Development of Integrated Annotation Workflows for Human Whole Genome Sequencing

• Project/Area Number: 25430183
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Nagasaki University
• Principal Investigator: MISHIMA Hiroyuki 長崎大学, 原爆後障害医療研究所, 助教 (10513319)
• Co-Investigator(Renkei-kenkyūsha): YOSHIURA Koh-ihiro 長崎大学, 原爆後障害医療研究所, 教授 (00304931) ; KATAYAMA Toshiaki 情報, システム研究機構DBCLS, 助教 (60396869)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: ヒトゲノム / バイオインフォマティクス / 次世代シークエンサー / ワークフロー / データベース生物学 / Ruby / TogoWS / ゲノム / REST API / UCSCゲノムデータベース

Outline of Final Research Achievements

This study aims to build workflows for finding disease causing mutations using whole genome sequencing data. For the goal, the primary researcher extended TogoWS to support the UCSC genome database, several open-source tools, the Bio-Virtuoso Docker containers. Built workflows were applied for whole genome dataset of 12 individuals.

Research Products

• [Journal Article] Ultra-sensitive droplet digital PCR for detecting a low-prevalence somatic GNAQ mutation in Sturge-Weber syndrome. (2016)
  • Author(s): Uchiyama Y, Nakashima M, Watanabe S, Miyajima M, Taguri M, Miyatake S, Miyake N, Saitsu H, Mishima H, Kinoshita A, Arai H, Yoshiura K, Matsumoto N.
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 22985-22985
  • DOI: 10.1038/srep22985
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Metabolic autopsy with next generation sequencing in sudden unexpected death in infancy: Postmortem diagnosis of fatty acid oxidation disorders (2015)
  • Author(s): Yamamoto T, Mishima H, Mizukami H, Fukahori Y, Umehara T, Murase T, Kobayashi M, Mori S, Nagai T, Fukunaga T, Yamaguchi S, Yoshiura K, Ikematsu K
  • Journal Title: Molecular Genetics and Metabolism Report Volume: 5 Pages: 26-32
  • DOI: 10.1016/j.ymgmr.2015.09.005
  • NAID: 120006986854
  • Peer Reviewed
• [Journal Article] Germline mutations causing familial lung cancer. (2015)
  • Author(s): Tomoshige K, Matsumoto K, Tsuchiya T, Oikawa M, Miyazaki T, Yamasaki N, Mishima H, Kinoshita A, Kubo T, Fukushima K, Yoshiura K, Nagayasu T.
  • Journal Title: Journal of Human Genetics Volume: 60 Issue: 10 Pages: 597-603
  • DOI: 10.1038/jhg.2015.75
  • Peer Reviewed
• [Journal Article] Novel compound heterozygous DNA ligase IV mutations in an adolescent with a slowly-progressing radiosensitive-severe combined immunodeficiency (2015)
  • Author(s): Tamura S, Higuchi K, Tamaki M, Inoue C, Awazawa R, Mitsuki N, Nakazawa Y, Mishima H, Takahashi K, Kondo O, Imai K, Morio T, Ohara O,et al
  • Journal Title: Clin Immunol Volume: 160 Issue: 2 Pages: 255-260
  • DOI: 10.1016/j.clim.2015.07.004
  • Peer Reviewed / Open Access
• [Journal Article] Pregnancy-associated microRNAs in plasma as potential molecular markers of ectopic pregnancy (2015)
  • Author(s): Miura K, Higashijima A, Mishima H, Miura S, Kitajima M, Kaneuchi M, Yoshiura K, Masuzaki H
  • Journal Title: Fertility and Sterility Volume: 印刷中 Issue: 5 Pages: 1202-1208
  • DOI: 10.1016/j.fertnstert.2015.01.041
  • Peer Reviewed
• [Journal Article] Circulating levels of maternal plasma cell-free pregnancy-associated placenta-specific microRNAs are associated with placental weight. (2014)
  • Author(s): Miura K, Morisaki S, Abe S, Higashijima A, Hasegawa Y, Miura S, Tateishi S, Mishima H, Yoshiura K, Masuzaki H.
  • Journal Title: placenta Volume: 35 (10) Issue: 10 Pages: 848-851
  • DOI: 10.1016/j.placenta.2014.06.002
  • Peer Reviewed
• [Journal Article] Clinical applications of analysis of plasma circulating complete hydatidiform mole pregnancy-associated miRNAs in gestational trophoblastic neoplasia: A preliminary investigation. (2014)
  • Author(s): Miura K, Hasegawa Y, Abe S, Higashijima A, Miura S, Mishima H, Kinoshita A, Kaneuchi M, Yoshiura K, Masuzaki H.
  • Journal Title: Placenta Volume: 35 (9) Issue: 9 Pages: 787-789
  • DOI: 10.1016/j.placenta.2014.06.004
  • Peer Reviewed
• [Journal Article] Genome-wide association study of HPV-associated cervical cancer in Japanese women. (2014)
  • Author(s): Miura K, Mishima H, Kinoshita A, Hayashida C, Abe S, Tokunaga K, Masuzaki H, Yoshiura KI.
  • Journal Title: Journal of Medical Virology Volume: 86 (7) Issue: 7 Pages: 1153-1158
  • DOI: 10.1002/jmv.23943
  • Peer Reviewed
• [Journal Article] Single human papillomavirus 16 or 52 infection and later cytological findings in Japanese women with NILM or ASC-US. (2014)
  • Author(s): Abe S, Miura K, Kinoshita A, Mishima H, Miura S, Yamasaki K, Hasegawa Y, Higashijima A, Jo O, Yoshida A, Kaneuchi M, Yoshiura K, Masuzaki H.
  • Journal Title: Journal of Human Genetics Volume: 59 (5) Issue: 5 Pages: 251-255
  • DOI: 10.1038/jhg.2014.9
  • Peer Reviewed
• [Journal Article] Identification of endometrioid endometrial carcinoma-associated microRNAs in tissue and plasma. (2014)
  • Author(s): Tsukamoto O, Miura K, Mishima H, Abe S, Kaneuchi M, Higashijima A, Miura S, Kinoshita A, Yoshiura K, Masuzaki H.
  • Journal Title: Gynecologic Oncology Volume: 132 (3) Issue: 3 Pages: 715-721
  • DOI: 10.1016/j.ygyno.2014.01.029
  • Peer Reviewed
• [Journal Article] Predominantly placenta-expressed mRNAs in maternal plasma as predictive markers for twin-twin transfusion syndrome (2014)
  • Author(s): Miura K, Higashijima A, Miura S, Mishima H, Yamasaki K, Abe S, Hasegawa Y, Kaneuchi M, Yoshida A, Kinoshita A, Yoshiura KI, Masuzaki H.
  • Journal Title: Prenatal Diagnosis Volume: 34 Issue: 4 Pages: 345-349
  • DOI: 10.1002/pd.4307
  • Peer Reviewed
• [Journal Article] 全エクソーム解析における情報処理 (2013)
  • Author(s): 三嶋博之
  • Journal Title: 医学のあゆみ Volume: 245 Pages: 345-351
• [Presentation] io-Virtuoso: A package of Docker containers for multiple source data retrieval, RDF conversion, and triplesore deployment in a simplified manner. (2016)
  • Author(s): Hiroyuki Mishima, Koh-ichiro Yoshiura
  • Organizer: The 13th International Congress of Human Genetics
  • Place of Presentation: 京都府京都国際会館
  • Year and Date: 2016-04-02
  • Int'l Joint Research
• [Presentation] Exomiserを用いたエクソーム解析ワークフローと支援ツールの開発 (2015)
  • Author(s): 三嶋博之，吉浦孝一郎
  • Organizer: 日本人類遺伝学会第６０回大会
  • Place of Presentation: 東京都京王プラザホテル
  • Year and Date: 2015-10-14
• [Presentation] （1-2）Exomiserを用いた知識ベース疾患原因変異探索のためのワークフロー (2015)
  • Author(s): 三嶋博之，吉浦孝一郎
  • Organizer: NGS現場の会第四回研究会
  • Place of Presentation: つくば市つくば国際会議場
  • Year and Date: 2015-07-01
• [Presentation] ヒトの遺伝学と低酸素生物学はデータベース生物学の夢をみるか？ (2015)
  • Author(s): 三嶋博之
  • Organizer: 第13回がんとハイポキシア研究会
  • Place of Presentation: 三島市国立遺伝学研究所
  • Year and Date: 2015-06-06
  • Invited
• [Presentation] 多発性歯牙腫合併症例を含むSATB2遺伝子変異症候群の新規変異の同定 (2014)
  • Author(s): 三嶋博之
  • Organizer: 日本人類遺伝学会第５９回大会
  • Place of Presentation: 東京都江戸川区タワーホール深堀
  • Year and Date: 2014-11-20
• [Presentation] Handmaid Building of a High-Performance Computing Cluster and a Storage System for Bioinformatics (2014)
  • Author(s): Hiroyuki Mishima
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: 仙台市仙台国際センター
  • Year and Date: 2014-10-02 – 2014-10-04
• [Presentation] 公開セッション第一部・個人ゲノム解析技術の現在と未来／解析結果 (2014)
  • Author(s): 三嶋博之
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: 仙台市仙台国際センター
  • Year and Date: 2014-10-02 – 2014-10-04
  • Invited
• [Presentation] 次世代シークエンサーで挑む口唇口蓋裂と乳歯歯胚異常の遺伝学 (2014)
  • Author(s): 三嶋博之
  • Organizer: 北海道大学大学院歯学研究科歯学研究セミナー
  • Place of Presentation: 札幌市北海道大学
  • Year and Date: 2014-05-16
  • Invited
• [Presentation] (2-47-B) TogoWS RESTサービスによるUCSCゲノムデータベースの利用 (2013)
  • Author(s): 三嶋博之，西澤達也，片山俊明
  • Organizer: NGS現場の会第三回研究会
  • Place of Presentation: 神戸市神戸国際会議場
• [Presentation] （O44）TogoWS REST サービスによるUCSCゲノムデータベースの利用
  • Author(s): 三嶋博之，西澤達也，吉浦孝一郎，片山俊明
  • Organizer: 日本人類遺伝学会第５８回大会
  • Place of Presentation: 仙台市江陽グランドホテル
• [Presentation] Gene Hunting: できること・できないこと
  • Author(s): 三嶋博之
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: 東京都江戸川区タワーホール深堀
• [Book] 次世代シークエンサーDRY解析教本：1-2 コマンドラインの使い方 (2015)
  • Author(s): 三嶋博之，清水厚志
  • Total Pages: 399
  • Publisher: 学研メディカル秀潤社
• [Book] 実験医学増刊・今日から使えるデータベース・ウェブツール達人になるための実線ガイド100 (2014)
  • Author(s): 三嶋博之
  • Total Pages: 6
  • Publisher: 羊土社
• [Remarks] Hgvd2annovar / Hgvd2BED / Hgvd2VCF
  • URL: https://github.com/misshie/hgvd2annovar
• [Remarks] Bio-Virtuoso
  • URL: https://github.com/misshie/bio-virtuoso
• [Remarks] Ruby UCSC API
  • URL: https://github.com/misshie/bioruby-ucsc-api
• [Remarks] Rakefiles for workflows
  • URL: https://github.com/misshie/Workflows
• [Remarks] Hgvd2annovar / Hgvd2BED
  • URL: https://github.com/misshie/hgvd2annovar
• [Remarks] TogoWS
  • URL: http://togows.org/
• [Remarks] GitHub - Ruby UCSC API
  • URL: https://github.com/misshie/bioruby-ucsc-api
• [Remarks] RubyGems - bio-ucsc-api
  • URL: http://rubygems.org/gems/bio-ucsc-api