Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population

Sung Mi Cho; Ju Young Kim; Ha Jung Ryu; Jae Jung Kim; Hyun Hee Kim; Joo Hyun Park; Hung Tae Kim; Kyung Hee Kim; Hye Young Cho; Bermseok Oh; Chan Park; Kuchan Kimm; Inho Jo; Jong Eun Lee; Hyoung Doo Shin; Jong Keuk Lee

doi:10.1016/j.humimm.2004.04.005

Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population

Sung Mi Cho, Ju Young Kim, Ha Jung Ryu, Jae Jung Kim, Hyun Hee Kim, Joo Hyun Park, Hung Tae Kim, Kyung Hee Kim, Hye Young Cho, Bermseok Oh, Chan Park, Kuchan Kimm, Inho Jo, Jong Eun Lee, Hyoung Doo Shin, Jong Keuk Lee

Department of Molecular Medicine

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	710-718
Number of pages	9
Journal	Human Immunology
Volume	65
Issue number	7
DOIs	https://doi.org/10.1016/j.humimm.2004.04.005
State	Published - Jul 2004

Bibliographical note

Funding Information:
This work was supported by an intramural grant of the National Institute of Health, Korea. I.J. was supported in part by an IMT-2000 research grant (01-PJ11-PG9-01BT05-0003) from the Ministry of Health and Welfare and the Ministry of Science and Technology, Korea.

Keywords

Korean
SNP
SSCP
TNF-TNFR superfamily

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.humimm.2004.04.005

Cite this

Cho, S. M., Kim, J. Y., Ryu, H. J., Kim, J. J., Kim, H. H., Park, J. H., Kim, H. T., Kim, K. H., Cho, H. Y., Oh, B., Park, C., Kimm, K., Jo, I., Lee, J. E., Shin, H. D., & Lee, J. K. (2004). Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population. Human Immunology, 65(7), 710-718. https://doi.org/10.1016/j.humimm.2004.04.005

@article{88bc0b71ed754ce48f77732430574ff1,

title = "Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population",

abstract = "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.",

keywords = "Korean, SNP, SSCP, TNF-TNFR superfamily",

author = "Cho, {Sung Mi} and Kim, {Ju Young} and Ryu, {Ha Jung} and Kim, {Jae Jung} and Kim, {Hyun Hee} and Park, {Joo Hyun} and Kim, {Hung Tae} and Kim, {Kyung Hee} and Cho, {Hye Young} and Bermseok Oh and Chan Park and Kuchan Kimm and Inho Jo and Lee, {Jong Eun} and Shin, {Hyoung Doo} and Lee, {Jong Keuk}",

note = "Funding Information: This work was supported by an intramural grant of the National Institute of Health, Korea. I.J. was supported in part by an IMT-2000 research grant (01-PJ11-PG9-01BT05-0003) from the Ministry of Health and Welfare and the Ministry of Science and Technology, Korea.",

year = "2004",

month = jul,

doi = "10.1016/j.humimm.2004.04.005",

language = "English",

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Cho, SM, Kim, JY, Ryu, HJ, Kim, JJ, Kim, HH, Park, JH, Kim, HT, Kim, KH, Cho, HY, Oh, B, Park, C, Kimm, K, Jo, I, Lee, JE, Shin, HD & Lee, JK 2004, 'Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population', Human Immunology, vol. 65, no. 7, pp. 710-718. https://doi.org/10.1016/j.humimm.2004.04.005

TY - JOUR

T1 - Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population

AU - Cho, Sung Mi

AU - Kim, Ju Young

AU - Ryu, Ha Jung

AU - Kim, Jae Jung

AU - Kim, Hyun Hee

AU - Park, Joo Hyun

AU - Kim, Hung Tae

AU - Kim, Kyung Hee

AU - Cho, Hye Young

AU - Oh, Bermseok

AU - Park, Chan

AU - Kimm, Kuchan

AU - Jo, Inho

AU - Lee, Jong Eun

AU - Shin, Hyoung Doo

AU - Lee, Jong Keuk

N1 - Funding Information: This work was supported by an intramural grant of the National Institute of Health, Korea. I.J. was supported in part by an IMT-2000 research grant (01-PJ11-PG9-01BT05-0003) from the Ministry of Health and Welfare and the Ministry of Science and Technology, Korea.

PY - 2004/7

Y1 - 2004/7

N2 - 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.

AB - 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.

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KW - SNP

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ER -

Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population

Abstract

Bibliographical note

Keywords

UN SDGs

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