Loss of heterozygosity testing using real-time PCR analysis of single nucleotide polymorphisms

  • Tamara ČačevEmail author
  • Mladen Jokić
  • Radan Spaventi
  • Krešimir Pavelić
  • Sanja Kapitanović
Original Paper


Purpose: Colon cancer is a genetic disease, caused by mutations in different oncogenes and tumor-suppressor genes. The aim of this study is to evaluate the usefulness of real-time PCR SNP analysis as a new technique in the loss of heterozygosity (LOH) analysis at the E-cadherin gene locus in sporadic colon cancer. Methods: One-hundred cases of human sporadic colon cancer and corresponding normal tissue samples were analyzed using two flanking polymorphic markers commonly used in the LOH analysis at the E-cadherin gene locus by conventional VNTR–LOH analysis. Two intragenic E-cadherin SNP markers were analyzed using real-time PCR SNP analysis. Results: LOH (17.6%) was detected using flanking markers, however, no LOH was detected when the intragenic E-cadherin SNP markers were introduced into our study. Since these markers are intragenic they more accurately represent the status of the E-cadherin gene than the previously used flanking markers. Conclusion: In conclusion, real-time PCR SNP analysis was found to be more accurate, faster, simpler, and a more high-throughput method than the conventional VNTR–LOH analysis.


Real-time PCR SNP analysis E-cadherin gene 



This work was supported in part by grants number 0098108 and 0098109, from the Ministry of Science and Technology, Republic of Croatia.


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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Tamara Čačev
    • 1
    Email author
  • Mladen Jokić
    • 1
  • Radan Spaventi
    • 1
    • 2
  • Krešimir Pavelić
    • 1
  • Sanja Kapitanović
    • 1
  1. 1.Division of Molecular MedicineRuđer Bošković InstituteZagrebCroatia
  2. 2.PLIVA Research Institute Ltd.ZagrebCroatia

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