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Related Concept Videos

Fixation and Sectioning01:03

Fixation and Sectioning

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Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...
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Related Experiment Video

Updated: Mar 21, 2026

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

Camilla Lagheden1, Carina Eklund1, Sara Nordqvist Kleppe1

  • 1Department of Laboratory Medicine, Karolinska Institutet, F56 Huddinge, 14188 Stockholm, Sweden.

Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology
|May 6, 2016
PubMed
Summary

A new, xylene-free DNA extraction method significantly improves human papillomavirus (HPV) detection rates in formalin-fixed paraffin-embedded (FFPE) samples. This robust method enhances HPV genotyping from FFPE tissues, offering a safer and more effective alternative.

Keywords:
DNA-extractionFormalin-Fixed paraffin-Embedded (FFPE)GenotypingHuman papillomavirus (HPV)Xylene

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Area of Science:

  • Molecular Biology
  • Virology
  • Cancer Research

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for human papillomavirus (HPV) DNA extraction and genotyping.
  • Traditional xylene-based DNA extraction methods are laborious, inefficient, and pose health risks.

Purpose of the Study:

  • To evaluate a novel, xylene-free DNA extraction method for HPV genotyping in FFPE samples.
  • To compare the efficacy of a CDC-developed, xylene-free method against the standard xylene-based protocol.

Main Methods:

  • Fifty FFPE cervical cancer samples and corresponding blank controls were analyzed.
  • DNA was extracted using both standard xylene and a modified xylene-free method with an additional heating step (120°C for 20 min).
  • Extracted DNA was tested for beta-globin, HPV16, and general HPV types using real-time PCR, MGP-PCR, and Luminex assays.

Main Results:

  • The xylene-free method with heating significantly increased HPV detection from 70% to 86% (p=0.039).
  • 100% HPV type concordance was achieved between the two methods for all evaluable samples.
  • The modified method demonstrated improved DNA extraction efficiency from FFPE specimens.

Conclusions:

  • A standardized, xylene-free DNA extraction protocol offers a robust and improved method for HPV-DNA typing in FFPE samples.
  • This method addresses the demand for safer and more efficient molecular diagnostics in cancer research.
  • The proposed protocol shows general utility for FFPE-based HPV analysis.