Small Nucleolar RNA Score: An Assay to Detect Formalin-Overfixed Tissue

Wim Ammerlaan*, Johanna Trouet, Michael C. Sachs, Ping Guan, Latarsha Carithers, Pauline Lambert, Sonia Frasquilho, Laurent Antunes, Olga Kofanova, Daniel Rohrer, Dana R. Valley, Alex Blanski, Scott Jewell, Helen Moore, Fay Betsou

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

4 Citations (Scopus)

Abstract

Although there are millions of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown fixation conditions. We analyzed FFPE tissue biospecimens as part of the NCI Biospecimen Preanalytical Variables (BPV) program to identify microRNA (miRNA) markers for fixation time. miRNA was extracted from kidney and ovary tumor FFPE blocks (19 patients, cold ischemia ≤2 hours) with 6, 12, 24, and 72 hours fixation times, then analyzed using the WaferGen SmartChip platform (miRNA chip with 1036 miRNA targets). For fixation time, principal component analysis of miRNA chip expression data separated 72 hours fixed samples from 6 to 24 hours fixed samples. A set of small nuclear RNA (snRNA) targets was identified that best determines fixation time and was validated using a second independent cohort of seven different tissue types. A customized assay was then developed, based on a set of 24 miRNA and snRNA targets, and a simple "snoRNA score" defined. This score detects FFPE tissue samples with fixation for 72 hours or more, with 79% sensitivity and 80% specificity. It can therefore be used to assess the fitness-for-purpose of FFPE samples for DNA or RNA-based research or clinical assays, which are known to be of limited robustness to formalin overfixation.

Original languageEnglish
Pages (from-to)467-476
Number of pages10
JournalBiopreservation and Biobanking
Volume16
Issue number6
DOIs
Publication statusPublished - Dec 2018

Keywords

  • biobank
  • formalin fixation
  • miRNA
  • quality control
  • tissue

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