Cancer Research

Get the most out of FFPE samples

FFPE in focus series

QIAGEN scientists share their expertise

The archives of formalin-fixed, paraffin-embedded (FFPE) tissue sections stored around the world represent a valuable and extensive source of material for biomedical research. FFPE tissue is a precious but challenging sample type that requires highly efficient methods for analyte purification and downstream molecular analysis, that can deal with the nature of FFPE samples. Sign in for our tips and tricks series and benefit from the expertise of QIAGEN scientists.

Webinars, videos and more

Nucleic acid preparation

Pre-analytical considerations

Martin Schlumpberger: FFPE samples – the basics

Martin kicks off the web seminar series by highlighting various factors impacting molecular analysis from FFPE samples and key challenges and considerations while working with this precious yet challenging sample type.

Daniel Groelz: Preanalytical considerations – standards and how to implement in your laboratory

Daniel talks about pre-analytical factors that influence nucleic acid analyses from FFPE samples, international initiatives and requirements to standardize pre-analytical workflows and ways to implement these standards in your laboratory.

Martin Schlumpberger: Nucleic acid preparation – DNA, RNA and retrieving both from the same FFPE sample

Martin discusses key considerations to achieve and verify high yields and quality of DNA and RNA from FFPE samples such as efficient deparaffinization, crosslink and artifact removal, DNA/RNA integrity control and its impact on downstream analysis.

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DNA methylation

Ioanna Andreou: Detection of methyl markers in NGS from FFPE samples

Ioanna talks about DNA methylation analysis from FFPE samples by targeted methylation sequencing. She will discuss a single day to sequencer workflow using unique molecular index (UMI) and single primer extension (SPE) technologies.

Norbert Hochstein: Methylation analysis by Pyrosequencing – impact of amplicon length and DNA input quantity

Norbert gives an overview of a Pyrosequencing workflow for methylation analysis followed by key findings of his Pyrosequencing study using FFPE samples and the impacts of amplicon length and DNA input quantity on results.

miRNA expression

Francesca Di Pasquale: miRNA analysis by PCR

Francesca discusses common challenges when working with miRNA from FFPE samples and key considerations for primer design, quality control and data normalization for miRNA expression analysis by qPCR.

Marie-Louise Lunn: miRNA FFPE ISH in cancer biomarker development

Marie-Louise talks about optimized miRNA in situ hybridization for localization studies using locked nucleic acids (LNAs). She will discuss an optimized, non-toxic, one-day protocol, along with controls needed, for ISH protocol optimization.

Any questions about FFPE analysis?

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RNA-seq and multimodal NGS

Jonathan Shaffer: Whole transcriptome NGS of FFPE samples

Jon introduces a new technology to efficiently remove rRNA from FFPE samples during whole transcriptome RNA-seq that dramatically increases the reads mapped to genes and detected genes, leading to robust differential expression analysis.

Jonathan Shaffer: Multimodal NGS analysis from FFPE samples

Jon talks about a new workflow – multimodal NGS – for simultaneous profiling of both DNA variants and RNA fusions. He will discuss, with examples, how this solution allows consolidated DNA and RNA targeted library preparation from FFPE samples.

Leif Schauser: NGS data analysis using QIAGEN CLC Genomics Workbench

Leif introduces the QIAGEN CLC Genomics Workbench for NGS data analysis and the key features that are relevant to FFPE. In a live demo, he will guide you through the key steps of DNA-seq and RNA-seq data analysis workflows.

Technical guidelines

Successful biomarker profiling from FFPE samples

FFPE tissue sections are a precious but challenging sample type that requires highly efficient methods for analyte purification and downstream molecular analysis.
Learn about the latest methods and critical considerations for the preparation of FFPE samples and the preanalytical workflow steps for molecular analysis.

Download guideline

Products

Discover the real potential of FFPE samples

From sample preparation to data analysis, for molecular analysis by NGS, digital PCR, PCR or qPCR – Discover QIAGEN’s Sample to Insight solutions for successful molecular analysis from FFPE samples

Download overview

Product in focus:

QIAamp DNA FFPE Advanced Kit

This next-generation kit for isolating DNA from FFPE tissue samples will enable you to increase your amplifiable DNA yields. The xylene-free, no-wash deparaffinization, double-lyse protocol, can also be automated.

Learn more

Any questions about FFPE analysis?

Send us your questions via email, and we will do our best to get them answered.

Ask us