Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue
Publication date
2019-01-01
Authors
Strengman, Eric
Barendrecht-Smouter, Francoise A.S.
de Voijs, Carmen
de Vree, Paula
Nijman, Isaac J.
de Leng, Wendy W J
Editors
Murray, Sarah S.
Advisors
Supervisors
Document Type
Part of book
Metadata
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License
taverne
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.
Keywords
Ampliseq, Formalin-fixed paraffin-embedded, Mutation analysis, Next-generation sequencing, Targeted sequencing, Variant calling, Taverne, Molecular Biology, Genetics, Journal Article
Citation
Strengman, E, Barendrecht-Smouter, F A S, de Voijs, C, de Vree, P, Nijman, I J & de Leng, W W J 2019, Amplicon-Based Targeted Next-Generation Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue. in S S Murray (ed.), Tumor profiling : methods and protocols. vol. 1908, Methods in Molecular Biology, vol. 1908, Springer Science + Business Media, New York, pp. 1-17. https://doi.org/10.1007/978-1-4939-9004-7_1