Exome sequencing for disease gene discovery in rheumatoid arthritis

• Project/Area Number: 22510213
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Medical genome science
• Research Institution: Tokai University
• Principal Investigator: MITSUNAGA Shigeki 東海大学, 医学部, 教授 (20510051)
• Co-Investigator(Kenkyū-buntansha): INOKO Hidetoshi 東海大学, 医学部, 教授 (10101932) ; INOUE Ituro 東海大学, 医学部, 教授 (00192500) ; SHIINA Takashi 東海大学, 医学部, 准教授 (00317744)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2011: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2010: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 疾患関連遺伝子 / 稀少変異 / 関節リウマチ / エクソーム解析 / 感受性遺伝子 / 稀少変異体 / 次世代シーケンサ / 希少変異体 / Long-Range PCR / Exome解析

Research Abstract

The butyrophilin-like protein 2 gene (BTNL2) within the class III region of the Major Histocompatability Complex (MHC) genomic region was identified as a rheumatoid arthritis (RA) susceptibility gene by exome sequencing (19 RA cases) with stepwise filtering analysis and then validated by Sanger sequencing and association analysis using 432 cases and 432 controls. Logistic regression of the Sanger-sequenced single nucleotide variants (SNVs) in an association study of 432 cases and 432 controls showed that twelve non-synonymous SNPs in BTNL2 were significantly associated with RA. The lowest p values were obtained from 3 SNPs, rs41521946, rs28362677, and rs28362678, which were in absolute linkage disequilibrium: p = 4.55E-09, OR = 1.88, 95% CI = 1.52 - 2.33. The BTNL2 locates on chromosome 6 between HLA-DRB1 and NOTCH4 and is 170 kb apart from these two genes. Although DRB1 and NOTCH4 were reported to be RA-susceptible, the 3 BTNL2 SNPs retained significant association with RA when evaluated by the logistic regression with the adjustment for RA-susceptible HLA-DRB1 alleles in Japanese or rs2071282-T in NOTCH4: p = 0.0156 and p = 0.00368, respectively. These results suggest that the 3 non-synonymous SNPs in BTNL2 confer RA-risk independently from HLA-DRB1 and NOTCH4

Research Products

• [Journal Article] Detection of Ancestry Informative HLA Alleles Confirms the Admixed Origins of Japanese Population (2013)
  • Author(s): Nakaoka H, Mitsunaga S, Hosomichi K, Shyh-Yuh L,Sawamoto T, Fujiwara T, Tsutsui N, Suematsu K, Shinagawa A, Inoko H, Inoue I.
  • Journal Title: PLoS One Volume: 8(4)
  • Peer Reviewed
• [Journal Article] Improved loop-mediated isothermal amplification for HLA-DRB1 genotyping using RecA and a restriction enzyme for enhanced amplification specificity. (2013)
  • Author(s): Mitsunaga S, Shimizu S, Okudaira Y, Oka A, Tanaka M, Kimura M, Kulski JK, Inoue I, Inoko H.
  • Journal Title: Immunogenetics
  • Peer Reviewed
• [Journal Article] Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2 (2013)
  • Author(s): Mitsunaga S, Hosomichi K, Okudaira Y, Nakaoka H, Kunii N, Suzuki Y, Kuwana M, Sato S, Kaneko Y, Homma Y, Kashiwase K, Azuma F, Kulski JK, Inoue I, Inoko H.
  • Journal Title: J Hum Gene Volume: 58(4) Pages: 210-5
  • NAID: 40019642228
  • Peer Reviewed
• [Journal Article] Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. (2013)
  • Author(s): Mitsunaga S, Hosomichi K, Okudaira Y, Nakaoka H, Kunii N, Suzuki Y, Kuwana M, Sato S, Kaneko Y, Homma Y, Kashiwase K, Azuma F, Kulski JK, Inoue I, Inoko H.
  • Journal Title: J Hum Genet. Volume: 58 Issue: 4 Pages: 210-215
  • DOI: 10.1038/jhg.2013.2
  • NAID: 10031169422
  • Peer Reviewed
• [Journal Article] Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population. (2013)
  • Author(s): Nakaoka H, Mitsunaga S, Hosomichi K, Shyh-Yuh L, Sawamoto T, Fujiwara T, Tsutsui N, Suematsu K, Shinagawa A, Inoko H, Inoue I.
  • Journal Title: PLoS One. Volume: 8 Issue: 4 Pages: e60793-e60793
  • DOI: 10.1371/journal.pone.0060793
  • Peer Reviewed
• [Journal Article] Improved loop-mediated isothermal amplification for HLA-DRB1 genotyping using RecA and a restriction enzyme for enhanced amplification specificity (2013)
  • Author(s): Mitsunaga S, Shimizu S, Okudaira Y, Oka A, Tanaka M, Kimura M, Kulski JK, Inoue I, Inoko H
  • Journal Title: Immunogenet Volume: 65(6) Issue: 6 Pages: 405-415
  • DOI: 10.1007/s00251-013-0690-0
  • Peer Reviewed
• [Journal Article] Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. (2012)
  • Author(s): Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, Oka A, Umemura T, Joshita S, Takahashi O, Hayashi Y, Paumen M, Katsuyama Y, Mitsunaga S, Ota M, Kulski JK, Inoko H.
  • Journal Title: Tissue Antigens Volume: 80(4) Pages: 305-16
  • Peer Reviewed
• [Journal Article] Associations between six classical HLA loci and rheumatoid arthritis: a comprehensive analysis. (2012)
  • Author(s): Mitsunaga S, Suzuki Y, Kuwana M, Sato S, Kaneko Y, Homma Y, Narita A, Kashiwase K, Okudaira Y, Inoue I, Kulski JK, Inoko H
  • Journal Title: Tissue Antigens Volume: 80(1) Pages: 16-25
  • Peer Reviewed
• [Journal Article] Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. (2012)
  • Author(s): Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, Oka A, Umemura T, Joshita S, Takahashi O, Hayashi Y, Paumen M, Katsuyama Y, Mitsunaga S, Ota M, Kulski JK, Inoko H
  • Journal Title: Tissue Antigens. Volume: 80 Issue: 4 Pages: 305-16
  • DOI: 10.1111/j.1399-0039.2012.01941.x
  • Peer Reviewed
• [Journal Article] A systems genetics approach provides a bridge from discovered genetic variants to biological pathways in rheumatoid arthritis. (2011)
  • Author(s): Nakaoka H, Cui T, Tajima A, Oka A, Mitsunaga S, Kashiwase K, Homma Y, Sato S, Suzuki Y, Inoko H, Inoue I.
  • Journal Title: PLoS One Volume: 6(9)
  • Peer Reviewed
• [Journal Article] Exact break point of a 50 kb deletion 8 kb centromeric of the HLA-A locus with HLA-A*24:02: the same deletion observed in other A*24 alleles and A*23:01 allele (2011)
  • Author(s): Mitsunaga S, Okudaira Y, Kunii N, Cui T, Hosomichi K, Oka A, Suzuki Y, Homma Y, Sato S, Inoue I, Inoko H
  • Journal Title: Immunogenetics Volume: 63(8) Pages: 467-74
  • Peer Reviewed
• [Journal Article] Particular human leukocyte antigen alleles are associated with biochemical traits in the Japanese population (2011)
  • Author(s): Mitsunaga S, Homma Y, Narita A, Kashiwase K, Okudaira Y, Shiina Y, Inoue I, Inoko H.
  • Journal Title: Hum Immuno Volume: 72(7) Pages: 566-70
  • Peer Reviewed
• [Journal Article] Particular human leukocyte antigen alleles are associated with biochemical traits in the Japanese population (2011)
  • Author(s): Mitsunaga Shigeki; Homma Yasuhiko; Narita Akira, et al
  • Journal Title: HUMAN IMMUNOLOGY Volume: 72:7 Issue: 7 Pages: 566-570
  • DOI: 10.1016/j.humimm.2011.03.011
  • Peer Reviewed
• [Journal Article] A Systems Genetics Approach Provides a Bridge from Discovered Genetic Variants to Biological Pathways in Rheumatoid Arthritis (2011)
  • Author(s): Nakaoka Hirofumi; Cui Tailin; Tajima Atsushi, et al
  • Journal Title: PLOS ONE Volume: 6:9 Issue: 9 Pages: e25389-e25389
  • DOI: 10.1371/journal.pone.0025389
  • Peer Reviewed
• [Journal Article] Exact break point of a 50 kb deletion 8 kb centromeric of the HLA-A locus with HLA-A^*24:02 : the same deletion observed in other A^*24 alleles and A^*23:01 allele
  • Author(s): Shigeki Mitsunaga, Yuko Okudaira, Nanae Kunii, et al.
  • Journal Title: Immunogenetics Volume: (in press)
  • Peer Reviewed
• [Journal Article] Genome情報と薬剤応答
  • Author(s): 光永滋樹、猪子英俊
  • Journal Title: International Review of Thrombosis Volume: (印刷中)
• [Presentation] Integrative analysis of whole-gene co-expression network and exome sequence data to characterize pathways relevant to rheumatoid arthritis. (2012)
  • Author(s): Hirofumi Nakaoka, Shigeki Mitsunaga, Hidetoshi Inoko, Ituro Inoue:
  • Organizer: 62nd Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: San Francisco, CA
• [Presentation] 関節リウマチとHLA 6座との関連解析 (2012)
  • Author(s): 奥平裕子、光永滋樹、鈴木康夫、桑名正隆、佐藤慎二、金子祐子、本間康彦、成田暁、柏瀬貢一、井ノ上逸朗、猪子英俊
  • Organizer: 第21回日本組織適合性学会大会
  • Place of Presentation: 東京 明治大学駿河台キャンパス
• [Presentation] 関節リウマチとHLA 6座との関連解析 (2012)
  • Author(s): 奥平裕子、光永滋樹、鈴木康夫、桑名正隆、佐藤慎二、金子祐子、本間康彦、成田暁、柏瀬貢一、井ノ上逸朗、猪子英俊
  • Organizer: 第21回日本組織適合性学会大会
  • Place of Presentation: 東京 明治大学駿河台キャンパス
• [Presentation] HLA研究の臨床応用を目指した８桁レベルHLAタイピング法の開発 (2012)
  • Author(s): 椎名隆、鈴木進悟、尾崎有紀、吉川枝里、重成敦子、光永滋樹、猪子英俊
  • Organizer: 第21回日本組織適合性学会大会
  • Place of Presentation: 東京 明治大学駿河台キャンパス
• [Presentation] HLA遺伝子における超高解像度DNAタイピング法（SS-SBT法） (2012)
  • Author(s): 尾崎有紀、鈴木進悟、重成敦子、吉川枝里、岡 晃、光永滋樹、稲岡斉彦、大澤資樹、椎名隆、猪子英俊
  • Organizer: 日本DNA多型学会第21回学術集会
  • Place of Presentation: 京都 京都教育文化センター
• [Presentation] エクソーム解析による関節リウマチ感受性遺伝子の探索 (2011)
  • Author(s): 奥平裕子、光永滋樹、國井七絵、細道一善、田中政之、林英樹、河田寿子、鈴木康夫、佐藤慎二、本間康彦、井ノ上逸朗、猪子英俊
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜市パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] 日本人集団におけるHLAと生化学検査値の関連 (2011)
  • Author(s): 奥平裕子、光永滋樹、成田暁、柏瀬貢一、椎名豊、本間康彦、井ノ上逸朗、猪子英俊
  • Organizer: 第20回日本組織適合性学会大会
  • Place of Presentation: 静岡市ツインメッセ静岡
  • Year and Date: 2011-08-29
• [Presentation] エクソーム解析による関節リウマチ感受性遺伝子の探索 (2011)
  • Author(s): 奥平裕子、光永滋樹、國井七絵、細道一善、田中政之、林英樹、河田寿子、鈴木康夫、佐藤慎二、本間康彦、井ノ上逸朗、猪子英俊
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜 パシフィコ横浜
• [Presentation] 関節リウマチにおけるシステムズ・ジェネティクス・アプローチ~感受性遺伝子座から生物学的経路の推定 (2011)
  • Author(s): 中岡 博史, 崔 泰林, 田嶋 敦, 光永滋樹, 猪子 英俊, 井ノ上 逸朗
  • Organizer: 日本人類遺伝学会第56回大会
  • Place of Presentation: 千葉 幕張メッセ
• [Presentation] 関節リウマチ感受性遺伝子における希少多型・変異の探索 (2010)
  • Author(s): 國井七絵、光永滋樹, 他
  • Organizer: BMB2010
  • Place of Presentation: 神戸ポートアイランド(兵庫県)
  • Year and Date: 2010-12-09
• [Presentation] A*24:02を有するHLA-A遺伝子近傍の欠失領域の解析 (2010)
  • Author(s): 奥平裕子、光永滋樹、崔 泰林、河田寿子、細道一善、山口香織、岡 晃、井ノ上逸朗、猪子英俊
  • Organizer: 第19回日本組織適合性学会大会
  • Place of Presentation: 東京 東京大学本郷キャンパス
• [Presentation] 関節リウマチの病型とHLAとの関連解析 (2010)
  • Author(s): 國井七絵、 光永滋樹、奥平裕子、成田暁、鈴木康夫、本間康彦、桑名正隆、柏瀬貢一、井ノ上逸朗、猪子英俊
  • Organizer: 第19回日本組織適合性学会大会
  • Place of Presentation: 東京東京大学本郷キャンパス
• [Presentation] HLA-DRB1*14:54 の分布 (2010)
  • Author(s): 勝山喜彦、太田雅穂、吉川枝里、光永滋樹、益尾清恵、猪子英俊
  • Organizer: 第19回日本組織適合性学会大会
  • Place of Presentation: 東京 東京大学本郷キャンパス
• [Presentation] 関節リウマチ感受性遺伝子における希少多型・変異の探索 (2010)
  • Author(s): 國井七絵、光永滋樹、細道一善、奥平裕子、鈴木康夫、本間康彦、井ノ上逸朗、猪子英俊
  • Organizer: 第33回日本分子生物学会年会・ 第83回日本生化学会大会合同大会
  • Place of Presentation: 神戸 ポートアイランド
• [Presentation] A systematic approach to constructing genomic risk prediction model of common disease and assessing its clinical validity: A case study of rheumatoid arthritis (2010)
  • Author(s): 中岡 博史, 崔 泰林, 田嶋 敦, 光永滋樹, 井ノ上 逸朗
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会
  • Place of Presentation: 神戸 ポートアイランド