FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
- Jeffery M. Vahrenkamp1,
- Kathryn Szczotka2,
- Mark K. Dodson2,
- Elke A. Jarboe3,
- Andrew P. Soisson2 and
- Jason Gertz1
- 1Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA;
- 2Department of Obstetrics and Gynecology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA;
- 3Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
Abstract
The majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE) samples. For clinical molecular tests to have wide-reaching impact, they must be applicable to FFPE material. Accurate quantitative measurements of RNA derived from FFPE specimens is challenging because of low yields and high amounts of degradation. Here, we present FFPEcap-seq, a method specifically designed for sequencing capped 5′ ends of RNA derived from FFPE samples. FFPEcap-seq combines enzymatic enrichment of 5′ capped RNAs with template switching to create sequencing libraries. We find that FFPEcap-seq can faithfully capture mRNA expression levels in FFPE specimens while also detecting enhancer RNAs that arise from distal regulatory regions. FFPEcap-seq is a fast and straightforward method for making high-quality 5′ end RNA-seq libraries from FFPE-derived RNA.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.249656.119.
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Freely available online through the Genome Research Open Access option.
- Received February 20, 2019.
- Accepted October 3, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
