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Updated: May 17, 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

Data analysis considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues.

Sharoni Jacobs

    Cold Spring Harbor Protocols
    |November 3, 2012
    PubMed
    Summary

    This study details methods for reliable copy number analysis using Whole Genome Sampling Analysis (WGSA) on challenging Formalin-Fixed Paraffin-Embedded (FFPE) DNA samples, overcoming degradation and contamination issues.

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Formalin-Fixed Paraffin-Embedded (FFPE) samples are crucial for clinical archives but pose challenges for molecular analysis due to DNA degradation and contamination.
    • High-quality DNA from blood, tissue, or cell lines is typically required for accurate Whole Genome Sampling Analysis (WGSA).
    • Existing methods struggle with the compromised quality of DNA extracted from FFPE samples.

    Purpose of the Study:

    • To establish a reliable protocol for copy number analysis of degraded and contaminated DNA from FFPE samples.
    • To adapt the Whole Genome Sampling Analysis (WGSA) assay for FFPE-derived DNA.
    • To enable accurate genomic profiling of archived clinical specimens.

    Main Methods:

    • Whole Genome Sampling Analysis (WGSA) assay.

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    Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
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    Comparative Lesions Analysis Through a Targeted Sequencing Approach
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  • Affymetrix GeneChip Mapping Arrays.
  • Specific DNA extraction and purification techniques tailored for FFPE samples.
  • Quality control measures to assess DNA integrity and purity.

    • Main Results:

    • Development of a robust workflow for FFPE DNA processing.
    • Demonstration of reliable copy number predictions from degraded FFPE DNA.
    • Successful application of WGSA to FFPE samples, overcoming common limitations.

    Conclusions:

    • The described methodology enables accurate copy number analysis from FFPE samples.
    • This approach expands the utility of archived FFPE specimens for genomic studies.
    • The protocol facilitates the use of FFPE samples in molecular diagnostics and research.