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Related Concept Videos

DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

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Related Experiment Video

Updated: Jun 10, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
08:30

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

Multicentre validation study of nucleic acids extraction from FFPE tissues.

Serena Bonin1, Falk Hlubek, Jean Benhattar

  • 1ACADEM Department-University of Trieste and ICGEB, University of Trieste, Cattinara Hospital, 34149 Trieste, Italy.

Virchows Archiv : an International Journal of Pathology
|July 29, 2010
PubMed
Summary

Standardized nucleic acid extraction from formalin-fixed paraffin-embedded (FFPE) tissues is crucial for molecular pathology. Silica columns are recommended for DNA, while commercial kits yield better RNA, with proteinase-K digestion impacting results.

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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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Last Updated: Jun 10, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
08:30

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
13:24

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Area of Science:

  • Molecular Pathology
  • Diagnostic Laboratory Science
  • Biotechnology

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are the primary specimens in diagnostic pathology laboratories worldwide.
  • Current diagnostic molecular pathology tests often rely on laboratory-developed assays, highlighting a need for standardized nucleic acid extraction procedures.

Purpose of the Study:

  • To evaluate and compare routine nucleic acid extraction methods from FFPE tissues used by European diagnostic laboratories.
  • To identify optimal protocols for DNA and RNA extraction from FFPE samples for molecular pathology applications.

Main Methods:

  • Thirteen European laboratories participated in the IMPACTS program, isolating nucleic acids from four FFPE tissue types using their standard protocols (homemade and commercial kits).
  • Extracted nucleic acid quality was assessed via PCR amplification of control gene fragments and RT-PCR for RNA integrity.
  • DNA recovery methods were evaluated for suitability in array applications and accurate DNA quantification.

Main Results:

  • Most DNA extraction protocols, except one homemade method, yielded comparable DNA quality for PCR amplification.
  • Silica-based adsorption columns are recommended for DNA extraction when accurate quantification or array applications are required.
  • Commercial chromatography column-based kits provided the highest quantity and best assayable RNA, with successful RT-PCR amplification of 200-250 bp products.
  • Optimizing proteinase-K digestion time improved RNA extraction results, even with commercial kits.

Conclusions:

  • Standardized quality control methods for nucleic acid extracts are essential to prevent false negatives and ensure data comparability across diagnostic laboratories.
  • Specific recommendations for DNA (silica columns) and RNA (commercial chromatography kits) extraction from FFPE tissues are provided based on performance.
  • Further optimization, such as modifying proteinase-K digestion, can enhance nucleic acid extraction efficiency from FFPE samples.