Clinical application of cytokine-related gene polymorphism analysis using a newly developed DNA chip in critically ill patients.
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.
Otani
Shunsuke
S
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
Oda
Shigeto
S
Sadahiro
Tomohito
T
Nakamura
Masataka
M
Watanabe
Eizo
E
Nakada
Taka-aki
TA
Abe
Ryuzo
R
Tokuhisa
Takeshi
T
Hirasawa
Hiroyuki
H
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*
D053583:Interleukin-1beta; D015850:Interleukin-6; D014409:Tumor Necrosis Factor-alpha