POLYMORPHISMS IN THE TNF–ALPHA GENE AND EXTENDED HLA AND TNF–ALPHA HAPLOTYPES IN KOREANS

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TITLE: POLYMORPHISMS IN THE TNF–ALPHA GENE AND EXTENDED HLA AND TNF–ALPHA HAPLOTYPES IN KOREANS–A FAMILY STUDY

Y. J. Park,¹ H. J. Park,¹ M. H. Park.¹

¹Department of Clinical Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea

Tumor necrosis factor alpha (TNF–alpha) is known to play an important role in various conditions such as inflammation, autoimmunity, apoptosis, insulin resistance and sleep induction. Five single nucleotide polymorphisms (SNPs) are known to affect the transcriptional activities of TNF–alpha: –1031 T/C, –863 C/A, –857 C/T, –308 G/A and –238 G/A. We have investigated 5 SNP loci of the promoter region of TNF–alpha gene, the distribution of 5–locus TNF–alpha haplotypes, and their haplotypic associations with HLA–A, –B and –DRB1 loci in 196 parents from 98 unrelated Korean families with 291 children. TNF–alpha SNPs were typed using PCR–single strand conformation polymorphism (SSCP) and PCR–RFLP methods. We used HLA data of these individuals, typed in a previous study: HLA–A, –B, and –DR by serologic method and HLA–DRB1 by PCR–SSCP method. %The allele frequencies of –1031C, –863A, –857T, –308A, and –238A, which are known as the high–producer type, were 17.9%, 14.3%, 14.3%, 6.1%, and 3.6%, respectively. The frequency of –308A allele, known to be associated with autoimmune disease, was 6.1% in Koreans which was lower than Caucasians (14–17%) and somewhat higher than Japanese (1.7%). Five TNF–alpha haplotypes (–1031/–863/–857/–308/–238) were identified: TCCGG (61.7%), CACGG (14.3%), TCTGG (14.3%), TCCAG (6.1%), and CCCGA (3.6%). Significant positive associations (P < 0.001) were observed between TCCGG and B7, B13, B62; between CACGG and A31, B51, B61, DRB1*0701; between TCTGG and B35, B54, B59, DRB1*0405, DRB1*0407; between TCCAG and A3, A33, B58, DRB1*0301, DRB1*1302; and between CCCGA and B14, B38, B48, B57, DRB1*0404, DRB1*1401. Five most common extended haplotypes (frequency > 1.5%) comprised around 15% of total haplotypes: A33–B44–TCCGG–DRB1*1302 (5.1%), A24–B7–TCCGG–DRB1*0101 (3.6%), A30–B13–TCCGG–DRB1*0701 (2.3%), A33–B44–CACGG–DRB1*0701 (2.3%), and A1–B37–TCCGG–DRB1*1001 (1.5%). A total of 223 HLA haplotypes and 239 extended HLA–TNF haplotypes were identified, indicating that most of HLA haplotypes are almost exclusively associated with particular TNF–alpha haplotypes.