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FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.


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.

SUBMITTER: Vahrenkamp JM 

PROVIDER: S-EPMC6836741 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.

Vahrenkamp Jeffery M JM   Szczotka Kathryn K   Dodson Mark K MK   Jarboe Elke A EA   Soisson Andrew P AP   Gertz Jason J  

Genome research 20191024 11


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 enzym  ...[more]

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