使用靶向下一代测序检测基因融合：一项比较评估。
Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation.
机构信息
Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
Institute of Pathology, University Hospital Erlangen, Erlangen, Germany.
出版信息
BMC Med Genomics. 2021 Feb 27;14(1):62. doi: 10.1186/s12920-021-00909-y.
BACKGROUND
Gene fusions represent promising targets for cancer therapy in lung cancer. Reliable detection of multiple gene fusions is therefore essential.
METHODS
Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).
RESULTS
The Illumina assay detected all tested fusions and showed the smallest number of false positive results. Both, the ArcherDX and Qiagen panels missed only one fusion event. Among the RNA-based assays, the Qiagen panel had the highest number of false positive events. The Oncomine Focus Assay (Thermo Fisher Scientific) was the least adequate assay for our purposes, seven fusions were not covered by the assay and two fusions were classified as uncertain. The DNA-based SureSelect XT HS Custom Panel (Agilent) missed three fusions and nine fusions were only called by one software version. Additionally, many false positive fusions were observed.
CONCLUSIONS
In summary, especially RNA-based parallel sequencing approaches are potent tools for reliable detection of targetable gene fusions in clinical diagnostics.
背景
基因融合是肺癌治疗中很有前途的靶点。因此，可靠地检测多种基因融合是至关重要的。
方法
评估了五种市售的平行测序检测方法，以检测八种细胞系和 18 个携带多种已知基因融合的 FFPE 组织样本中的基因融合。比较了四种基于 RNA 的检测方法和一种基于 DNA 的检测方法；两种是基于杂交捕获的，即 TruSight Tumor 170 检测（Illumina）和 SureSelect XT HS 定制面板（Agilent），三种是基于扩增子的，即 Archer FusionPlex 肺面板（ArcherDX）、QIAseq RNAscan 定制面板（Qiagen）和 Oncomine Focus 检测（Thermo Fisher Scientific）。
结果
Illumina 检测方法检测到了所有测试的融合，并显示出最少的假阳性结果。ArcherDX 和 Qiagen 面板都只错过了一个融合事件。在基于 RNA 的检测方法中，Qiagen 面板的假阳性事件最多。Oncomine Focus 检测（Thermo Fisher Scientific）是最不适合我们目的的检测方法，七种融合未被该检测方法覆盖，两种融合被归类为不确定。基于 DNA 的 SureSelect XT HS 定制面板（Agilent）错过了三个融合，九个融合仅被一个软件版本调用。此外，还观察到许多假阳性融合。
结论
总之，特别是基于 RNA 的平行测序方法是可靠检测临床诊断中可靶向基因融合的有力工具。
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