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pISSN 2384-2458 eISSN 2288-7261
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Original Article

Lab Med Qual Assur 2021; 43(1): 25-30

Published online March 31, 2021


Copyright © Korean Association of External Quality Assessment Service.

Frequency of Benign Variants Associated with Hematologic Malignancy in the Catalogue of Somatic Mutations in Cancer

Kyoung-Jin Park1 and Jong-Ho Park2

1Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang; 2Department of Laboratory Medicine, Samsung Medical Center, Seoul, Korea

Correspondence to:Kyoung-Jin Park
Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, 55 Hwasu-ro 14 beon-gil, Deogyang-gu, Goyang 10475, Korea
Tel +82-31-810-7082
E-mail unmar21@gmail.com

Received: October 17, 2020; Revised: November 10, 2020; Accepted: November 16, 2020

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.


Background: The presence of benign variants in mutation databases is a well-documented pitfall when interpreting clinical variants associated with hematologic malignancy. The aim of this study was to investigate the frequency of benign or likely benign (B/LB) variants associated with hematologic malignancy in the Catalogue of Somatic Mutations in Cancer (COSMIC), which is one of the most commonly used databases for cancer.
Methods: A total of 12,149,816 coding variants were downloaded from COSMIC (release ver. 91, April 2020), and 123,211 variants in 99 genes associated with hematologic malignancy were analyzed. The genes were selected according to the criteria recommended by the World Health Organization and National Comprehensive Cancer Network guidelines. The variant classification was performed based on standardized interpretation guidelines.
Results: The frequency of B/LB variants was 3.2% (3,890/123,211) of the COSMIC variants. In addition, 44.9% (1,748/3,890) of B/LB variants were observed in at least two cancer samples. In terms of drug response and cancer susceptibility, 2.9% (112/3,890) of the B/LB variants were clinically significant.
Conclusions: This study revealed that a significant number of B/LB variants were registered in COSMIC. This study highlights the importance of the reinterpretation of cancer variants reported from mutation databases and could be a good starting point for an in-depth review of somatic mutations essential for precision oncology.

Keywords: Catalogue of Somatic Mutations in Cancer, Database, Mutation

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