Comparison of three methods for genotyping the UGT1A1 (TA)n repeat polymorphism

Linnea M. Baudhuin, W Edward Jr. Highsmith, Jennifer Skierka, Leonard Holtegaard, Brenda E. Moore, Dennis J. O'Kane

Research output: Contribution to journalArticle

23 Scopus citations

Abstract

Objectives: The UGT1A1 promoter contains a (TA)n repeat polymorphism. The 7 repeat allele is associated with decreased enzyme activity and patients homozygous for this allele treated with irinotecan may experience life-threatening toxicity. Here, we have compared three methods [DNA sequencing, fragment analysis, and the Invader® assay (Third Wave Technologies)] for genotyping this polymorphism. Results: All of the DNA samples (n = 119) had concordant genotype calls between the sequencing and size-based methods. The Invader® method was also concordant if the genotypes were 6/6, 6/7, or 7/7. Both the size-based method and the Invader® method had straightforward data analysis, while interpretation of the sequencing results was occasionally more challenging. The Invader® method required more concentrated DNA for analysis, was more expensive, and had a limited genotyping spectrum. Conclusion: All three methods were valuable for genotyping the UGT1A1 (TA)n repeat, with the sequencing and size-based assays having the fewest drawbacks.

Original languageEnglish (US)
Pages (from-to)710-717
Number of pages8
JournalClinical Biochemistry
Volume40
Issue number9-10
DOIs
StatePublished - Jun 2007

    Fingerprint

Keywords

  • Capillary electrophoresis
  • Fragment analysis
  • Genotyping
  • Irinotecan
  • Sequencing
  • TATA box
  • UGT1A1

ASJC Scopus subject areas

  • Clinical Biochemistry

Cite this

Baudhuin, L. M., Highsmith, W. E. J., Skierka, J., Holtegaard, L., Moore, B. E., & O'Kane, D. J. (2007). Comparison of three methods for genotyping the UGT1A1 (TA)n repeat polymorphism. Clinical Biochemistry, 40(9-10), 710-717. https://doi.org/10.1016/j.clinbiochem.2007.03.007