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Expert series on successful biomarker profiling from FFPE samples

FFPE specimens are valuable yet challenging sample sources for biomedical research. Optimizing each step of the molecular analysis workflow is key to getting the best insights from these precious starting materials. In our upcoming 4-part web seminar series, we will discuss the latest tips and tricks for successful biomarker profiling from FFPE samples. Join us and benefit from the expertise of our scientists.


Successful biomarker profiling from FFPE samples – the tips and tricks series

Module 1 – Pre-analytical considerations and nucleic acid preparation

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 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 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.

Module 2 – DNA methylation analysis

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 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.

Module 3 – miRNA expression analysis

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 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.

Module 4 – RNA-seq, multimodal NGS and NGS data analysis

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.

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 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.


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