NIH, National Cancer Institute, Division of Cancer Treatment and Diagnosis (DCTD) NIH - National Institutes of Health National Cancer Institute DCTD - Division of Cancer Treatment and Diagnosis
Advanced SearchBrowse by AnalyteBrowse by Pre-analytical FactorSearch SOPsSOP Compendiums

An exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samples.

Author(s): Mojica WD, Stein L, Hawthorn L

Publication: BMC Clin Pathol, 2007, Vol. 7, Page 7

PubMed ID: 17683544 PubMed Review Paper? No

Purpose of Paper

The purpose of this paper was to compare the quantity, quality, and expression profiles of RNA extracted from case-matched tissue procured in three different manners: exfoliated and enriched fresh cells, laser-capture microdissected formalin-fixed, paraffin-embedded (FFPE) cells, and laser-capture microdissected fresh-frozen, Optimal Cutting Media-embedded cells.

Conclusion of Paper

The authors report that the exfoliation and enrichment strategy resulted in better quality and quantity RNA than that extracted from laser-capture microdissected FFPE tissue, and equivalent to laser-capture microdissected fresh-frozen tissue. They conclude that exfoliation and enrichment is superior to FFPE for RNA procurement, and is an economical alternative to laser-capture microdissection from fresh-frozen tissue.

Studies

  1. Study Purpose

    The purpose of this study was to compare the quantity, quality, and expression profile of RNA extracted from tissue procured in three different manners: exfoliated and enriched fresh cells, laser-capture microdissected FFPE cells, and laser-capture microdissected fresh-frozen, Optimal Cutting Media-embedded cells.

    Summary of Findings:

    While RNA of sufficient quantity and quality was extracted from all specimens, cells freshly captured by exfoliation and enriched using antibody coated magnet beads yielded more total RNA, by approximately 30-fold, than cells obtained by laser-capture mirodissection of frozen or FFPE specimens. RNA quality was also superior in exfoliated and enriched cells, as determined by OD 260/280 ratios and the presence of 18S and 28S ribosomal bands. Comparison of microarray results among cell capture methods revealed that the number of genes exhibiting a 2-fold or greater difference in expression was highest among FFPE laser-capture specimens, with 25% of the genes analyzed differing from freshly exfoliated and enriched cells, and 19% of genes differing from frozen laser-capture microdissection cells. The number of genes exhibiting a significant difference in expression was minimal (1.9%) among freshly exfoliated and enriched cells and frozen laser-capture microdissected cells.

    Biospecimens
    Preservative Types
    • None (Fresh)
    • OCT
    • Formalin
    Diagnoses:
    • Neoplastic - Normal Adjacent
    Platform:
    AnalyteTechnology Platform
    RNA Automated electrophoresis/Bioanalyzer
    RNA DNA microarray
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Aliquots and Components Cell capture method Exfoliation and enrichment
    Laser-capture microdissection
    Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
    None (fresh)
    OCT
    View more

You Recently Viewed  

News and Announcements

  • Most Downloaded SOPs in 2024
  • New Articles on the GTEx Project are Now FREELY Available!
  • Just Published!
    • More...