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

Simple salting-out method for DNA extraction from formalin-fixed, paraffin-embedded tissues

Author(s): Rivero Elena RC, Neves Adriana C, Silva-Valenzuela Maria G, Sousa Suzana OM, Nunes Fabio D

Publication: Pathol Res Pract, 2006, Vol. 202, Page 523

PubMed ID: 16723190 PubMed Review Paper? No

Purpose of Paper

Comparative analysis of DNA yield and integrity using different methods of DNA extraction (sodium acetate, phenol-chloroform, and a commercial kit) from formalin fixed paraffin embedded (FFPE) tissues.

Conclusion of Paper

All three methods of DNA extraction produced comparable results in terms of DNA yield, quality, and successful PCR amplification of different size products.

Studies

  1. Study Purpose

    To assess DNA yield and size distribution after extraction from FFPE tissues using three distinct methods (sodium acetate, phenol-chloroform, and an unspecified commercial isolation kit).

    Summary of Findings:

    The quantity of DNA from FFPE tissue was comparable among extraction methods, with all methods producing adequate amounts of DNA. Further, the size distribution of DNA was identical among extraction methods.

    Biospecimens
    Preservative Types
    • Formalin
    Diagnoses:
    • Neoplastic - Carcinoma
    Platform:
    AnalyteTechnology Platform
    DNA Electrophoresis
    DNA Spectrophotometry
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Analyte Extraction and Purification Analyte isolation method Phenol-choloroform extraction
    An unspecified commercial DNA isolation kit
    Salting out extraction (ammonium acetate)
    Simple salting out method (4M ammonium acetate)
  2. Study Purpose

    To assess the molecular applicability of DNA extracted from FFPE tissue by different methods via PCR analysis of representative genes (beta-globin, adenomatous polyposi coli (APC)) and a spectrum of amplicon sizes (167-536 bp).

    Summary of Findings:

    PCR amplification of shorter products (<268 bp) was successful for all DNA extraction methods and cases examined, but amplification of longer products (536 bp) was successful on a case by case basis and did not appear to be method dependent.

    Biospecimens
    Preservative Types
    • Formalin
    Diagnoses:
    • Neoplastic - Carcinoma
    Platform:
    AnalyteTechnology Platform
    DNA PCR
    Pre-analytical Factors:
    ClassificationPre-analytical FactorValue(s)
    Analyte Extraction and Purification Analyte isolation method Phenol-chloroform extraction
    An unspecified commercial DNA isolation kit
    Salting out extraction (ammonium acetate)
    PCR Specific Targeted nucleic acid APC
    beta-globin
    PCR Specific Length of gene fragment 167 bp
    268 bp
    536 bp

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