Department of Pathology, Molecular Oncology and Genetics Diagnostics, SUNY Upstate Medical University, Syracuse, NY 13210, USA.
Department of Pathology, Moffitt Cancer Center, Tampa, FL 33612, USA.
Genes (Basel). 2022 Apr 1;13(4):630. doi: 10.3390/genes13040630.
The detection of and mutations by next generation sequencing (NGS) is challenging due to high GC content and Internal Tandem Duplications (ITDs). Recent advances have been made to surmount these challenges. In this study, we compare three commercial kits and evaluate the performance of these more advanced hybrid-capture and AMP-chemistry based methods.
Amplicon-based TSM 54-Gene Panel (Illumina) was evaluated against hybridization-capture SOPHiA Genetics MSP, OGT SureSeq, and AMP chemistry-based VariantPlex (Archer) for wet-lab workflow and data-analysis pipelines. Standard kit directions and commercial analysis pipelines were followed. Seven and 10 -positive cases were identified that previously were missed on an amplicon NGS assay. The average reads, coverage uniformity, and the detection of or mutations were compared.
All three panels detected all 10 mutations and all 10 ITDs with 100% sensitivity. In addition, there was high concordance (100%) between all three panels detecting 47/47 confirmed variants in a set of core myeloid genes.
The results show that the NGS assays are now able to reliably detect mutations and ITDs. These assays may allow foregoing additional orthogonal testing for and .
由于高 GC 含量和内部串联重复（ITD），下一代测序（NGS）检测 和 突变具有挑战性。最近已经取得了一些进展来克服这些挑战。在这项研究中，我们比较了三种商业试剂盒，并评估了这些更先进的基于杂交捕获和 AMP 化学的方法的性能。
我们评估了基于扩增子的 TSM 54 基因panel（Illumina）与杂交捕获的 SOPHiA Genetics MSP、OGT SureSeq 和基于 AMP 化学的 VariantPlex（Archer）在湿实验室工作流程和数据分析管道方面的性能。我们遵循了标准试剂盒的说明和商业分析管道。确定了 7 个 和 10 个 阳性病例，这些病例之前在扩增子 NGS 检测中被遗漏。比较了平均读取量、覆盖均匀性和 或 突变的检测。
所有三个面板都以 100%的灵敏度检测到了所有 10 个 突变和所有 10 个 ITD。此外，在一组核心髓系基因中，所有三个面板检测到的 47/47 个确认变体之间具有高度一致性（100%）。
结果表明，NGS 检测现在能够可靠地检测 突变和 ITD。这些检测方法可能可以避免对 和 进行额外的正交检测。
