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

Cold Spring Harbor Protocols

|November 3, 2012

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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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.