Genotypic and phenotypic analysis of the polymorphic thiopurine S‐methyltransferase gene (TPMT) in a European population

Abstract

1 Characterization of allelic variants of the TPMT gene (TPMT) responsible for changes in TPMT activity, and elucidation of the mechanism by which these alleles act, are required because of the clinical importance of this polymorphism for patients receiving thiopurine drugs. 2 We de®ned the mutational and allelic spectrum of TPMT in a group of 191 Europeans. Using PCR ± SSCP, we screened for mutation the entire coding sequence, the exon-intron boundaries, the promoter region and the 3'-¯anking region of the gene. Six mutations were detected throughout the ten exons and seven TPMT alleles were characterized. Four of them, TPMT*2, *3A, *3C and *7, harbouring the known mutations, G238C, G460A, A719G or T681G, were nonfunctional and accounted for 0.5, 5.7, 0.8 and 0.3% of the allele totality, respectively. 3 Within the promoter region, six alleles corresponding to a variable number of tandem repeats (VNTR), were identi®ed. VNTR*V4 and *V5a which harbour four or ®ve repeats of a 17 ± 18 bp unit, were the most frequent (55% and 34%, respectively). The other VNTR alleles, having from ®ve to eight repeats, were rarer. 4 The TPMT phenotype was correctly predicted by genotyping for 87% of individuals. A clear negative correlation between the total number of repeats from both alleles and the TPMT activity level was observed, indicating that VNTRs contribute to interindividual variations of TPMT activity. Therefore, additional analysis of the promoter region of TPMT can improve the phenotype prediction rate by genotyping.

Thiopurine methyltransferase phenotypes and genotypes in Brazilians

“…In our study, the mutations 238G.C, 460G.A and 719A.G were not detected in four individuals with intermediate activity. This apparent discordance between phenotype and genotype might be due to one of the rarer mutations lying on the open reading frame of the TPMT gene, to variable number of tandem repeats on its promoter, previously reported but not examined in this study, or to yet unidentified mutations [9,10]. Moreover, the possibility that intermediate activity can be observed in the absence of genetic TPMT deficiency should not be overlooked.…”

“…This contrasts with the wide differences in the frequencies of these alleles in other ethnic groups ( Table 2, other studies). Thus, among Caucasians, TPMT Ã 3A is three-to five-fold more frequent than TPMT Ã 3C [3,9,11] whereas, in Africans, TPMT Ã 3A is not detected and TPMT Ã 3C frequency is 5-7% [12,13]. In African-Americans, these two alleles coexist, but TPMT Ã 3C is three-fold more frequent than TPMT Ã 3A [3].…”

Thiopurine S-methyltransferase pharmacogenetics: insights, challenges and future directions

“…The *14 SNP disrupts the translation initiation codon (Lindqvist et al, 2004) and prevents translation of the enzyme protein , while *4 and *15 involve alterations in canonical mRNA splice site sequences (Otterness et al, 1998;Lindqvist et al, 2004) and *3D contains a premature stop codon (Otterness et al, 1997). There is also a polymorphic GC-rich variable number of tandem repeats (VNTR) present in the 5 0 -flanking region of TPMT that can vary from 3 to 9 repeat elements (SpireVayron de la Moureyre et al, 1998Moureyre et al, , 1999Yan et al, 2000). This VNTR has been reported to modulate TPMT activity as a result of altered transcription.…”

“…As might be anticipated, many techniques have been used to genotype TPMT, beginning with RFLP assays and later extending to allele-specific amplification, direct sequencing, SSCP, DHPLC and -more recently -use of a variety of high throughput platforms (Yates et al, 1997;Spire-Vayron de la Moureyre et al, 1998;Schaeffeler et al, 2003Schaeffeler et al, , 2004. However, beyond all of the usual issues associated with genotyping, TPMT pharmacogenetics serves to highlight -in a very practical sense -a limitation common to all of these genotyping methods, their inability to determine haplotype directly.…”

Thiopurine methyltransferase polymorphisms in a Brazilian population

“…20 Furthermore, bimodal or trimodal activity patterns have been shown in several populations. 16,[21][22][23][24][25][26][27][28][29][30][31][32][33][34] Since ethnic differences have been demonstrated worldwide, it remains to be elucidated in Brazil, the fifth largest populated country in the world. The present-day Brazilian populations reflects the result of five centuries of interethnic crosses between peoples from almost all continents (Europeans, African, Asians) as well as autochthonous Amerindians, all forming one of the most heterogeneous populations in the world.…”