Single Nucleotide Polymorphism (SNP) Discovery within the UGT1A Gene Complex: Allelic Frequencies and Ethnic Differences.

Abstract The UDP-glycosyltransferase (UGT1A) gene complex plays an important role in the hepatic metabolism of many chemicals, toxins, and drugs including bilirubin and acetaminophen. In this large gene complex that spans over 200kb, there are at least 13 different coding regions that can serve as exon 1, followed by a common sequence that contains exons 2–5. These variable exon 1 sequences confer different chemical specificities for binding compounds, while exons 2–5 provide glycosyltransferase function (glucuronidation) that enhances water solubility and excretion. Mutations and polymorphisms within the UGT1A complex may help explain the phenotypic variability that is observed in drug metabolism for patients with hematological diseases. To date, several important polymorphisms have been identified in the coding regions of the UGT1A1 and UGT1A6 exon 1 sequences, but formal single nucleotide polymorphism (SNP) discovery has not been reported. Using genomic DNA obtained from a cohort of Thai patients with beta-thalassemia/HbE (n=37) and African-American patients with sickle cell anemia (n=12), flanking and coding sequences for UGT1A1 exon 1 (1.5kb), UGT1A6 exon 1 (1.5kb), and UGT1A common exons 2–5 (2.5kb) were fully sequenced in both directions. Polymorphisms that occurred more than once were compared to wildtype sequences obtained from NCBI, Accession Number AF297093. Single Nucleotide Polymorphisms in the UGT1A gene complex SNP NCBI nucleotide Location African-American Thai * indicates a SNP previously identified in NCBI g/c 109183 5′ 1A6 Exon 1 .875/.125 .676/.324 c/g 109301 5′ 1A6 Exon 1 .833/.167 1.000/.000 g/t 109628 1A6 Exon 1 .458/.542 .662/.338 c/t 109713 1A6 Exon 1 1.000/.000 .905/.095 a/g * 109924 1A6 Exon 1 .542/.458 .689/.311 a/g * 110150 1A6 Exon 1 .708/.292 .689/.311 a/c * 110161 1A6 Exon 1 .625/.375 .662/.338 t/g 110236 1A6 Exon 1 .750/.250 .973/.027 c/t 174679 5′ 1A1 Exon 1 .500/.500 .770/.230 g/c 174979 5′ 1A1 Exon 1 1.000/.000 .946/.054 g/a * 175253 1A1 Exon 1 1.000/.000 .932/.068 a/g 182226 Intron 2 .955/.045 .689/.311 t/c 182521 Intron 2 .850/.150 .905/.095 c/t 187524 3′ Exon 5 .417/.583 .865/.135 c/g * 187652 3′ Exon 5 .625/.375 .851/.149 c/g * 187753 3′ Exon 5 .587/.417 .838/.162 In addition to the well-described UGT1A1 (TA)n promoter polymorphism, a total of 16 SNPs were identified in these regions, including 10 that have not been previously reported. Four novel promoter SNPs were identified, along with three new UGT1A6 exon 1 coding SNPs and three non-coding SNPs within the common exon 2–5 region. The alellic frequencies for these SNPs can only be estimated from this small sample size, but indicate substantial differences between Thai and African-American patients. A larger sample size will be used to determine a more accurate allelic frequency for each SNP, and to identify haplotype associations. These novel SNPs within the UGT1A gene complex may have important effects on drug metabolism and may explain some of the phenotypic variability observed in these patient populations.