OBJECTIVES: 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. DESIGN AND 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.
OBJECTIVES: 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. DESIGN AND 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.