Lab Med Qual Assur.  2022 Dec;44(4):216-225. 10.15263/jlmqa.2022.44.4.216.

Performance Evaluation of BRCA1/2 Genetic Test Using Next-Generation Sequencing Based on Target Capture Method

• Kim A
• Kim JH
• Seo SH
• Lee S
• Lee W
• Chun S

• KMID: 2538681
• DOI: http://doi.org/10.15263/jlmqa.2022.44.4.216

Abstract

Background
BRCA1 and BRCA2 pathogenic variants are important genetic factors associated with cancers and biomarkers of breast and ovarian cancer. Although Sanger sequencing is regarded as the gold standard for BRCA1/2 testing, this method is time-consuming and labor-intensive. In this study, we performed next-generation sequencing (NGS) using DxSeq BRCA1/2 (Dxome, Korea), a kit in which the target capture method is applied to detect BRCA1/2 variants, and compared the performance of the kit with that of Sanger sequencing and BRCAaccuTest (NGeneBio, Korea), another approved kit based on the amplicon NGS method.
Methods
A total of 114 samples was evaluated using BRCA1/2 testing. All samples were confirmed using Sanger sequencing. We performed NGS analysis with the DxSeq BRCA1/2 and compared the results with those of Sanger sequencing and the BRCAaccuTest.
Results
Comparison of the sequencing results obtained using NGS with DxSeq BRCA1/2 and Sanger sequencing showed that the clinical sensitivity, clinical specificity, positive predictive value, and negative predictive value were 100%. The overall agreement between DxSeq BRCA1/2 and BRCAaccuTest was 89.1%. The BRCAaccuTest did not detect five cases: four insertion-deletion variants and one copy number variation.
Conclusions
DxSeq BRCA1/2, an NGS kit based on the target capture method, showed similar performed as that of Sanger sequencing. In addition, the performance of this kit was superior to that of another NGS kit using the amplicon method. Thus, the DxSeq BRCA1/2 kit can be used to detect genetic causes of breast and ovarian cancer in clinical laboratories

Keyword

BRCA1 genes; BRCA2 genes; Next-generation sequencing