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Updated: Jun 12, 2026

Robust Detection of Gene Amplification in Formalin-Fixed Paraffin-Embedded Samples by Fluorescence In Situ Hybridization
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High-efficiency genotype analysis from formalin-fixed, paraffin-embedded tumor tissues.

M J Sikora1, J N Thibert, J Salter

  • 1Department of Pharmacology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA.

The Pharmacogenomics Journal
|June 16, 2010
PubMed
Summary

This study enhances single-nucleotide polymorphism (SNP) genotyping from archival formalin-fixed, paraffin-embedded (FFPE) samples. Optimized methods increase SNP determinations from FFPE DNA, enabling more extensive retrospective pharmacogenetic research.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biotechnology

Background:

  • Archival formalin-fixed, paraffin-embedded (FFPE) samples are valuable for retrospective pharmacogenetic studies.
  • Assaying single-nucleotide polymorphisms (SNPs) from FFPE DNA is crucial for genetic association studies.

Purpose of the Study:

  • To develop and validate methods for increasing the number of SNP determinations from FFPE samples.
  • To optimize DNA extraction and assay conditions for FFPE-derived DNA.
  • To assess the feasibility of using tumor cores for SNP genotyping.

Main Methods:

  • Quantification of amplification-quality DNA (AQ-DNA) from FFPE samples.
  • Optimization of Taqman-based SNP assays with minimal AQ-DNA input.
  • DNA extraction from FFPE tumor sections and matched tumor/stromal cores.

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  • Genotyping of seven SNPs to assess method accuracy and concordance.

    • Main Results:

    • Optimized methods significantly increased the number of SNP determinations possible from FFPE samples.
    • AQ-DNA quantification reduced the sample input required for SNP assays.
    • Tumor cores yielded sufficient AQ-DNA for over 1000 SNP determinations.
    • Genotype concordance between tumor cores and sections ranged from 92.3% to 100% for single SNPs.

    Conclusions:

    • The described methods greatly expand the scope of genetic association studies using limited archival FFPE specimens.
    • Optimized SNP genotyping from FFPE samples, particularly using tumor cores, enhances retrospective pharmacogenetic research capabilities.
    • This approach maximizes the utility of archival FFPE blocks for genetic analysis.