Lab Med Qual Assur.  2022 Sep;44(3):174-180. 10.15263/jlmqa.2022.44.3.174.

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

• Hong J
• Yu J
• Gu H
• Lee J
• Lee W
• Chun S
• Min WK

• KMID: 2534082
• DOI: http://doi.org/10.15263/jlmqa.2022.44.3.174

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 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.

Keyword

Cell line; Circulating tumor DNA; Liquid biopsy; Quality control