Whole genome association study of rheumatoid arthritis using 27 039 microsatellites

Gen Tamiya; Minori Shinya; Tadashi Imanishi; Tomoki Ikuta; Satoshi Makino; Koichi Okamoto; Koh Furugaki; Toshiko Matsumoto; Shuhei Mano; Satoshi Ando; Yásuyuki Nozaki; Wataru Yukawa; Ryo Nakashige; Daisuke Yamaguchi; Hideo Ishibashi; Manabu Yonekura; Yuu Nakami; Seiken Takayama; Takaho Endo; Takuya Saruwatari; Masaru Yagura; Yoko Yoshikawa; Kei Fujimoto; Akira Oka; Suenori Chiku; Samuel E.V. Linsen; Marius J. Giphart; Jerzy K. Kulski; Toru Fukazawa; Hiroshi Hashimoto; Minoru Kimura; Yuuichi Hoshina; Yasuo Suzuki; Tomomitsu Hotta; Joji Mochida; Takatoshi Minezaki; Koichiro Komai; Shunichi Shiozawa; Atsuo Taniguchi; Hisashi Yamanaka; Naoyuki Kamatani; Takashi Gojobori; Seiamak Bahram; Hidetoshi Inoko

doi:10.1093/hmg/ddi234

Whole genome association study of rheumatoid arthritis using 27 039 microsatellites

Gen Tamiya, Minori Shinya, Tadashi Imanishi, Tomoki Ikuta, Satoshi Makino, Koichi Okamoto, Koh Furugaki, Toshiko Matsumoto, Shuhei Mano, Satoshi Ando, Yásuyuki Nozaki, Wataru Yukawa, Ryo Nakashige, Daisuke Yamaguchi, Hideo Ishibashi, Manabu Yonekura, Yuu Nakami, Seiken Takayama, Takaho Endo, Takuya SaruwatariMasaru Yagura, Yoko Yoshikawa, Kei Fujimoto, Akira Oka, Suenori Chiku, Samuel E.V. Linsen, Marius J. Giphart, Jerzy K. Kulski, Toru Fukazawa, Hiroshi Hashimoto, Minoru Kimura, Yuuichi Hoshina, Yasuo Suzuki, Tomomitsu Hotta, Joji Mochida, Takatoshi Minezaki, Koichiro Komai, Shunichi Shiozawa, Atsuo Taniguchi, Hisashi Yamanaka, Naoyuki Kamatani, Takashi Gojobori, Seiamak Bahram, Hidetoshi Inoko^*

^*Corresponding author for this work

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

109 Scopus citations

Abstract

A major goal of current human genome-wide studies is to identify the genetic basis of complex disorders. However, the availability of an unbiased, reliable, cost efficient and comprehensive methodology to analyze the entire genome for complex disease association is still largely lacking or problematic. Therefore, we have developed a practical and efficient strategy for whole genome association studies of complex diseases by charting the human genome at 100 kb intervals using a collection of 27 039 microsatellites and the DNA pooling method in three successive genomic screens of independent case-control populations. The final step in our methodology consists of fine mapping of the candidate susceptible DNA regions by single nucleotide polymorphisms (SNPs) analysis. This approach was validated upon application to rheumatoid arthritis, a destructive joint disease affecting up to 1% of the population. A total of 47 candidate regions were identified. The top seven loci, withstanding the most stringent statistical tests, were dissected down to individual genes and/or SNPs on four chromosomes, including the previously known 6p21.3-encoded Major Histocompatibility Complex gene, HLA-DRB1. Hence, microsatellite-based genome-wide association analysis complemented by end stage SNP typing provides a new tool for genetic dissection of multifactorial pathologies including common diseases.

Original language	English (US)
Pages (from-to)	2305-2321
Number of pages	17
Journal	Human Molecular Genetics
Volume	14
Issue number	16
DOIs	https://doi.org/10.1093/hmg/ddi234
State	Published - Aug 15 2005
Externally published	Yes

Bibliographical note

Funding Information:
We would like to thank M. Tomizawa, E. Tokubo, A. Takaki, H. Ando, S. Adachi, K. Yoshida, Y. Makino, K. Kobayashi, T. Shinomiya, S. Harada, M. Matsuzawa and S. Yamamoto for technical assistance, T. Ichihara (Nisshinbo Research and Development Center), N. Yasuda and T. Tamura (JBIRC), S. Hashimoto and H. Sano (JBiC), Y. Eguchi (MKI), M. Morikawa (GenoDive Pharm) for suggestions or help in this work and finally J.-L. Mandel, M. Koenig (both at IGBMC) and J. Sibilia (Strasbourg University Hospital) for critical reading of the manuscript. This work was performed under the management of Japan Biological Informatics Consortium (JBIC) and supported by grants from the New Energy and Industrial Technology Development Organization (NEDO). This research was also supported by ‘Special Coordination Funds for Promoting Science and Technology’ from the Japan Science and Technology Agency and ‘Research for the Future Program’ from the Japan Society for the Promotion Science. S.B. and H.I. wish to thank an INSERM-JSPS collaborative grant. Funding to pay the Open Access publication charges for this article was provided by the grant from NEDO.

ASJC Scopus subject areas

Molecular Biology
Genetics
Genetics(clinical)

UN SDGs

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

Access to Document

10.1093/hmg/ddi234

Cite this

Tamiya, G., Shinya, M., Imanishi, T., Ikuta, T., Makino, S., Okamoto, K., Furugaki, K., Matsumoto, T., Mano, S., Ando, S., Nozaki, Y., Yukawa, W., Nakashige, R., Yamaguchi, D., Ishibashi, H., Yonekura, M., Nakami, Y., Takayama, S., Endo, T., ... Inoko, H. (2005). Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Human Molecular Genetics, 14(16), 2305-2321. https://doi.org/10.1093/hmg/ddi234

@article{f2f77c00172a4a62804d53f39306a02c,

title = "Whole genome association study of rheumatoid arthritis using 27 039 microsatellites",

abstract = "A major goal of current human genome-wide studies is to identify the genetic basis of complex disorders. However, the availability of an unbiased, reliable, cost efficient and comprehensive methodology to analyze the entire genome for complex disease association is still largely lacking or problematic. Therefore, we have developed a practical and efficient strategy for whole genome association studies of complex diseases by charting the human genome at 100 kb intervals using a collection of 27 039 microsatellites and the DNA pooling method in three successive genomic screens of independent case-control populations. The final step in our methodology consists of fine mapping of the candidate susceptible DNA regions by single nucleotide polymorphisms (SNPs) analysis. This approach was validated upon application to rheumatoid arthritis, a destructive joint disease affecting up to 1% of the population. A total of 47 candidate regions were identified. The top seven loci, withstanding the most stringent statistical tests, were dissected down to individual genes and/or SNPs on four chromosomes, including the previously known 6p21.3-encoded Major Histocompatibility Complex gene, HLA-DRB1. Hence, microsatellite-based genome-wide association analysis complemented by end stage SNP typing provides a new tool for genetic dissection of multifactorial pathologies including common diseases.",

author = "Gen Tamiya and Minori Shinya and Tadashi Imanishi and Tomoki Ikuta and Satoshi Makino and Koichi Okamoto and Koh Furugaki and Toshiko Matsumoto and Shuhei Mano and Satoshi Ando and Y{\'a}suyuki Nozaki and Wataru Yukawa and Ryo Nakashige and Daisuke Yamaguchi and Hideo Ishibashi and Manabu Yonekura and Yuu Nakami and Seiken Takayama and Takaho Endo and Takuya Saruwatari and Masaru Yagura and Yoko Yoshikawa and Kei Fujimoto and Akira Oka and Suenori Chiku and Linsen, {Samuel E.V.} and Giphart, {Marius J.} and Kulski, {Jerzy K.} and Toru Fukazawa and Hiroshi Hashimoto and Minoru Kimura and Yuuichi Hoshina and Yasuo Suzuki and Tomomitsu Hotta and Joji Mochida and Takatoshi Minezaki and Koichiro Komai and Shunichi Shiozawa and Atsuo Taniguchi and Hisashi Yamanaka and Naoyuki Kamatani and Takashi Gojobori and Seiamak Bahram and Hidetoshi Inoko",

note = "Funding Information: We would like to thank M. Tomizawa, E. Tokubo, A. Takaki, H. Ando, S. Adachi, K. Yoshida, Y. Makino, K. Kobayashi, T. Shinomiya, S. Harada, M. Matsuzawa and S. Yamamoto for technical assistance, T. Ichihara (Nisshinbo Research and Development Center), N. Yasuda and T. Tamura (JBIRC), S. Hashimoto and H. Sano (JBiC), Y. Eguchi (MKI), M. Morikawa (GenoDive Pharm) for suggestions or help in this work and finally J.-L. Mandel, M. Koenig (both at IGBMC) and J. Sibilia (Strasbourg University Hospital) for critical reading of the manuscript. This work was performed under the management of Japan Biological Informatics Consortium (JBIC) and supported by grants from the New Energy and Industrial Technology Development Organization (NEDO). This research was also supported by {\textquoteleft}Special Coordination Funds for Promoting Science and Technology{\textquoteright} from the Japan Science and Technology Agency and {\textquoteleft}Research for the Future Program{\textquoteright} from the Japan Society for the Promotion Science. S.B. and H.I. wish to thank an INSERM-JSPS collaborative grant. Funding to pay the Open Access publication charges for this article was provided by the grant from NEDO.",

year = "2005",

month = aug,

day = "15",

doi = "10.1093/hmg/ddi234",

language = "English (US)",

volume = "14",

pages = "2305--2321",

journal = "Human Molecular Genetics",

issn = "0964-6906",

publisher = "Oxford University Press",

number = "16",

}

Tamiya, G, Shinya, M, Imanishi, T, Ikuta, T, Makino, S, Okamoto, K, Furugaki, K, Matsumoto, T, Mano, S, Ando, S, Nozaki, Y, Yukawa, W, Nakashige, R, Yamaguchi, D, Ishibashi, H, Yonekura, M, Nakami, Y, Takayama, S, Endo, T, Saruwatari, T, Yagura, M, Yoshikawa, Y, Fujimoto, K, Oka, A, Chiku, S, Linsen, SEV, Giphart, MJ, Kulski, JK, Fukazawa, T, Hashimoto, H, Kimura, M, Hoshina, Y, Suzuki, Y, Hotta, T, Mochida, J, Minezaki, T, Komai, K, Shiozawa, S, Taniguchi, A, Yamanaka, H, Kamatani, N, Gojobori, T, Bahram, S & Inoko, H 2005, 'Whole genome association study of rheumatoid arthritis using 27 039 microsatellites', Human Molecular Genetics, vol. 14, no. 16, pp. 2305-2321. https://doi.org/10.1093/hmg/ddi234

TY - JOUR

T1 - Whole genome association study of rheumatoid arthritis using 27 039 microsatellites

AU - Tamiya, Gen

AU - Shinya, Minori

AU - Imanishi, Tadashi

AU - Ikuta, Tomoki

AU - Makino, Satoshi

AU - Okamoto, Koichi

AU - Furugaki, Koh

AU - Matsumoto, Toshiko

AU - Mano, Shuhei

AU - Ando, Satoshi

AU - Nozaki, Yásuyuki

AU - Yukawa, Wataru

AU - Nakashige, Ryo

AU - Yamaguchi, Daisuke

AU - Ishibashi, Hideo

AU - Yonekura, Manabu

AU - Nakami, Yuu

AU - Takayama, Seiken

AU - Endo, Takaho

AU - Saruwatari, Takuya

AU - Yagura, Masaru

AU - Yoshikawa, Yoko

AU - Fujimoto, Kei

AU - Oka, Akira

AU - Chiku, Suenori

AU - Linsen, Samuel E.V.

AU - Giphart, Marius J.

AU - Kulski, Jerzy K.

AU - Fukazawa, Toru

AU - Hashimoto, Hiroshi

AU - Kimura, Minoru

AU - Hoshina, Yuuichi

AU - Suzuki, Yasuo

AU - Hotta, Tomomitsu

AU - Mochida, Joji

AU - Minezaki, Takatoshi

AU - Komai, Koichiro

AU - Shiozawa, Shunichi

AU - Taniguchi, Atsuo

AU - Yamanaka, Hisashi

AU - Kamatani, Naoyuki

AU - Gojobori, Takashi

AU - Bahram, Seiamak

AU - Inoko, Hidetoshi

N1 - Funding Information: We would like to thank M. Tomizawa, E. Tokubo, A. Takaki, H. Ando, S. Adachi, K. Yoshida, Y. Makino, K. Kobayashi, T. Shinomiya, S. Harada, M. Matsuzawa and S. Yamamoto for technical assistance, T. Ichihara (Nisshinbo Research and Development Center), N. Yasuda and T. Tamura (JBIRC), S. Hashimoto and H. Sano (JBiC), Y. Eguchi (MKI), M. Morikawa (GenoDive Pharm) for suggestions or help in this work and finally J.-L. Mandel, M. Koenig (both at IGBMC) and J. Sibilia (Strasbourg University Hospital) for critical reading of the manuscript. This work was performed under the management of Japan Biological Informatics Consortium (JBIC) and supported by grants from the New Energy and Industrial Technology Development Organization (NEDO). This research was also supported by ‘Special Coordination Funds for Promoting Science and Technology’ from the Japan Science and Technology Agency and ‘Research for the Future Program’ from the Japan Society for the Promotion Science. S.B. and H.I. wish to thank an INSERM-JSPS collaborative grant. Funding to pay the Open Access publication charges for this article was provided by the grant from NEDO.

PY - 2005/8/15

Y1 - 2005/8/15

N2 - A major goal of current human genome-wide studies is to identify the genetic basis of complex disorders. However, the availability of an unbiased, reliable, cost efficient and comprehensive methodology to analyze the entire genome for complex disease association is still largely lacking or problematic. Therefore, we have developed a practical and efficient strategy for whole genome association studies of complex diseases by charting the human genome at 100 kb intervals using a collection of 27 039 microsatellites and the DNA pooling method in three successive genomic screens of independent case-control populations. The final step in our methodology consists of fine mapping of the candidate susceptible DNA regions by single nucleotide polymorphisms (SNPs) analysis. This approach was validated upon application to rheumatoid arthritis, a destructive joint disease affecting up to 1% of the population. A total of 47 candidate regions were identified. The top seven loci, withstanding the most stringent statistical tests, were dissected down to individual genes and/or SNPs on four chromosomes, including the previously known 6p21.3-encoded Major Histocompatibility Complex gene, HLA-DRB1. Hence, microsatellite-based genome-wide association analysis complemented by end stage SNP typing provides a new tool for genetic dissection of multifactorial pathologies including common diseases.

AB - A major goal of current human genome-wide studies is to identify the genetic basis of complex disorders. However, the availability of an unbiased, reliable, cost efficient and comprehensive methodology to analyze the entire genome for complex disease association is still largely lacking or problematic. Therefore, we have developed a practical and efficient strategy for whole genome association studies of complex diseases by charting the human genome at 100 kb intervals using a collection of 27 039 microsatellites and the DNA pooling method in three successive genomic screens of independent case-control populations. The final step in our methodology consists of fine mapping of the candidate susceptible DNA regions by single nucleotide polymorphisms (SNPs) analysis. This approach was validated upon application to rheumatoid arthritis, a destructive joint disease affecting up to 1% of the population. A total of 47 candidate regions were identified. The top seven loci, withstanding the most stringent statistical tests, were dissected down to individual genes and/or SNPs on four chromosomes, including the previously known 6p21.3-encoded Major Histocompatibility Complex gene, HLA-DRB1. Hence, microsatellite-based genome-wide association analysis complemented by end stage SNP typing provides a new tool for genetic dissection of multifactorial pathologies including common diseases.

UR - http://www.scopus.com/inward/record.url?scp=26444577151&partnerID=8YFLogxK

U2 - 10.1093/hmg/ddi234

DO - 10.1093/hmg/ddi234

M3 - Article

C2 - 16000323

AN - SCOPUS:26444577151

SN - 0964-6906

VL - 14

SP - 2305

EP - 2321

JO - Human Molecular Genetics

JF - Human Molecular Genetics

IS - 16

ER -

Whole genome association study of rheumatoid arthritis using 27 039 microsatellites

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this