Genomic structure and multiple single-nucleotide polymorphisms (SNPs) of the thiopurine S-methyltransferase (TPMT) gene

Seki, Toyokazu; Tanaka, Toshihiro; Nakamura, Yusuke

doi:10.1007/s100380070020

Cited by 44 publications

(42 citation statements)

References 13 publications

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“…Repetitive elements were excluded from the search by invoking the REPEAT MASKER computer program, in the manner described previously (Seki et al 2000). PCR reactions and DNA sequencing were carried out, as previously described (Saito et al 2001).…”

Section: Discovery Of Snps In the Tfap2b Gene And Genotypingmentioning

confidence: 99%

Genetic variations in the gene encoding TFAP2B are associated with type 2 diabetes mellitus

et al. 2005

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To search a gene(s) conferring susceptibility to type 2 diabetes mellitus, we genotyped nearly 60,000 gene-based SNPs for Japanese patients and found evidence that the gene at chromosome 6p12 encoding transcription-factor-activating protein 2b (TFAP2B) 283-292 DOI 10.1007/s10038-005-0253-9 locus: v 2 =10.9, P=0.0009; odds ratio=1.57, 95% CI 1.20-2.06, intron 1+774 (G/T); v 2 =11.6, P=0.0006; odds ratio=1.60, 95% CI 1.22-2.09, intron 1+2093 (A/C); v 2 =12.2, P=0.0004; odds ratio=1.61, 95% CI 1.23-2.11]. The association of TFAP2B with type 2 diabetes was also observed in the UK population. These results suggest that TFAP2B might be a new candidate for conferring susceptibility to type 2 diabetes and contribute to the pathogenesis of type 2 diabetes.

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Section: Discovery Of Snps In the Tfap2b Gene And Genotypingmentioning

confidence: 99%

Genetic variations in the gene encoding TFAP2B are associated with type 2 diabetes mellitus

et al. 2005

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“…Dye-terminated PCR amplifications were analyzed with an ABI 3700 autosequencer (PE Applied Biosystems). Detection of polymorphism was carried out using the PolyPhred computer program (Nickerson et al 1997), which automatically detects the presence of heterozygous SNPs by fluorescence-based sequencing of PCR products Seki et al 2000;Yamada et al 2000;Iida et al 2001). Allele frequencies were estimated individually by comparing the peak levels of signals among all 192 chromosomes.…”

Section: Detection Of Snps and Insertion/deletion Polymorphismsmentioning

confidence: 99%

Identification of single-nucleotide polymorphisms (SNPs) of human N-acetyltransferase genes NAT1, NAT2, AANAT, ARD1, and L1CAM in the Japanese population

et al. 2001

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By direct sequencing of regions of the human genome containing five genes belonging to the acetyltransferase family, arylamine N-acetyltransferase (NAT1), arylamine N-acetyltransferase (NAT2), arylalkylamine Nacetyltransferase (AANAT), L1 cell adhesion molecule (L1CAM), and the human homolog of Saccharomyces cerevisiae N-acetyltransferase ARD1, we identified 53 single-nucleotide polymorphisms (SNPs) and two insertion/ deletion polymorphisms in 48 healthy Japanese volunteers. NAT1 and NAT2 are so-called drug-metabolizing enzymes. In the NAT1 gene we found two SNPs and a 3-bp insertion/ deletion polymorphism that corresponded to the NAT1*3,

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“…DNA sequencing was done with the BigDye Terminator Cycle Sequencing FS (PE Biosystems, Foster City, CA, USA) and determined with an ABI PRISM 377-96 sequencer (Applied Biosystems, Foster City, CA, USA), as described by Seki et al (2000). Results were processed with Sequencher, version 3.0 (Hitachi Software, Yokohama, Japan), to compare sequences and to locate polymorphisms (Nakajima et al 1999).…”

Section: Direct Sequencingmentioning

confidence: 99%

Linkage disequilibrium and haplotype analysis among eight novel single-nucleotide polymorphisms in the human tissue-type plasminogen activator (t-PA) gene

et al. 2001

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Tissue-type plasminogen activator (t-PA), a serine protease, activates the conversion of plasminogen to the fibrinolytic protein, plasmin. The t-PA gene, mapped to chromosome 8p12-p11.2, contains 14 exons. An Alu insertion/deletion (I/D) polymorphism in this gene has been associated with an increased risk for myocardial infarction. In the work reported here we sequenced 11 kilobases (kb) of genomic DNA from 50 normal Japanese volunteers (100 alleles), to include all 14 exons of the t-PA gene, flanking intronic sequences, and 6 kb of the 5Ј sequence. These experiments identified eight novel single-nucleotide polymorphisms (SNPs), in addition to the known Alu I/D polymorphism, from which genotypic data we constructed 12 haplotypes in the tested population. Two-way comparisons of SNPs and the Alu polymorphism revealed strong linkage disequilibrium between the Alu site and SNPs at positions 20,209 ( 2 ϭ 92.263) and 27,555 ( 2 ϭ 47.53), and between SNPs at positions 27,849 and 28,902 ( 2 ϭ 66.331). A phylogenic tree was constructed to infer a process of genome construction that would reflect the sequence variations we observed. Our results help to explain the lack of agreement among results of various disease-association studies in which a contribution of the human t-PA gene has been suspected but not always confirmed.

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Genomic structure and multiple single-nucleotide polymorphisms (SNPs) of the thiopurine S-methyltransferase (TPMT) gene

Cited by 44 publications

References 13 publications

Genetic variations in the gene encoding TFAP2B are associated with type 2 diabetes mellitus

Genetic variations in the gene encoding TFAP2B are associated with type 2 diabetes mellitus

Identification of single-nucleotide polymorphisms (SNPs) of human N-acetyltransferase genes NAT1, NAT2, AANAT, ARD1, and L1CAM in the Japanese population

Linkage disequilibrium and haplotype analysis among eight novel single-nucleotide polymorphisms in the human tissue-type plasminogen activator (t-PA) gene

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