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KMID : 0985420220440030174
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Laboratory Medicine and Quality Assurance
2022 Volume.44 No. 3 p.174 ~ p.180
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Establishment of External Quality Assessment Material Preparation Method for Next-Generation Sequencing-Based Liquid Biopsy Scheme
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Hong Jin-Young
Yu Joon-Sang
Gu Hyun-Jung
Lee Ju-Hee
Lee Woo-Chang
Chun Sa-Il
Min Won-Ki
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Abstract
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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 cellfree 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.
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KEYWORD
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Cell line, Circulating tumor DNA, Liquid biopsy, Quality control
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