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Related Experiment Video

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

Sample processing considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues.

Sharoni Jacobs

    Cold Spring Harbor Protocols
    |November 3, 2012
    PubMed
    Summary

    Whole Genome Sampling Analysis (WGSA) is effective for copy number analysis in high-quality DNA. This study details strategies for adapting WGSA for challenging, degraded DNA from formalin-fixed, paraffin-embedded (FFPE) samples.

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Whole Genome Sampling Analysis (WGSA) with Affymetrix GeneChip Mapping Arrays is a standard for DNA copy number analysis.
    • Formalin-fixed, paraffin-embedded (FFPE) samples are common in clinical archives but pose challenges due to DNA degradation and modification.
    • Existing WGSA protocols are optimized for high-quality DNA, limiting their application to FFPE samples.

    Purpose of the Study:

    • To describe methods for successfully applying WGSA and Affymetrix GeneChip Mapping Arrays to FFPE DNA.
    • To address the challenges of DNA quality inherent in FFPE sample processing for copy number analysis.

    Main Methods:

    • DNA extraction and purification protocols specifically adapted for FFPE samples.
    • Quality control measures for assessing FFPE DNA integrity and suitability for WGSA.

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    Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization
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    Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization

    Published on: July 12, 2024

    Related Experiment Videos

    Last 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

    Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization
    03:55

    Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization

    Published on: July 12, 2024

  • WGSA assay optimization for degraded and modified FFPE DNA.
  • Hybridization and analysis of FFPE DNA on Affymetrix GeneChip Mapping Arrays.

    • Main Results:

    • Demonstration of successful copy number analysis using WGSA on FFPE-derived DNA.
    • Identification of key processing steps critical for obtaining reliable results from FFPE samples.
    • Validation of the adapted WGSA workflow for FFPE samples.

    Conclusions:

    • WGSA can be effectively utilized for copy number analysis in FFPE samples with appropriate pre-processing strategies.
    • The described methods enable the use of valuable archived FFPE clinical samples for genomic copy number studies.
    • This work expands the utility of WGSA for retrospective genomic analysis of clinical specimens.