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
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Comparison of Snap Freezing versus Ethanol Fixation for Gene Expression Profiling of Tissue Specimens

Author(s): Perlmutter MA, Best CJ, Gillespie JW, Gathright Y, González S, Velasco A, Linehan WM, Emmert-Buck MR, Chuaqui RF

Publication: J Mol Diagn, 2004, Vol. 6, Page 371

PubMed ID: 15507677 PubMed Review Paper? No

Purpose of Paper

To evaluate the preservation of RNA quality and mRNA expression profiles in cells microdissected from ethanol fixed paraffin embedded (EFPE) prostate tissue sections using microarray and matched OCT frozen controls.

Conclusion of Paper

RNA yield and quality were reduced in EFPE tissues compared to OCT frozen controls. The observed RNA degradation in EFPE samples may have translated to altered present call rates compared to OCT frozen controls. Significantly lower 3'/5' reference gene ratios in EFPE samples suggest incomplete transcript amplification. However, comparative analysis of genes differentially expressed among tissue processing regimes and tumor status suggest that the skewed EFPE tissue microarray data retains biological relevance and is not solely an artifact of fixation or processing.

Studies

  1. Study Purpose

    Comparative analysis of RNA yield and quality in OCT frozen and ethanol fixed (70% ethanol at 4 degrees overnight) paraffin embedded (EFPE) prostate tissue specimens.

    Summary of Findings:

    RNA yield and quality were reduced in EFPE microdissected cells as compared to frozen OCT controls. RNA from EFPE tissue was fragmented with a maximum transcript size of 1 kb.

    Biospecimens
    Preservative Types
    • Ethanol
    • OCT
    Diagnoses:
    • Neoplastic - Benign
    • Neoplastic - Carcinoma
    Platform:
    AnalyteTechnology Platform
    RNA Electrophoresis
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Preservation Type of fixation/preservation OCT
    Ethanol
    View more
  2. Study Purpose

    Comparative analysis of gene expression profiles in OCT frozen and EFPE prostate tissue specimens after amplification and subsequent microarray analysis.

    Summary of Findings:

    The 3'/5' ratios for GAPDH and beta-actin reference genes were significantly reduced in EFPE samples compared to OCT frozen controls. The average present call rate was reduced in EFPE samples (4.5%) compared to frozen controls (26.1%). However, in EFPE samples, benign and tumor samples yielded distinguishable expression profiles, and 90% of the genes expressed in EFPE samples were also present in OCT frozen controls.

    Biospecimens
    Preservative Types
    • Ethanol
    • OCT
    Diagnoses:
    • Neoplastic - Carcinoma
    • Neoplastic - Benign
    Platform:
    AnalyteTechnology Platform
    RNA DNA microarray
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Biospecimen Preservation Type of fixation/preservation OCT
    Ethanol
    View more

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