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.
OBJECTIVE
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.


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.
Papatheodorou
Athanasios
A
Lecturer Medical Genetics, University of Athens, Medical School, Department of Medical Genetics, Thivon and Levadias, Athens, Greece.
Latsi
Panagiota
P
Vrettou
Christina
C
Dimakou
Aikaterini
A
Chroneou
Alexia
A
Makrythanasis
Periklis
P
Kaliakatsos
Marios
M
Orfanidou
Dora
D
Roussos
Charis
C
Kanavakis
Emmanuel
E
Tzetis
Maria
M
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000465:Algorithms; D000483:Alleles; D016022:Case-Control Studies; D020022:Genetic Predisposition to Disease; D006115:Greece; D006239:Haplotypes; D006579:Heterozygote; D006801:Humans; D008875:Middle Aged; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D029424:Pulmonary Disease, Chronic Obstructive / Q000235:genetics*; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*; D044465:White People / Q000235:genetics*
D014409:Tumor Necrosis Factor-alpha