Anchored multiplex FOR for targeted next-generation sequencing
Anchored multiplex FOR for targeted next-generation sequencing
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DOI：
10.1038/nm.3729
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发表时间：
2014-12-01
期刊：
影响因子：
82.9
通讯作者：
Le, Long Phi
中科院分区：
文献类型：
--
作者：
Zheng, Zongli;Liebers, Matthew;Le, Long Phi
我们描述了一种用于下一代测序的快速目标富集方法，称为锚定多重PCR（AMP），该方法与福尔马林固定石蜡包埋（FFPE）标本的低核酸输入兼容。AMP可有效检测基因重排（无需事先了解融合伴侣）、单核苷酸变异、插入、缺失和拷贝数变化。与参考检测相比，使用319份FFPE样本验证基因重排组显示100%灵敏度（95%置信限：96.5-100%）和100%特异性（95%置信限：99.3-100%）。基于我们对986个临床FFPE样本进行AMP的经验，我们展示了其作为稳健的临床测定和强大的发现工具的潜力，我们使用它来鉴定新的治疗重要基因融合：胶质母细胞瘤中的ARHGEF 2-NTRK 1和CHTOP-NTRK 1，肺癌中的MSN-ROS 1、TRIM 4-BRAF、VAMP 2-NRG 1、TPM 3-NTRK 1和RUFY 2-RET，胆管癌中的FGFR 2-CREB 5和甲状腺癌中的PPL-NTRK 1。AMP是用于研究和临床应用的可扩展且高效的下一代测序靶点富集方法。
We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5-100%) and 100% specificity (95% confidence limit: 99.3-100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.