Discrepancies between VEGF-1154 G>A polymorphism analysis performed in peripheral blood samples and FFPE tissue

Giorgia Marisi, Alessandro Passardi, Daniele Calistri, Wainer Zoli, Dino Amadori, Paola Ulivi

Research output: Contribution to journalArticle

Abstract

Single nucleotide polymorphisms (SNPs) may be associated with the response or toxicity to different types of treatment. Although SNP analysis is usually performed on DNA from peripheral blood, formalin fixed paraffin-embedded (FFPE) tissue is often used for retrospective studies. We analyzed VEGF(-2578C>A,-1498C>T,-1154G>A,-634C>G, +936C>T) and eNOS(+894G>T,-786T>C, VNTR (variable number of tandem repeats) 27bp intron 4) polymorphisms by direct sequencing or Real Time PCR in 237 patients with advanced colorectal cancer. Peripheral blood was used for 153 patients, whereas only FFPE tumor tissue was available for 84 patients. All SNP frequencies were in Hardy-Weinberg Equilibrium (HWE), with the exception of VEGF-1154, which was only in HWE in peripheral blood specimens. We therefore analyzed this SNP in DNA extracted from FFPE tumor tissue compared to FFPE healthy tissue and peripheral blood from 20 patients. Numerous heterozygous patients in peripheral blood DNA were homozygous for the A-allele in both tumor and healthy FFPE tissues. Our findings indicate that, although FFPE tissue might be a suitable specimen for genotyping, VEGF-1154 does not give reliable results on this type of material. As other SNPs may also have this limitation, genotype concordance should first be confirmed by comparing results obtained from FFPE and fresh sample analyses.

Original languageEnglish
Pages (from-to)13333-13343
Number of pages11
JournalInternational Journal of Molecular Sciences
Volume15
Issue number8
DOIs
Publication statusPublished - Jul 30 2014

Keywords

  • (mCRC)
  • Formalin fixed paraffin-embedded (FFPE) tissue
  • Growth factor (VEGF)
  • Metastatic colorectal cancer
  • Peripheral blood
  • Single nucleotide polymorphisms (SNPs)
  • Vascular endothelial

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Spectroscopy
  • Inorganic Chemistry
  • Catalysis
  • Molecular Biology
  • Computer Science Applications
  • Medicine(all)

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