A clinical PCR fragment analysis assay for TA repeat sizing in the UGT1A1 promoter region

Background A genetic TA repeat length polymorphism in the UGT1A1 promoter has been shown to affect UDP-glucuronosyltyransferase (UGT1A1) expression levels with significant clinical implications. The presence of 7 TA repeats has been associated with lowered UGT1A1 expression and the mild hyperbilinrubinemia manifested in Gilbert's syndrome. Furthermore, cancer patients carrying this variant exhibit irinotecan-related toxicity and require lower doses of this chemotherapeutic agent compared to patients carrying the 6 TA repeat allele. This polymorphism is very common and, therefore, necessitates the development of reliable means of detecting it in the clinical laboratory to deliver better personalized therapy regimens. Methods We used 45 whole blood samples from patients previously tested with the FDA-approved Invader UGT1A1 assay (Hologic, Madison, WI) to assess extraction method, analytical sensitivity, accuracy and precision of this assay. In addition, cell line controls were used to test for the common and rare alleles of this polymorphism. The assay was based on PCR amplification and capillary electrophoresis for accurate sizing of the TA repeat copy number. Results All samples tested and controls gave the expected results. Conclusions We have developed and validated a simple and sensitive PCR fragment analysis assay for accurately determining TA repeat length in the UGT1A1 promoter. At our medical center, this testing is used primarily for guiding irinotecan dosing decisions for our cancer patients.