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UGT1A1 Fragment Analysis: Genotyping the (TA)n Variable Repeat Polymorphism for Clinical Applications.

Ryan N Baugher1, Kristen M Pike1, Teri M Plona1

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Summary

A new PCR and fragment analysis assay accurately genotypes UGT1A1 variants, improving pharmacogenomics by correcting previous genotyping errors for drug dosing.

Keywords:
UGT1A1clinicalfragment analysisirinotecanpharmacogenomics

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Area of Science:

  • Pharmacogenomics
  • Molecular Diagnostics
  • Clinical Chemistry

Background:

  • The UGT1A1 gene is crucial for drug metabolism, with specific variants (rs3064744) impacting irinotecan and atazanavir dosing.
  • Existing genotyping methods may lack the precision to accurately determine UGT1A1 TA repeat lengths, affecting pharmacogenomic applications.

Purpose of the Study:

  • To develop and validate a precise Polymerase Chain Reaction (PCR) and fragment analysis assay for UGT1A1 genotyping.
  • To improve the accuracy of UGT1A1 variant determination compared to existing assays like PharmacoScan.

Main Methods:

  • A CLIA-validated PCR assay using SuperFi Master Mix and GC Enhancer with a FAM-labeled forward primer.
  • Fragment analysis via capillary electrophoresis with HiDi Formamide and LIZ 500 size standard.
  • Data analysis using GeneMapper software, identifying peaks by area under the curve (AUC) against known controls.

Main Results:

  • The assay achieved 100% concordance across all CLIA validation parameters: accuracy, precision, reportable range, reference range, analytical specificity, and sensitivity.
  • Clinical implementation revealed discrepancies in 74 out of 940 samples (7.8%) when compared to PharmacoScan results for UGT1A1 rs3064744.

Conclusions:

  • The developed assay serves as a valuable supplemental tool in pharmacogenomics, significantly improving the accuracy of UGT1A1 genotyping.
  • The assay identified a 7.8% correction rate in patient samples, including a 2.77% miscalling rate of the UGT1A1*37 variant by previous methods.