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

UGT1A1 is involved in glucuronidation of drugs and plays a large role in metabolism. Genotyping variants of differing dinucleotide TA repeat length within the TATA box of the UGT1A1 region (dbSNP ID rs3064744) are utilized in the dosing of irinotecan and atazanavir for pharmacogenomics purposes. Here we describe a CLIA-validated PCR and fragment analysis assay that distinguishes between UGT1A1*36 (TA)₅, UGT1A1*1 (TA)₆, UGT1A1*28 (TA)₇, and UGT1A1*37 (TA)₈, as well as potential heterozygous combinations. This development offers a more determinant genotype than assays like PharmacoScan can accurately establish alone.

PCR was performed using 2X Platinum SuperFi PCR Master Mix, 5X SuperFi GC Enhancer, a FAM-labeled forward primer, reverse primer, and 0.5 ng/μL-20 ng/μL DNA. MiniGene plasmids for each variant served as controls. QC was performed using the Agilent Bioanalyzer 2100 or TapeStation 4200; fragment analysis was performed with HiDi Formamide and LIZ 500 size standard and processed via capillary electrophoresis. Data were analyzed using the GeneMapper version 5 software and peaks with the largest area under the curve (AUC) were identified and compared with known sizes of controls.

Per CLIA regulations, the assay passed validation with 100% concordance for all parameters: accuracy, precision, reportable range, reference range, analytical specificity, and analytical sensitivity. Following validation, clinical assay implementation for 940 samples run on PharmacoScan showed disagreement for 74 samples at UGT1A1 rs3064744.

Clinical implementation as a supplemental assay to other pharmacogenomics offerings resulted in a correction rate of the loci within patient samples of 7.8%, with 2.77% caused by miscalling UGT1A1*37 variant.