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Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
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FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
Jeffery M Vahrenkamp1, Kathryn Szczotka2, Mark K Dodson2
1Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA.
Genome Research
|October 26, 2019
Summary
We developed FFPEcap-seq, a new method for RNA sequencing from challenging formalin-fixed paraffin-embedded (FFPE) cancer samples. This technique accurately measures mRNA and enhancer RNA expression from degraded FFPE specimens.
Area of Science:
- Molecular Biology
- Genomics
- Cancer Research
Background:
- Formalin-fixed paraffin-embedded (FFPE) samples are the standard for clinical cancer specimens.
- Accurate RNA quantification from FFPE is difficult due to low yields and degradation.
- Clinical molecular tests require methods applicable to FFPE material.
Purpose of the Study:
- To develop a method for high-quality RNA sequencing from FFPE samples.
- To enable accurate measurement of mRNA and enhancer RNA expression from FFPE specimens.
- To facilitate the clinical application of molecular tests on FFPE samples.
Main Methods:
- FFPEcap-seq combines enzymatic enrichment of 5' capped RNAs.
- Template switching is used to create sequencing libraries.
- The method is designed for FFPE-derived RNA.
Main Results:
- FFPEcap-seq faithfully captures mRNA expression levels in FFPE specimens.
- The method detects enhancer RNAs from distal regulatory regions.
- FFPEcap-seq generates high-quality 5' end RNA-seq libraries.
Conclusions:
- FFPEcap-seq is a fast and straightforward method for 5' end RNA sequencing.
- This method overcomes challenges associated with RNA analysis in FFPE samples.
- FFPEcap-seq has the potential to broaden the impact of clinical molecular tests.
