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pISSN 2950-9114 eISSN 2950-9122
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Original Article

Lab Med Qual Assur 2022; 44(3): 174-180

Published online September 30, 2022

https://doi.org/10.15263/jlmqa.2022.44.3.174

Copyright © Korean Association of External Quality Assessment Service.

Establishment of External Quality Assessment Material Preparation Method for Next-Generation Sequencing-Based Liquid Biopsy Scheme

Jinyoung Hong *, Joonsang Yu *, Hyunjung Gu , Juhee Lee , Woochang Lee , Sail Chun , and Won-Ki Min

Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea

Correspondence to:Woochang Lee
Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Korea
Tel +82-2-3010-4506
E-mail wlee1@amc.seoul.kr
*These authors contributed equally to this work and shared the first authorship.

Received: February 24, 2022; Revised: May 9, 2022; Accepted: May 30, 2022

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background: Next-generation sequencing (NGS)-based liquid biopsy testing using peripheral blood is a minimally invasive technique that can identify the characteristics of tumor-derived circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA). External quality assessment (EQA) should be implemented to ensure the reliability of NGS-based liquid biopsy tests. This study aims to establish a method for producing EQA materials for NGS-based liquid biopsy tests.
Methods: Eight cell lines harboring clinically important somatic mutations were selected for further analysis. Genomic DNA from the cell lines was extracted and fragmented using an ultrasonicator (Covaris Inc., USA). Two EQA materials were produced by spiking fragmented DNA into fresh frozen plasma and frozen at –70℃. The manufactured EQA materials were evaluated using a cfDNA gene panel (Dxome, Korea) using NextSeq Dx (Illumina, USA).
Results: After sonication, the average sizes of the fragmented DNA were 203 and 201 bp, respectively. The results of the cell-free NGS panel showed a combination of different variants between the two EQA materials, and clinically important somatic mutations were detected as intended.
Conclusions: In this study, a method for manufacturing materials for an NGS-based liquid biopsy test EQA scheme is presented. EQA materials with conditions similar to ctDNA clinical specimens can be produced at a relatively low cost using cell line-derived DNA and an ultrasonicator. The distribution of adequate EQA materials can improve the reliability of NGS-based liquid biopsy tests.

Keywords: Cell line, Circulating tumor DNA, Liquid biopsy, Quality control

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