Aim: To genotype cytokine polymorphisms in the Macedonian population as a part of the international project Cytokine Polymorphism Component (CPC).
Methods: The sample consisted of 125 healthy unrelated individuals, 46 men and 79 women, aged 20-35 years. All individuals were of Macedonian origin and nationality, Christian Orthodox religion, and residents of different regions of the Republic of Macedonia. Blood samples were collected after written consent was obtained, DNA was isolated from peripheral blood leukocytes by the phenol-chloroform extraction method, and the samples were stored in the Anthropology section of the Macedonian Human DNA Bank (hDNAMKD). Fourteen cytokine genes were identified as candidates: gamma-interferon (IFNgamma); interleukin (IL) 1 alpha (IL-1alpha); IL-1 beta (IL-1beta); IL-1 receptor (IL-1R); IL-1R antagonist (IL-1RA); IL-2; IL-4; IL-4 receptor alpha (IL-4Ralpha); IL-6; IL-10; IL-12B; TGF beta 1 (TGF-beta1); and TNF alpha (TNF-alpha). Cytokine genotyping for the anthropology samples was performed by polymerase chain reaction with sequence-specific priming (PCR-SSP) (Heidelberg kit). The population genetics analysis package, PyPop, was used for the analysis of the cytokine data for this report.
Results: The frequency of alleles for some single nucleotide polymorphisms (SNP) varied from 0.967 for TGF-beta1 cdn25/G and 0.920 for TNF-alpha -238/G, to 0.914 for IL-1alpha -889/C, indicating common "wild type" allele in those cytokines. For the most SNPs, the test of neutrality showed negative value for F(nd) statistic, which indicated balancing selection operating on the alleles at that locus. F(nd) was negative and significantly different from 0 for IFNgamma UTR5644 and TGF-beta1 cdn10 (P=0.006 and P=0.007, respectively). Most of SNPs showed a good fit with HWP expectations. A few SNPs (IL-1alpha -889, IL-1beta -511, IL-1beta+3962, and IFNgammaUTR5644) were not in HWP (P< or =0.005), and Guo and Thompson Hardy Weinberg Output (GTHWO) was significant (P< or =0.005). The most frequent haplotypes for TGF-beta1 were TG (0.491) and CG (0.476), with the absence of TGF-beta1/TC haplotype in the sample from the Macedonian population. Test of neutrality showed negative value for F(nd) statistic (Ewens-Watterson test of neutrality) which indicated balancing selection operating on the haplotypes at that locus, except for the IL-4 haplotypes, where it showed a positive value for F(nd) statistic, but without significance. F(nd) was negative and significantly different from 0 for IL-10 haplotypes (P=0.002). In the sample from the Macedonian population, D' was equal to 1 in all haplotypes with P values <0.0001, except for TNF-alpha (P< or =0.012), which indicated that one or more haplotypes were missing.
Conclusion: The analysis of cytokine alleles, genotypes, and haplotypes in the sample from the Macedonian population showed a good fit with Hardy Weinberg equilibrium for most of SNPs and can be used for anthropological comparisons, as well as for association studies with different diseases.