基于扩增子的福尔马林固定石蜡包埋组织靶向新一代测序

Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue.

作者信息

Strengman Eric, Barendrecht-Smouter Francoise A S, de Voijs Carmen, de Vree Paula, Nijman Isaac J, de Leng Wendy W J

机构信息

Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.

Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.

出版信息

Methods Mol Biol. 2019;1908:1-17. doi: 10.1007/978-1-4939-9004-7_1.

DOI:10.1007/978-1-4939-9004-7_1

PMID:30649717

Abstract

Next-generation sequencing (NGS) is rapidly becoming the method of choice for mutation analysis in both research and diagnostics. The benefit of targeted NGS compared to whole-genome and whole-exome sequencing is that smaller amounts of input material can be used as well as qualitatively suboptimal tissue samples, like formalin-fixed, paraffin-embedded archival tissue.Here, we describe the protocol for targeted next-generation sequencing using the Ion Torrent PGM platform in combination with Ion Ampliseq NGS gene panels for formalin-fixed, paraffin-embedded tissues. Both the manual and the automated workflow are described as well as the bioinformatics for data analysis.

摘要

新一代测序（NGS）正迅速成为研究和诊断中突变分析的首选方法。与全基因组测序和全外显子组测序相比，靶向NGS的优势在于可以使用少量的输入材料以及质量欠佳的组织样本，如福尔马林固定、石蜡包埋的存档组织。在此，我们描述了使用Ion Torrent PGM平台结合Ion Ampliseq NGS基因面板对福尔马林固定、石蜡包埋组织进行靶向新一代测序的方案。文中介绍了手动和自动工作流程以及数据分析的生物信息学方法。