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

Area of Science:

• Biomedical Research
• Molecular Biology
• Pathology

Background:

• Millions of formalin-fixed paraffin-embedded (FFPE) tissue blocks exist for research.
• Variable quality of FFPE tissues, often due to unknown fixation conditions, poses a challenge.
• The NCI Biospecimen Preanalytical Variables (BPV) program aims to standardize biospecimen quality.

Purpose of the Study:

• To identify microRNA (miRNA) markers to determine FFPE tissue fixation time.
• To develop a reliable method for assessing FFPE sample quality for research.

Main Methods:

• miRNA was extracted from kidney and ovary tumor FFPE blocks with varying fixation times (6, 12, 24, 72 hours).
• Analysis was performed using the WaferGen SmartChip platform, targeting 1036 miRNA.
• Principal component analysis identified small nuclear RNA (snRNA) targets indicative of fixation time.

Main Results:

• Principal component analysis distinguished 72-hour fixed samples from shorter fixation times.
• A set of snRNA targets was identified and validated across seven tissue types.
• A customized assay with 24 miRNA and snRNA targets yielded a "snoRNA score".

Conclusions:

• The "snoRNA score" can detect FFPE samples fixed for 72 hours or more with 79% sensitivity and 80% specificity.
• This score aids in assessing FFPE sample suitability for DNA or RNA-based research and clinical assays.
• The method addresses limitations in research robustness due to formalin over-fixation.