Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system
Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system
复制标题
DOI：
10.1038/modpathol.2016.81
复制
发表时间：
2016-07-01
期刊：
影响因子：
7.5
通讯作者：
Tanaka, Shinya
中科院分区：
文献类型：
--
作者：
Yuzawa, Sayaka;Nishihara, Hiroshi;Tanaka, Shinya
最近使用下一代测序仪进行的遗传分析揭示了各种肿瘤中的许多遗传改变，包括脑膜瘤，这是最常见的原发性脑肿瘤。然而，在肿瘤基因分型的临床应用中，它们作为常规实验室检查的用途并不具有成本效益。为建立脑膜瘤的临床测序系统并探讨基因型的临床意义，我们回顾性地对103例脑膜瘤进行了靶向扩增子测序，并评估了其与临床病理特征的相关性。我们设计了针对八个基因的扩增子测序板，包括NF 2（神经纤维蛋白2），TRAF 7，KLF 4，AKT 1和SMO。使用Illumina MiSeq对从103例脑膜瘤标本的PAX基因固定石蜡包埋组织中提取的基因组DNA制备的文库进行测序。在某些情况下，NF 2的损失也证实了间期荧光原位杂交。我们通过靶向扩增子测序在103例病例中的81例（79%）中鉴定出NF 2缺失和/或NF 2、TRAF 7、KLF 4、AKT 1和SMO中至少一种突变。根据基因状态，我们将脑膜瘤分为三个基因型组：NF 2型，TRAKLS型（TRAF 7、AKT 1、KLF 4和/或SMO突变）和“未另行分类”型。基因型与肿瘤体积、肿瘤位置、磁共振成像结果（如邻近骨改变和不均匀钆增强）以及组织病理学亚型显著相关。此外，多因素分析显示基因型与复发风险独立相关。总之，我们建立了一个快速的临床测序系统，使最终确认脑膜瘤基因型在7天内周转时间。我们的方法将为神经病理学家和神经外科医生带来多方面的好处，以准确的诊断和适当的术后管理。
Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgenefixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.