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


CONCLUSIONS
All three methods were valuable for genotyping the UGT1A1 (TA)n repeat, with the sequencing and size-based assays having the fewest drawbacks.
Baudhuin
Linnea M
LM
Mayo Clinic and Foundation, Department of Laboratory Medicine and Pathology, Hilton 730, Rochester, MN 55905, USA. baudhuin.linnea@mayo.edu
Highsmith
W Edward
WE
Skierka
Jennifer
J
Holtegaard
Leonard
L
Moore
Brenda E
BE
O'Kane
Dennis J
DJ
D001741:Black or African American / Q000235:genetics; D000483:Alleles; D002166:Camptothecin / Q000009:adverse effects / Q000031:analogs & derivatives; D005838:Genotype; D014453:Glucuronosyltransferase / Q000235:genetics*; D006801:Humans; D000077146:Irinotecan; D016133:Polymerase Chain Reaction / Q000191:economics / Q000379:methods; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods; D013997:Time Factors; D000099148:UGT1A1 Enzyme
D002166:Camptothecin; D014453:Glucuronosyltransferase; D000077146:Irinotecan; D000099148:UGT1A1 Enzyme