DNA amplification by polymerase chain reaction from brain tissues embedded in paraffin.

Author(s): Gall K, Pavelic J, Jadro-Santel D, Poljak M, Pavelic K

Publication: Int J Exp Pathol, 1993, Vol. 74, Page 333-7

PubMed ID: 8398805 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare amplicon abundance of a 317 bp beta-actin DNA fragment in brain specimens that had been fixed with 1 of 6 fixatives and embedded in paraffin.

   Summary of Findings:

   The authors report that DNA amplified from tissue fixed in 10% neutral buffered formalin, AMeX, or Carnoy's produced equally abundant 317 bp amplicons after 40 PCR cycles. Amplicons were less abundant (paraformaldehyde and acetone fixed specimens) or absent (Bouin's fixed specimens) with other fixatives examined.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin
   • Other Preservative

   Diagnoses:

   • Autopsy
   • Neoplastic - Benign
   • Normal

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Acetone Bouin's fixative Formalin (buffered) Carnoy's solution Paraformaldehyde AMeX

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2. Study Purpose

   The purpose of this study was to evaluate three different deparaffinization durations, and an additional phenol/chloroform extraction step for isolation of DNA from formalin-fixed paraffin-embedded (FFPE) brain specimens.

   Summary of Findings:

   PCR amplification was equivalent after deparaffinization in xylene for 4 hours or overnight, while less abundant amplicons resulted with shorter incubations. Addition of a phenol/chloroform extraction step after proteinase K extraction did not improve PCR results.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin

   Diagnoses:

   • Autopsy
   • Neoplastic - Benign
   • Normal

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Deparaffinization	Xylene (overnight incubation) Xylene (2 x 120 min incubations) Xylene (2 x 60 min incubations) Xylene (2 x 30 min incubations)
   Analyte Extraction and Purification	Analyte isolation method	Phenol/chloroform extraction No phenol/chloroform extraction

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3. Study Purpose

   This study compared PCR efficiency among DNA extracted from formalin-fixed paraffin blocks stored at room temperature for extended periods of time (10 versus 39 years).

   Summary of Findings:

   The duration of paraffin block storage of formalin-fixed brain specimens did not affect PCR amplification of a 317 bp beta-actin DNA fragment.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Sarcoma

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	3 mon 1 yr 10 yr 39 yr

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