Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population

Yoichiro Kamatani, Koichi Matsuda, Tetsuya Ohishi, Shigeru Ohtsubo, Keiko Yamazaki, Aritoshi Iida, Naoya Hosono, Michiaki Kubo, Wako Yumura, Kosaku Nitta, Toyomasa Katagiri, Yasushi Kawaguchi, Naoyuki Kamatani, Yusuke Nakamura

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Abstract

Systemic lupus erythematosus (SLE) is one of the common autoimmune diseases, with complex genetic components. Here, we report on a case-control association study of 178 SLE patients and 899 control subjects, using genome-wide gene-based single nucleotide polymorphism (SNP) markers. An SNP, rs3130342, in a 5' flanking region of the TNXB gene revealed a significant association with SLE [P = 0.000000930, odds ratio (OR) 3.11, with 95% confidence interval (95%CI) of 1.89-5.28] in a Japanese population. This association was replicated independently with 203 cases and 294 controls (P = 0.0440, OR 1.52, with 95%CI of 1.01-2.78). Although a copy number variation (CNV) of the C4 gene adjacent to the TNXB gene was reported to be associated with SLE, our analysis on this CNV revealed that the association of CNV of the C4 gene was weaker than the SNP in the TNXB gene and likely to reflect the linkage disequilibrium between C4 CNV and this particular SNP. Stratified analysis also revealed that the association of SNP rs3130342 with SLE was independent of the HLA-DRB1*1501 allele that has been shown to be associated with SLE. Our findings strongly imply that the TNXB gene is a candidate gene susceptible to SLE in the Japanese population.

Original languageEnglish
Pages (from-to)64-73
Number of pages10
JournalJournal of Human Genetics
Volume53
Issue number1
DOIs
Publication statusPublished - 01-01-2008

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Systemic Lupus Erythematosus
Single Nucleotide Polymorphism
Population
Genes
Odds Ratio
Confidence Intervals
HLA-DRB1 Chains
5' Flanking Region
Linkage Disequilibrium
Autoimmune Diseases
Case-Control Studies
Alleles
Genome

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Kamatani, Yoichiro ; Matsuda, Koichi ; Ohishi, Tetsuya ; Ohtsubo, Shigeru ; Yamazaki, Keiko ; Iida, Aritoshi ; Hosono, Naoya ; Kubo, Michiaki ; Yumura, Wako ; Nitta, Kosaku ; Katagiri, Toyomasa ; Kawaguchi, Yasushi ; Kamatani, Naoyuki ; Nakamura, Yusuke. / Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population. In: Journal of Human Genetics. 2008 ; Vol. 53, No. 1. pp. 64-73.
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Kamatani, Y, Matsuda, K, Ohishi, T, Ohtsubo, S, Yamazaki, K, Iida, A, Hosono, N, Kubo, M, Yumura, W, Nitta, K, Katagiri, T, Kawaguchi, Y, Kamatani, N & Nakamura, Y 2008, 'Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population', Journal of Human Genetics, vol. 53, no. 1, pp. 64-73. https://doi.org/10.1007/s10038-007-0219-1

Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population. / Kamatani, Yoichiro; Matsuda, Koichi; Ohishi, Tetsuya; Ohtsubo, Shigeru; Yamazaki, Keiko; Iida, Aritoshi; Hosono, Naoya; Kubo, Michiaki; Yumura, Wako; Nitta, Kosaku; Katagiri, Toyomasa; Kawaguchi, Yasushi; Kamatani, Naoyuki; Nakamura, Yusuke.

In: Journal of Human Genetics, Vol. 53, No. 1, 01.01.2008, p. 64-73.

Research output: Contribution to journalArticle

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T1 - Identification of a significant association of a single nucleotide polymorphism in TNXB with systemic lupus erythematosus in a Japanese population

AU - Kamatani, Yoichiro

AU - Matsuda, Koichi

AU - Ohishi, Tetsuya

AU - Ohtsubo, Shigeru

AU - Yamazaki, Keiko

AU - Iida, Aritoshi

AU - Hosono, Naoya

AU - Kubo, Michiaki

AU - Yumura, Wako

AU - Nitta, Kosaku

AU - Katagiri, Toyomasa

AU - Kawaguchi, Yasushi

AU - Kamatani, Naoyuki

AU - Nakamura, Yusuke

PY - 2008/1/1

Y1 - 2008/1/1

N2 - Systemic lupus erythematosus (SLE) is one of the common autoimmune diseases, with complex genetic components. Here, we report on a case-control association study of 178 SLE patients and 899 control subjects, using genome-wide gene-based single nucleotide polymorphism (SNP) markers. An SNP, rs3130342, in a 5' flanking region of the TNXB gene revealed a significant association with SLE [P = 0.000000930, odds ratio (OR) 3.11, with 95% confidence interval (95%CI) of 1.89-5.28] in a Japanese population. This association was replicated independently with 203 cases and 294 controls (P = 0.0440, OR 1.52, with 95%CI of 1.01-2.78). Although a copy number variation (CNV) of the C4 gene adjacent to the TNXB gene was reported to be associated with SLE, our analysis on this CNV revealed that the association of CNV of the C4 gene was weaker than the SNP in the TNXB gene and likely to reflect the linkage disequilibrium between C4 CNV and this particular SNP. Stratified analysis also revealed that the association of SNP rs3130342 with SLE was independent of the HLA-DRB1*1501 allele that has been shown to be associated with SLE. Our findings strongly imply that the TNXB gene is a candidate gene susceptible to SLE in the Japanese population.

AB - Systemic lupus erythematosus (SLE) is one of the common autoimmune diseases, with complex genetic components. Here, we report on a case-control association study of 178 SLE patients and 899 control subjects, using genome-wide gene-based single nucleotide polymorphism (SNP) markers. An SNP, rs3130342, in a 5' flanking region of the TNXB gene revealed a significant association with SLE [P = 0.000000930, odds ratio (OR) 3.11, with 95% confidence interval (95%CI) of 1.89-5.28] in a Japanese population. This association was replicated independently with 203 cases and 294 controls (P = 0.0440, OR 1.52, with 95%CI of 1.01-2.78). Although a copy number variation (CNV) of the C4 gene adjacent to the TNXB gene was reported to be associated with SLE, our analysis on this CNV revealed that the association of CNV of the C4 gene was weaker than the SNP in the TNXB gene and likely to reflect the linkage disequilibrium between C4 CNV and this particular SNP. Stratified analysis also revealed that the association of SNP rs3130342 with SLE was independent of the HLA-DRB1*1501 allele that has been shown to be associated with SLE. Our findings strongly imply that the TNXB gene is a candidate gene susceptible to SLE in the Japanese population.

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