Development and assessment of a pathogenic mutations search method for individuals who are difficult to identify the mutations in standard-exome analysis
Project/Area Number |
16K07211
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Research Category |
Grant-in-Aid for Scientific Research (C)
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Allocation Type | Multi-year Fund |
Section | 一般 |
Research Field |
Medical genome science
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Research Institution | Tokyo Medical and Dental University |
Principal Investigator |
Miya Fuyuki 東京医科歯科大学, 難治疾患研究所, 講師 (50415311)
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Project Period (FY) |
2016-04-01 – 2019-03-31
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Project Status |
Completed (Fiscal Year 2018)
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Budget Amount *help |
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2018: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2017: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2016: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
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Keywords | エクソーム解析 / 疾患遺伝子変異 / 遺伝性疾患 / 次世代シーケンサー / CNV解析 / ミトコンドリア / 全ゲノムシーケンス / 疾患原因変異同定手法開発 / 次世代シーケンスのバイオインフォマティクス / 生体生命情報学 / 脳神経疾患 / バイオテクノロジー / 遺伝子 / 遺伝学 |
Outline of Final Research Achievements |
Whole-exome sequencing (WES) using next generation sequencing is a useful method to identify disease-causing mutations. However, often no candidate mutations are identified using commonly available methods. The reported success rate of WES for Mendelian diseases is around 30% worldwide. We have developed an integrative analysis methodology to identify pathogenic mutations. The analysis methodology consists of the following 6 methods: 1) standard variants calling method, 2) detection of intermediate-size insertions and deletions (indels) using our own developed method, 3) copy number variants analysis for WES data, 4) analysis of mitochondrial DNA for WES data, and 5) domain enrichment analysis for candidate mutations. Through this combinatorial method, it becomes possible to identify variants and structural abnormalities that had been difficult to search and identify previously. Also, the method makes it possible to expand the limits of mutation detection of standard WES analysis.
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Academic Significance and Societal Importance of the Research Achievements |
我々の研究成果で疾患の遺伝子変異を同定する新たな手法論を構築し発表することで、その同定率を10%以上増やすことができた。解析手法を改良することによって、未同定疾患原因変異の新たな発見も可能であることを証明したことで、将来的な解析への応用は当然であるが、過去データの再検証で新規原因変異が同定されることも期待される。病気の原因変異が分かると、病気のメカニズム解明や薬剤ターゲット候補の発見、将来の発症予測、等に役立たせることができ、本成果は今後その一助になると考えられる。
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Report
(4 results)
Research Products
(50 results)
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[Journal Article] Genome-wide association study suggests four variants influencing outcomes with ranibizumab therapy in exudative age-related macular degeneration.2018
Author(s)
Akiyama M, Takahashi A, Momozawa Y, Arakawa S, Miya F, Tsunoda T, Ashikawa K, Oshima Y, Yasuda M, Yoshida S, Enaida H, Tan X, Yanagi Y, Yasukawa T, Ogura Y, Nagai Y, Takahashi K, Fujisawa K, Inoue M, Arakawa A, Tanaka K, Yuzawa M, Kadonosono K, Sonoda KH, Ishibashi T, Kubo M.
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Journal Title
J Hum Genet
Volume: 63
Issue: 10
Pages: 1083-1091
DOI
Related Report
Peer Reviewed
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[Journal Article] Discovery of a Cynomolgus Monkey Family With Retinitis Pigmentosa2018
Author(s)
Ikeda Yasuhiro、Nishiguchi Koji M.、Miya Fuyuki、Shimozawa Nobuhiro、Funatsu Jun、Nakatake Shunji、Fujiwara Kohta、Tachibana Takashi、Murakami Yusuke、Hisatomi Toshio、Yoshida Shigeo、Yasutomi Yasuhiro、Tsunoda Tatsuhiko、Nakazawa Toru、Ishibashi Tatsuro、Sonoda Koh-Hei
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Journal Title
Investigative Opthalmology & Visual Science
Volume: 59
Issue: 2
Pages: 826-826
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Structural Basis and Genotype-Phenotype Correlations of INSR Mutations Causing Severe Insulin Resistance.2017
Author(s)
Hosoe J, Kadowaki H, Miya F, Aizu K, Kawamura T, Miyata I, Satomura K, Ito T, Hara K, Tanaka M, Ishiura H, Tsuji S, Suzuki K, Takakura M, Boroevich KA, Tsunoda T, Yamauchi T, Shojima N, Kadowaki T
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Journal Title
Diabetes
Volume: 66
Issue: 10
Pages: 2713-2723
DOI
NAID
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis2017
Author(s)
Ishigaki Kazuyoshi、Kochi Yuta、Suzuki Akari、Tsuchida Yumi、Tsuchiya Haruka、Sumitomo Shuji、Yamaguchi Kensuke、Nagafuchi Yasuo、Nakachi Shinichiro、Kato Rika、Sakurai Keiichi、Shoda Hirofumi、Ikari Katsunori、Taniguchi Atsuo、Yamanaka Hisashi、Miya Fuyuki、Tsunoda Tatsuhiko、et al.、Yamamoto Kazuhiko
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Journal Title
Nature Genetics
Volume: 49
Issue: 7
Pages: 1120-1125
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Identification of a human clonogenic progenitor with strict monocyte differentiation potential: A counterpart of mouse cMoPs2017
Author(s)
Kawamura S, Onai N, Miya F, Sato T, Tsunoda T, Kurabayashi K, Yotsumoto S, Kuroda S, Takenaka K, Akashi K, Ohteki T
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Journal Title
Immunity
Volume: 46
Issue: 5
Pages: 835-848
DOI
Related Report
Peer Reviewed / Acknowledgement Compliant
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[Journal Article] A combination of genetic and biochemical analyses for the diagnosis of PI3K-AKT-mTOR pathway-associated megalencephaly.2017
Author(s)
Negishi Y, Miya F, Hattori A, Johmura Y, Nakagawa M, Ando N, Hori I, Togawa T, Aoyama K, Ohashi K, Fukumura S, Mizuno S, Umemura A, Kishimoto Y, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Nakanishi M, Saitoh S.
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Journal Title
BMC Med Genet.
Volume: 18
Issue: 1
Pages: 4-4
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Role of a heterotrimeric G-protein, Gi2, in the corticogenesis: possible involvement in periventricular nodular heterotopia and intellectual disability.2016
Author(s)
Hamada, N., Negishi, Y., Mizuno, M., Miya, F., Hattori, A., Okamoto, N., Kato, M., Tsunoda, T., Yamasaki, M., Kanemura, Y., Kosaki, K., Tabata, H., Saitoh, S., Nagata, K.-I.
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Journal Title
J. Neurochem.
Volume: 140
Issue: 1
Pages: 82-95
DOI
Related Report
Peer Reviewed
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[Journal Article] Novel compound heterozygous variants in PLK4 identified in a patient with autosomal recessive microcephaly and chorioretinopathy.2016
Author(s)
Tsutsumi M, Yokoi S, Miya F, Miyata M, Kato M, Okamoto N, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S, *Kurahashi H.
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Journal Title
Eur J Hum Genet
Volume: 24
Issue: 12
Pages: 1702-1706
DOI
Related Report
Peer Reviewed / Acknowledgement Compliant
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[Journal Article] Novel Splicing Mutation in the ASXL3 gene causing Bainbridge-Ropers Syndrome.2016
Author(s)
Hori I, Miya F, Ohashi K, Negishi Y, Hattori A, Ando N, Okamoto N, Kato M, Tsunoda T, Yamasaki M, Kanemura Y, Kosaki K, Saitoh S.
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Journal Title
Am. J. Med. Genet. A
Volume: 170
Issue: 7
Pages: 1863-1867
DOI
Related Report
Peer Reviewed
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[Presentation] Identification of SLC12A2 as a Candidate Deafness Gene in Human.2019
Author(s)
utai H, Wasano K, Momozawa Y, Kamatani Y, Miya F, Masuda S, Morimoto N, Nara K, Takahashi S, Tsunoda T, Homma K, Michiaki Kubo M, Matsunaga T.
Organizer
Association for Research in Otolaryngology (ARO) 42nd Annual Midwinter Meeting
Related Report
Int'l Joint Research
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[Presentation] Structural basis of mutations of the tyrosine kinase domain in INSR and the relations with clinical severity.(インスリン受容体 tyrosine kinase domainをコードする遺伝子変異に伴うタンパク質立体障害と臨床的重症度の関連)2018
Author(s)
Hosoe J, Kadowaki H, Miya F, Takakura M, Tanaka M, Ishiura H, Tsuji S, Tsundoa T, Sshojima N, Yamauchi T, Kadowaki T.
Organizer
日本人類遺伝学会第63回大会
Related Report
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[Presentation] A de novo gain-of-function mutation in MYCN causes a novel megalencephaly syndrome2018
Author(s)
Kato K, Miya F, Hamada N, Negishi Y, Narumi-Kishimoto Y, Ozawa H, Ito H, Hori I, Hattori A, Okamoto N, Kato M, Tsunoda T, Kanemura Y, Kosaki K, Takahashi Y, Nagata K, Saitoh S.
Organizer
日本人類遺伝学会第63回大会
Related Report
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[Presentation] A de novo gain-of-function mutation in MYCN causes a novel megalencephaly syndrome2018
Author(s)
Kato K, Miya F, Hamada N, Negishi Y, Narumi-Kishimoto Y, Ozawa H, Ito H, Hori I, Hattori A, Okamoto N, Kato M, Tsunoda T, Kanemura Y, Kosaki K, Takahashi Y, Nagata K, Saitoh S
Organizer
The American Society of Human Genetics
Related Report
Int'l Joint Research
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[Presentation] PI3K-AKT-mTOR経路異常による巨脳症の臨床的・分子遺伝学的・生化学的検討 (Clinical, genetic, and biochemical analyses for PI3K-AKT-mTOR pathway-associated megalencephaly)2018
Author(s)
堀 いくみ, 宮 冬樹,中村 勇治,家田 大輔,根岸 豊,服部 文子,角田 達彦,金村 米博,小崎 健次郎,齋藤 伸治
Organizer
第60回日本小児神経学会学術集会
Related Report
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[Presentation] 既存のexome解析では疾患原因変異同定が困難な検体の原因変異探索手法の開発2017
Author(s)
宮 冬樹, 重水 大智, 金村 米博, 齋藤 伸治, 岡本 伸彦, 加藤 光広, 山崎 麻美, 松永 達雄, 務台 英樹, 小崎 健次郎, 角田 達彦
Organizer
日本人類遺伝学会 第62回大会
Related Report
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[Presentation] 疾患原因変異発見のための正確な中間サイズインデル検出法の開発2017
Author(s)
重水 大智, 宮 冬樹, 秋山 真太郎, 奥田 修二郎, Keith Boroevich, 藤本 明洋, 中川 英刀, 尾崎 浩一, 新飯田 俊平, 金村 米博, 岡本 伸彦, 齋藤 伸治, 加藤 光広, 山崎 麻美, 松永 達雄, 務台 英樹, 小崎 健次郎, 角田 達彦
Organizer
日本人類遺伝学会 第62回大会
Related Report
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[Presentation] インスリン受容体遺伝子フィブロロネクチンタイプ 3 ドメインにおける遺伝子変異の蛋白質立体構造への影響と臨床的重症度の関連2017
Author(s)
細江 隼, 門脇 弘子, 宮 冬樹, 高倉 美菜香, 会津 克哉, 宮田 市郎, 川村 智行, 里村 憲一, 伊東 建, 原 一雄, 田中 真生, 石浦 浩之, 辻 省次, 鈴木 顕, 角田 達彦, 庄嶋 伸浩, 山内 敏正, 門脇 孝
Organizer
日本人類遺伝学会 第62回大会
Related Report
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[Presentation] evere Insulin Resistance Caused by Mutations in INSR: Genotype-phenotype Correlations and Structural Characterization of the Mutations2017
Author(s)
Jun Hosoe, Hiroko Kadowaki, Fuyuki Miya, Ichiro Miyata, Aizu Katsuya, Tomoyuki Kawamura, Kenichi Satomura, Takeru Ito, Tatsuhiko Tsunoda, Toshimasa Yamauchi, Nobuhiro Shojima, Takashi Kadowaki
Organizer
The 77th Scientific Sessions of the American Diabetes Association
Related Report
Int'l Joint Research
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[Presentation] 既存のexome解析では疾患原因変異同定が困難な検体の原因変異探索手法の開発2017
Author(s)
宮 冬樹, 重水 大智, 齋藤 伸治, 須藤 章, 中川 英刀, 奥田 修二郎, 岡本 伸彦, 加藤 光広, 山崎 麻美, Keith A. Boroevich, 金村 米博, 小崎 健次郎, 角田 達彦
Organizer
次世代現場の会 第5回研究会
Related Report
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[Presentation] Novel compound heterozygous variants in PLK4 cause microcephaly and chorioretinopathy2017
Author(s)
横井摂理, 堤真紀子, 宮冬樹, 宮田昌史, 加藤光広, 岡本伸彦, 角田達彦, 山崎麻美, 金村米博, 小崎健次郎, 齋藤伸治, 倉橋浩樹
Organizer
第59回小児神経学会
Related Report
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[Presentation] A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations.2016
Author(s)
Fuyuki Miya, Mitsuhiro Kato, Tadashi Shiohama, Nobuhiko Okamoto, Shinji Saitoh, Mami Yamasaki, Daichi Shigemizu, Tetsuo Abe, Takashi Morizono, Keith A. Boroevich, Kenjiro Kosaki, Yonehiro Kanemura, Tatsuhiko Tsunoda.
Organizer
ICHG (The 13th International Congress of Human Genetics)
Place of Presentation
Kyoto International Conference Center, Kyoto, Japan
Year and Date
2016-04-03
Related Report
Int'l Joint Research
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