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Related Experiment Video

Updated: Nov 25, 2025

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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Tissue Preservation and FFPE Samples: Optimized Nucleic Acids Isolation in Ewing Sarcoma.

Laura Romero-Pérez1,2,3, Thomas G P Grünewald4

  • 1Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. Laura.romeroperez@dkfz-heidelberg.de.

Methods in Molecular Biology (Clifton, N.J.)
|December 16, 2020
PubMed
Summary

Preserving pediatric sarcoma samples using formalin-fixed paraffin-embedding (FFPE) is common but may degrade nucleic acids. This study details optimal sample preservation and nucleic acid isolation for Ewing sarcoma molecular testing.

Keywords:
DNAEwing sarcomaFFPE samplesMolecular assaysPreservationRNA

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Area of Science:

  • Pathology and Molecular Diagnostics
  • Pediatric Oncology
  • Genomics

Background:

  • Formalin-fixed paraffin-embedded (FFPE) samples are standard in pathology for long-term tissue preservation.
  • FFPE is suitable for techniques like immunohistochemistry and FISH, crucial for diagnosing pediatric sarcomas.
  • Emerging genomic technologies (NGS, microarrays) require high-quality nucleic acids (DNA/RNA) for pediatric sarcoma diagnosis and confirmation.

Purpose of the Study:

  • To outline ideal methods for preserving biopsy or resection samples, particularly for pediatric sarcoma.
  • To describe efficient nucleic acid isolation protocols for subsequent molecular assays.
  • To focus on optimizing preservation and isolation for Ewing sarcoma samples.

Main Methods:

  • Review and description of established FFPE sample preservation techniques.
  • Detailed protocol for isolating high-quality DNA and RNA from FFPE tissues.
  • Specific considerations for handling and processing Ewing sarcoma specimens.

Main Results:

  • FFPE preservation, while common, can impact nucleic acid integrity for advanced molecular analyses.
  • The described methods facilitate the isolation of sufficient DNA/RNA quantities from FFPE samples.
  • Successful application of protocols for subsequent molecular assays, including those for Ewing sarcoma.

Conclusions:

  • Optimized sample preservation and nucleic acid isolation are critical for utilizing advanced molecular techniques in pediatric sarcoma diagnostics.
  • The presented approach enhances the utility of FFPE samples for next-generation sequencing and microarray analysis in Ewing sarcoma.
  • This methodology supports accurate diagnosis and molecular subtyping of pediatric sarcomas.