DNA extraction by sonication: a comparison of fresh, frozen, and paraffin-embedded tissues extracted for use in polymerase chain reaction assays.

Author(s): Heller MJ, Robinson RA, Burgart LJ, TenEyck CJ, Wilke WW

Publication: Mod Pathol, 1992, Vol. 5, Page 203-6

PubMed ID: 1574499 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of preservation and DNA extraction method on PCR success. Normal adjacent kidney and lung tissue as well as liver from an autopsy were studied.

   Summary of Findings:

   A 174 bp fragment of beta globin was less often amplified when DNA was extracted from FFPE tissue by boiling than when DNA was extracted by sonication with beads. Amplification of a 123 bp fragment of beta globin was equally successful when DNA was extracted from fresh, frozen or FFPE tissue by sonication, with or without beads.

   Biospecimens

   • Tissue - Kidney
   • Tissue - Liver
   • Tissue - Lung

   Preservative Types

   • Formalin
   • Frozen
   • None (Fresh)

   Diagnoses:

   • Autopsy
   • Neoplastic - Normal Adjacent
   • Neoplastic - Carcinoma
   • Other diagnoses

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Preaquisition	Diagnosis/ patient condition	Hydrocephalus
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen None (fresh)
   Analyte Extraction and Purification	Analyte isolation method	Boiling method Sonication with glass beads Sonication without glass beads
   PCR Specific	Length of gene fragment	123 bp 174 bp
   PCR Specific	Targeted nucleic acid	Beta globin

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