title: Clinical application of cytokine-related gene polymorphism analysis using a newly developed DNA chip in critically ill patients.
abstract: OBJECTIVE
  To investigate the usefulness of analysis of single nucleotide polymorphism (SNP) using a newly developed DNA chip assay involving single base extension(SBE) and subsequent hybridization in cytokine-related genes in critical care patients.
  
  
  METHODS
  Genotyping was performed in 76 ICU patients admitted to the ICU. First, the DNA samples from 58 patients were subjected to PCR and SBE conditioning for DNA. Second, another 18 patients were subjected to genotyping for SNPs in IL-6 -596G/A, -572C/G, -174G/C, TNF-alpha -308G/A, -238G/A, IL-1beta -511C/T and -31T/C by both TaqMan and DNA chip method, and by DNA direct sequencing prospectively.
  
  
  RESULTS
  First, PCR and SBE condition were established with initial sample sets, which were consistent with results by TaqMan method. Second, no difference was observed between two assay methods in prospective validation set.
  
  
  CONCLUSIONS
  The genotyping assay using the new chip was developed and its usefulness was confirmed.
authors.affiliation: Department of Emergency and Critical Care Medicine, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo, Chiba, 260-8677, Japan. otani-shun@umin.ac.jp
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Otani
authors.forename: Shigeto
authors.initials: S
authors.lastname: Oda
authors.forename: Tomohito
authors.initials: T
authors.lastname: Sadahiro
authors.forename: Masataka
authors.initials: M
authors.lastname: Nakamura
authors.forename: Eizo
authors.initials: E
authors.lastname: Watanabe
authors.forename: Taka-aki
authors.initials: TA
authors.lastname: Nakada
authors.forename: Ryuzo
authors.initials: R
authors.lastname: Abe
authors.forename: Takeshi
authors.initials: T
authors.lastname: Tokuhisa
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hirasawa
mesh_terms: D016638:Critical Illness; D004252:DNA Mutational Analysis / Q000379:methods; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D007362:Intensive Care Units; D053583:Interleukin-1beta / Q000235:genetics*; D015850:Interleukin-6 / Q000235:genetics*; D046228:Microarray Analysis / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*
chemical_list: D053583:Interleukin-1beta; D015850:Interleukin-6; D014409:Tumor Necrosis Factor-alpha