Purification of DNA from formaldehyde fixed and paraffin embedded human tissue.

Author(s): Goelz SE, Hamilton SR, Vogelstein B

Publication: Biochem Biophys Res Commun, 1985, Vol. 130, Page 118-26

PubMed ID: 2992457 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare the quality and quantity of DNA extracted from freshly procured tissue specimens that were snap frozen with those that were fixed in formaldehyde and embedded in paraffin.

   Summary of Findings:

   DNA yields were comparable among FFPE and frozen specimens, although variability per mg of specimen was greater for FFPE specimens potentially due to paraffin contribution. DNA extracted from FFPE specimens generated Southern blot results comparable to frozen specimens.

   Biospecimens

   • Tissue - Placenta

   Preservative Types

   • Other Preservative
   • Frozen

   Diagnoses:

   • Normal
   • Neoplastic - Benign

   Platform:

   Analyte	Technology Platform
   DNA	Southern blot
   DNA	Electrophoresis
   DNA	Spectrophotometry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formaldehyde Snap frozen

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2. Study Purpose

   The purpose of this study was to compare tissue that had been prospectively collected for this experiment (i.e. surgically removed then immediately frozen, formaldehyde fixed and paraffin embedded) with archival FFPE tissue stored as paraffin blocks for up to 5 years.

   Summary of Findings:

   Examination of archival FFPE specimens, stored as paraffin blocks for up to 5 years, yielded DNA of variable quality. A relationship among extracted DNA quality and the duration of paraffin block storage was not observed, although the authors noted several potentially confounding variables associated with the unknown life cycle of an archived biospecimen. While DNA extracted from archival FFPE specimens were successfully analyzed by Southern blot, variability was greater for signal intensity and hybridization background noise.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Other Preservative
   • Frozen

   Diagnoses:

   • Normal
   • Neoplastic - Benign
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	Electrophoresis
   DNA	Southern blot

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	< 1 yr 1-3 yr 4-5 yr
   Biospecimen Preservation	Type of fixation/preservation	Formaldehyde Snap frozen

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