigated. The possible causes of ‘nonevaluable’ and ‘unacceptable’ variants were also explored. Among the six rounds of proficiency tests, the acceptance rates for all tested variants were above 80% and acceptance rates of 100% were identified in more than half of the variants in the target regions. Issues of variant classification and false-negative variants were addressed through the analysis of ‘non-evaluable’ variants. The significant causes of ‘unacceptable’ variants were identified as wrong protein or nucleotide numbering. In conclusion, the proficiency tests demonstrated the good analytical performance of the participating clinical laboratories. Although the findings identified some problems awaiting solutions, the proficiency tests may help clinical laboratories to improve their performance in detecting somatic variants by next-generation sequencing.

Keywords: Laboratory Proficiency Testing, External quality assurance, Nextgeneration sequencing, Somatic variant

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