Carrie Grimsley

Haplotype structure of the UDP-glucuronosyltransferase 1A1 promoter in different ethnic groups.

Genetic variation in UDP-glucuronosyltransferase 1A1 (UGT1A1)expression has several important clinical implications. UGT1A1 basal transcription is affected by a polymorphic (TA)n repeat, and another important regulatory element is the phenobarbital-responsive enhancer module (PBREM) which might contain variants affecting inducible gene expression. We assessed the extent of linkage disequilibrium between the (TA)n polymorphism and variants in the PBREM and UGT1A1 promoter. We also investigated the relationship between PBREM-(TA)n haplotypes and the glucuronidation rate of the UGT1A1 substrate SN-38. DNAs from 83 human livers were genotyped for the (TA)n polymorphism and microsomes from the same livers were phenotyped for SN-38 glucuronidation. The (TA)n polymorphism was genotyped in 24 additional African-Americans included in the Human Variation Panel (Coriell Institute). A 606-bp region spanning the PBREM was sequenced in 81 liver and a subset of 22 Human Variation Panel DNAs and six variants were found. The -3279G T and -3156G A variants are common (0.39 and 0.30, respectively). -3279G T is more common in Caucasians than African-Americans (P = 0.001). In Caucasians, linkage disequilibrium was highly significant between sites -3279, -3156, and the (TA)n polymorphism (P < 0.0001). In contrast, in African-Americans, only marginal levels of significance were observed between (TA)n and -3279 (P = 0.02) and between -3279 and -3156 (P = 0.04). Ten promoter haplotypes were identified. Haplotype I is the most common (0.39), from which haplotype II (0.15) differs at position -3279. SN-38G formation rates were correlated with (TA)n genotypes. This study showed that (i) common promoter variants are in linkage disequilibrium and (ii) the haplotype structure of promoter is probably different between Caucasians and African-Americans.

Population genetic studies of HLA-E: Evidence for Selection

HLA-E is a nonclassical, class I gene (Ib) of unknown function. The study was initiated to determine the amount and nature of the variation in the class Ib gene HLA-E in diverse ethnic groups. A single base-pair substitution (A-->G at 382, exon 3) resulting in a change from an arginine (R) to a glycine (G) at codon 107 was found. A glycine was present at position 107 in individuals from four ape species, suggesting that EG107 is the older of the two alleles. The two human alleles were present in all samples studied. The alleles were in linkage disequilibrium with HLA-A (W = 0.58), HLA-B (W = 0.59) and HLA-C (W = 0.55) in the Hutterites. The frequencies of the two HLA-E alleles were more equal than expectations based on neutrality in inbred and outbred Caucasian samples (Wattersons F = 0.506, p = 0.02 and F = 0.512, p = 0.047, respectively) and nearly significant in African-American and Hispanic samples (F = 0.513, p = 0.063 and F = 0.508, p = 0.053). These data suggest that this polymorphism arose before the expansion of Homo sapiens and has been maintained in diverse populations by stabilizing selection.

Population genetic studies of HLA-G: allele frequencies and linkage disequilibrium with HLA-A

HLA-G is a class I gene that is expressed in the extravillous cytotrophoblast. Although the function of this gene is still unknown, its expression at the maternal-fetal interface suggests that HLA-G may play a key role in the induction of tolerance during pregnancy. Preliminary to our studies of the effects of HLA-G polymorphisms on pregnancy outcome, we have defined HLA-G alleles in the Hutterites. We report here the presence of nine HLA-G alleles that differ with respect to nucleotide sequences, including four groups of alleles that differ with respect to amino acid sequences, and striking linkage disequilibrium between HLA-G and HLA-A alleles. The levels and sites of polymorphism in HLA-G suggest that this gene had a unique evolutionary history and may perform nonclassical functions at the maternal-fetal interface.

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster

Common polymorphisms within the human UGT1A gene locus are associated with irinotecan and tranilast toxicity. To uncover additional functional variation across this gene cluster, cross-species sequence comparisons were performed. Evolutionarily conserved segments (a total of 47.1 kb) were re-sequenced in 24 African-American, 24 European-American, and 24 Asian individuals, and 381 segregating sites (including 123 singletons) were identified. Highly conserved coding sites were less likely to be polymorphic than diverged sites (P<0.0001) but this pattern was not observed at non-coding sites (P=0.1025). Among coding variants, the distribution of those computationally predicted to affect function was skewed toward low frequencies. Some alleles occurred at similar frequencies in each population; others had wide disparities. Although strong linkage disequilibrium was detected among the hepatically expressed genes, the degree of linkage disequilibrium varied among populations. These results suggest that rare functional gene variants and inter-population variability must be considered in the interpretation of association studies between UGT1A and drug metabolism/toxicity phenotypes.

Pharmacogenetics of flavopiridol, glucuronidation

Clinical Pharmacology & Therapeutics (2003) 73, P60–P60; doi: