Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
06 05 2019
06 05 2019
Historique:
received:
07
01
2019
accepted:
08
04
2019
entrez:
8
5
2019
pubmed:
8
5
2019
medline:
24
10
2020
Statut:
epublish
Résumé
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
Identifiants
pubmed: 31061401
doi: 10.1038/s41598-019-43282-8
pii: 10.1038/s41598-019-43282-8
pmc: PMC6502812
doi:
Substances chimiques
Fixatives
0
MicroRNAs
0
Formaldehyde
1HG84L3525
RNA
63231-63-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6980Références
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