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

Area of Science:

• Pharmacogenomics
• Molecular Diagnostics
• Genetic Polymorphisms

Background:

• The UGT1A1 gene's (TA)n repeat polymorphism influences enzyme activity.
• The 7-repeat allele is linked to reduced UGT1A1 activity.
• Homozygosity for the 7-repeat allele increases risk of severe toxicity from irinotecan treatment.

Purpose of the Study:

• To compare the effectiveness of three genotyping methods for the UGT1A1 (TA)n repeat polymorphism.
• Evaluate DNA sequencing, fragment analysis, and the Invader assay for accuracy and practicality.
• Identify the most suitable method for clinical application in irinotecan therapy.

Main Methods:

• Genotyping of the UGT1A1 (TA)n repeat polymorphism in 119 DNA samples.
• Comparison of results from DNA sequencing, fragment analysis (size-based), and the Invader assay.
• Assessment of concordance, data analysis ease, cost, and DNA concentration requirements.

Main Results:

• DNA sequencing and fragment analysis showed concordant genotype calls for all samples.
• The Invader assay demonstrated concordance for common genotypes (6/6, 6/7, 7/7).
• Fragment analysis and Invader assay offered simpler data analysis; sequencing interpretation was sometimes challenging. Invader assay had higher costs and stricter DNA requirements.

Conclusions:

• All three methods are viable for UGT1A1 (TA)n repeat genotyping.
• DNA sequencing and size-based fragment analysis present fewer limitations.
• These findings aid in selecting optimal genotyping strategies for personalized irinotecan therapy.