Development of a novel microarray methodology for the study of SNPs in the promoter region of the TNF-alpha gene: their association with obstructive pulmonary disease in Greek patients.

OBJECTIVES: Polymorphisms in promoter region of TNF-alpha gene were shown to interfere with the transcriptional activity of the gene resulting in the production of different levels of TNF-alpha product suggesting their involvement in susceptibility or severity of many inflammatory diseases. We set up a case-control study consisting of 117 COPD (Chronic Obstructive Pulmonary Disease), 62 DB (bronchiectasis) patients and two control groups (109 smokers without COPD-healthy smokers control group and 212 general population subjects) to evaluate involvement of TNF-alpha gene polymorphisms in the abovementioned diseases in a homogeneous population.
METHODS: The novel methodology of the NanoChip Molecular Biology Workstation (MBW Nanogen http://www.nanogen.com) was employed to genotype the 5 promoter SNPs. RESULTS AND
CONCLUSIONS: Genotype frequencies of the 5 SNPs showed no significant difference between the COPD and DB patient groups and the healthy smokers group. Statistical difference (p=0.043) was only revealed between the haplotype frequencies in COPD patients compared to the general population control group. The NanoChip MBW is an accurate method for SNP screening.