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A multiplex MALDI-TOF MS approach facilitates genotyping of DNA from formalin-fixed paraffin-embedded tumour

Heike Horn1, Christiane Pott, Jörg Kalla

  • 1Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. heike.horn@ikp-stuttgart.de

Pharmacogenetics and Genomics
|August 31, 2010
PubMed
Abstract

Insights

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) reliably genotypes DNA from formalin-fixed paraffin-embedded (FFPE) tissues. This method is reproducible for multiplex reactions, enabling retrospective studies of FFPE cohorts.

Area of Science:

  • Genetics and Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Single-nucleotide polymorphisms (SNPs) significantly influence cancer susceptibility and pathogenesis.
  • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool for analyzing short DNA fragments.
  • Formalin-fixed paraffin-embedded (FFPE) tissues are valuable for retrospective studies but pose challenges for DNA analysis.

Purpose of the Study:

  • To assess the applicability of MALDI-TOF MS for genotyping DNA extracted from FFPE tissue samples.
  • To evaluate the performance of multiplex genotyping assays using FFPE DNA.
  • To determine the reliability and reproducibility of MALDI-TOF MS for FFPE DNA analysis in comparison to germline DNA.

Main Methods:

  • DNA was extracted from FFPE follicular lymphoma tumor specimens using phenol-chloroform and a commercial kit.
  • Thirty-one SNPs across 25 genes were analyzed using multiplex assays (7-plex to 24-plex).
  • Genotyping results from 64 FFPE tumor specimens were compared with matched germline DNA samples.

Main Results:

  • High call rates were achieved: 99.6% with phenol-chloroform extraction and 93.5% with a commercial kit.
  • Increasing multiplexity reduced genotyping call rates and quality, particularly with commercial kit-extracted DNA.
  • A perfect 100% concordance rate was observed between FFPE tumor DNA genotypes and matched germline DNA.

Conclusions:

  • MALDI-TOF MS-based genotyping of FFPE DNA is reliable and reproducible, even in multiplex reactions.
  • This technique facilitates the retrospective investigation of FFPE study cohorts.
  • The findings support the use of MALDI-TOF MS for targeted genotyping in FFPE samples.

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