title: 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.
abstract: 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.
authors.affiliation: Lecturer Medical Genetics, University of Athens, Medical School, Department of Medical Genetics, Thivon and Levadias, Athens, Greece.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Papatheodorou
authors.forename: Panagiota
authors.initials: P
authors.lastname: Latsi
authors.forename: Christina
authors.initials: C
authors.lastname: Vrettou
authors.forename: Aikaterini
authors.initials: A
authors.lastname: Dimakou
authors.forename: Alexia
authors.initials: A
authors.lastname: Chroneou
authors.forename: Periklis
authors.initials: P
authors.lastname: Makrythanasis
authors.forename: Marios
authors.initials: M
authors.lastname: Kaliakatsos
authors.forename: Dora
authors.initials: D
authors.lastname: Orfanidou
authors.forename: Charis
authors.initials: C
authors.lastname: Roussos
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Kanavakis
authors.forename: Maria
authors.initials: M
authors.lastname: Tzetis
mesh_terms: 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*
chemical_list: D014409:Tumor Necrosis Factor-alpha