Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population.
The tumor necrosis factor (TNF) and TNF receptor (TNF-TNFR) superfamily plays crucial roles in immune regulation and host immune responses. The superfamily has been also associated with many immune-mediated diseases such as asthma, rheumatoid arthritis, inflammatory bowel disease, and diabetes. In order to investigate genetic variants of the TNF-TNFR superfamily, a total of 63 known single nucleotide polymorphisms (SNPs) in the coding region (cSNPs) of the TNF-TNFR superfamily genes were selected from the public SNP database. Among 63 cSNPs tested in this study, only 24 SNPs (38%) were validated to be polymorphic in the Korean population by primer extension-based SNP genotyping. By means of the new enhanced single strand conformational polymorphism (SSCP) method, we also identified a total of 78 SNPs, including 48 known SNPs and 30 novel SNPs, in the 44 human TNF-TNFR superfamily genes. The newly discovered SNPs in the TNF-TNFR superfamily genes revealed that the Korean population had very different patterns of allele frequency compared with African or white populations, whereas Korean allele frequencies were highly similar to those of Asian (correlation coefficient r = 0.88, p < 0.046). A higher similarity of allele frequency was observed between Korean and Japanese populations (r = 0.90, p < 0.001). The validated SNPs in the TNF-TNFR superfamily would be valuable for association studies with several immune-mediated human diseases.
National Genome Research Institute, Seoul, South Korea.
Sung-Mi
SM
Cho
JuYoung
J
Kim
Ha-Jung
HJ
Ryu
Jae-Jung
JJ
Kim
Hyun-Hee
HH
Kim
Joo-Hyun
JH
Park
Hung-Tae
HT
Kim
Kyung-Hee
KH
Kim
Hye-Young
HY
Cho
Bermseok
B
Oh
Chan
C
Park
Kuchan
K
Kimm
Inho
I
Jo
Jong-Eun
JE
Lee
Hyoung Doo
HD
Shin
Jong-Keuk
JK
Lee
D000328:Adult; D000483:Alleles; D019943:Amino Acid Substitution / Q000235:genetics; D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D005006:Ethnicity / Q000235:genetics*; D005260:Female; D005787:Gene Frequency / Q000235:genetics; D006801:Humans; D007723:Korea; D008297:Male; D008875:Middle Aged; D005810:Multigene Family / Q000235:genetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D018807:Polymorphism, Single-Stranded Conformational; D018124:Receptors, Tumor Necrosis Factor / Q000235:genetics*; D017422:Sequence Analysis, DNA; D048069:Tumor Necrosis Factors / Q000235:genetics*; D044465:White People / Q000235:genetics
D018124:Receptors, Tumor Necrosis Factor; D048069:Tumor Necrosis Factors; D004247:DNA