Source:http://linkedlifedata.com/resource/pubmed/id/10599887
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rdf:type | |
lifeskim:mentions |
umls-concept:C0002085,
umls-concept:C0017349,
umls-concept:C0019721,
umls-concept:C0023746,
umls-concept:C0086418,
umls-concept:C0205147,
umls-concept:C0337112,
umls-concept:C0441704,
umls-concept:C0456387,
umls-concept:C0812246,
umls-concept:C1335439,
umls-concept:C1456820,
umls-concept:C1510438,
umls-concept:C1522492,
umls-concept:C1522669,
umls-concept:C1524075,
umls-concept:C1556094
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pubmed:issue |
5
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pubmed:dateCreated |
2000-1-11
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pubmed:abstractText |
Tumor necrosis factor alpha plays a substantial role in a number of conditions such as inflammation, autoimmunity, insulin resistance and sleep. Three new single nucleotide polymorphisms, -1,031 T/C, -863 C/A and -857 T/C, were recently identified in the upstream 5'-flanking region of TNFA in the Japanese population. In the present study, we developed polymerase chain reaction (PCR)-preferential homoduplex formation assay for the single-step allele typing of TNFA, and determined the genotypes of 271 healthy unrelated Japanese individuals. Four haplotypes, -1,031/-863/-857 TCC, TCT, CAC and CCC, were found to constitute the majority, if not all, of the TNFA alleles of healthy Japanese population. These alleles were designated as TNFA-U01, -U02 -U03 and -U04, respectively, in the order of frequency. Based on HLA-A, -B and -DRB1 genotypes together with TNFA genotypes, multi-locus haplotypes were analyzed. Significant positive associations were observed between TNFA-U01 and A*3303, B*5201, B*4403, B*4601, B*0702, DRB1*1502, DRB1*0101, DRB1*1302, between TNFA-U02 and B*5401, B*3501, DRB1*0405, DRB1*0407, between TNFA-U03 and B*4006, B*4002, DRB1*0803, DRB1*0802, DRB1*0403, DRB1*0901, and between TNFA-U04 and B*4801. Four-locus haplotype estimation revealed that A*3303-B*4403-TNFA-U01-DRB1*1302, A*2402-B*5201-TNFA-U01-DRB1*1502 and A*2402-B*5401-TNFA-U02-DRB1*0405 constitute major extended haplotypes in Japanese. Interestingly, TNFA alleles previously shown to have a higher promoter activity (U02, U03) were found to form haplotypes with certain DRB1 alleles associated with T helper 1 (Th1)-dominant diseases such as rheumatoid arthritis, insulin dependent diabetes mellitus and Crohn's disease in Japanese. In contrast, TNFA allele with a low promoter activity (U01) is in linkage disequilibrium with the DRB1 alleles associated with T helper 2 (Th2)-dominant diseases such as atopic dermatitis and ulcerative colitis. These observations raise the possibility that TNFA upstream promoter region polymorphisms contribute to some of the HLA-disease associations.
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pubmed:language |
eng
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pubmed:journal | |
pubmed:citationSubset |
IM
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pubmed:chemical |
http://linkedlifedata.com/resource/pubmed/chemical/5' Untranslated Regions,
http://linkedlifedata.com/resource/pubmed/chemical/HLA-A Antigens,
http://linkedlifedata.com/resource/pubmed/chemical/HLA-DR Antigens,
http://linkedlifedata.com/resource/pubmed/chemical/HLA-DRB1 Chains,
http://linkedlifedata.com/resource/pubmed/chemical/Tumor Necrosis Factor-alpha
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pubmed:status |
MEDLINE
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pubmed:month |
Nov
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pubmed:issn |
0001-2815
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pubmed:author | |
pubmed:issnType |
Print
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pubmed:volume |
54
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
478-84
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pubmed:dateRevised |
2011-11-17
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pubmed:meshHeading |
pubmed-meshheading:10599887-5' Untranslated Regions,
pubmed-meshheading:10599887-Alleles,
pubmed-meshheading:10599887-Genotype,
pubmed-meshheading:10599887-HLA-A Antigens,
pubmed-meshheading:10599887-HLA-DR Antigens,
pubmed-meshheading:10599887-HLA-DRB1 Chains,
pubmed-meshheading:10599887-Haplotypes,
pubmed-meshheading:10599887-Humans,
pubmed-meshheading:10599887-Japan,
pubmed-meshheading:10599887-Linkage Disequilibrium,
pubmed-meshheading:10599887-Polymerase Chain Reaction,
pubmed-meshheading:10599887-Promoter Regions, Genetic,
pubmed-meshheading:10599887-Tumor Necrosis Factor-alpha
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pubmed:year |
1999
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pubmed:articleTitle |
Allele typing of human TNFA 5'-flanking region using polymerase chain reaction-preferential homoduplex formation assay (PCR-PHFA): linkage disequilibrium with HLA class I and class II genes in Japanese.
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pubmed:affiliation |
Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Japan.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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