Genomics Approach to orofacial clefts focusing theubiquitin-proteasome system

• Project/Area Number: 23791230
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Embryonic/Neonatal medicine
• Research Institution: Nagasaki University
• Principal Investigator: MISHIMA Hiroyuki 長崎大学, 大学院・医歯薬学総合研究科, 助教 (10513319)
• Project Period (FY): 2011 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2011: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: 次世代シークエンサー / バイオインフォマティクス / オープンソース / 口唇口蓋裂 / 人類遺伝学 / 先天異常 / ユビキチン / プロテアソーム / オープンソースソフトウェア

Research Abstract

Next generation sequencers (NGS) can analyze samples more comprehensively and more accurately than quantitative PCR. Thus, the author started to build data analysis workflow for NGS data. Using the workflow, the research team including the author succeeded to find the UVSSA gene causing UV sensitive syndrome A. The author also published database accessing library for Ruby, the Ruby UCSC API. The author plan to finish analysis of orofacial cleft samples using build workflows.

Research Products

• [Journal Article] Copy number variation of the antimicrobial-gene, defensin beta 4, is associated with susceptibility to cervical cancer (2013)
  • Author(s): Abe S, Miura K, Kinoshita A, Mishima H, Miura S, Yamasaki K, Hasegawa Y, Higashijima A, Jo O, Sasaki K, Yoshida A, Yoshiura K, Masuzaki H
  • Journal Title: J Hum Genet
  • NAID: 10031177218
• [Journal Article] Characterization of placenta-specific microRNAs in fetal growth restriction pregnancy (2013)
  • Author(s): Higashijima A, Miura K, Mishima H, Kinoshita A, Jo O, Abe S, Hasegawa Y, Miura S, Yamasaki K, Yoshida A, Yoshiura K, Masuzaki H
  • Journal Title: Prenatal Diagnosis Volume: 33 Pages: 214-222
• [Journal Article] Copy number variation of the antimicrobial-gene, defensin beta 4, is associated with susceptibility to cervical cancer. (2013)
  • Author(s): Abe, S, Miura, K, Kinoshita, A, Mishima, H, Miura, S, Yamasaki, K, Hasegawa, Y, Higashijima, A, Jo, O, Sasaki, K, Yoshida, A, Yoshiura, KI, Masuzaki.
  • Journal Title: Journal of Human Genetics Volume: 58 Issue: 5 Pages: 250-253
  • DOI: 10.1038/jhg.2013.7
  • Peer Reviewed
• [Journal Article] Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations. (2012)
  • Author(s): Sasaki K, Mishima H, Miura K, Yoshiura K
  • Journal Title: Gene Volume: 512 Pages: 267-274
  • NAID: 120006985901
• [Journal Article] The Ruby UCSC API: accessing the UCSC genome database using Ruby (2012)
  • Author(s): Mishima H, Aerts J, Katayama T, Bonnal RJ, Yoshiura K
  • Journal Title: BMC Bioinformatics Volume: 13 Pages: 240-240
  • NAID: 120006985547
• [Journal Article] Mutations in UVSSA cause UV-sensitive syndrome and impair RNA polymerase IIo processing in transcription-coupled nucleotide-excision repair (2012)
  • Author(s): Nakazawa Y, Sasaki K, Mitsutake N, Matsuse M, Shimada M, Nardo T, Takahashi Y, Ohyama K, Ito K, Mishima H, Nomura M, Kinoshita A, Ono S, Takenaka K, Masuyama R, Kudo T, Slor H, Utani A, Tateishi S, Yamashita S, Stefanini M, Lehmann AR, Yoshiura K, Ogi T
  • Journal Title: Nature Genetics Volume: 44 Pages: 586-592
  • NAID: 120006985586
• [Journal Article] Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations (2012)
  • Author(s): Kensaku Sasaki
  • Journal Title: Gene Volume: 512 Issue: 2 Pages: 267-274
  • DOI: 10.1016/j.gene.2012.10.035
  • Peer Reviewed
• [Journal Article] The Ruby UCSC API: accessing the UCSC genome database using Ruby (2012)
  • Author(s): Hiroyuki Mishima
  • Journal Title: BMC Bioinformatics Volume: 13 Issue: 1 Pages: 1471-2105
  • DOI: 10.1186/1471-2105-13-240
  • NAID: 120006985547
  • Peer Reviewed
• [Journal Article] Biogem: an effective tool based approach for scaling up open source software development in bioinformatics (2012)
  • Author(s): Bonnal RJP, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P
  • Journal Title: Bioinformatics Volume: 28 Issue: 7 Pages: 1035-1037
  • DOI: 10.1093/bioinformatics/bts080
  • Peer Reviewed
• [Journal Article] Identification of Novel Schizophrenia Loci by Homozygosity Mapping Using DNA Microarray Analysis (2011)
  • Author(s): Kurotaki, et al
  • Journal Title: PLos One Volume: 6(5) Issue: 5 Pages: e20589-e20589
  • DOI: 10.1371/journal.pone.0020589
  • Peer Reviewed
• [Journal Article] Assembly defect due to a PSMB8 mutation reduces proteasome activity and causes the autoinflammatory disorder, Nakajo-Nishimura syndrome (2011)
  • Author(s): Arima, K., Kinoshita, A., Mishima, H., Kanazawa, N., Kaneko, T., Mizushima, T., Ichinose, K., Nakamura, H., Tsujino, A., Kawakami, A., Matsunaka, M., Kasagi, S., Kawano, S., Kumagai, S., Ohmura, K., Mimori, T., Hirano, M., Ueno, S., Tanaka, K., Tanaka, M., Toyoshima, I., Sugino, H., Yamakawa, A., Tanaka, K., Niikawa, N., Furukawa, F., Murata, S., Eguchi, K., Ida, H., Yoshiura, K.
  • Journal Title: Proc.Natl.Acad.Sci.USA Volume: 108 Issue: 36 Pages: 14914-14919
  • DOI: 10.1073/pnas.1106015108
  • Peer Reviewed
• [Journal Article] Agile parallel bioinformatics workflow management using Pwrake (2011)
  • Author(s): Mishima, et al
  • Journal Title: BMC Res Notes Volume: 4(1) Issue: 1 Pages: 331-331
  • DOI: 10.1186/1756-0500-4-331
  • NAID: 120006985006
  • Peer Reviewed
• [Presentation] ヒトゲノム変異解析ワークフローにおける公共データベース活用 (2012)
  • Author(s): 三嶋博之, 吉浦孝一郎
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡市福岡国際会議場・マリンメッセ福岡
  • Year and Date: 2012-12-13
• [Presentation] 次世代シークエンサーを用いたDisease Gene Hunting (2012)
  • Author(s): 三嶋博之
  • Organizer: 第24回日本小児口腔外科学会総会・学術大会
  • Place of Presentation: 名古屋市愛知学院大学
  • Year and Date: 2012-11-24
• [Presentation] Biogem, Ruby UCSC API, and Bioruby (2012)
  • Author(s): Hiroyuki Mishima, Raoul J.P. Bonnal, Naohisa Goto, Francesco Strozzi, Toshiaki Katayama, Pjotr Prins
  • Organizer: The 13th Annual Bioinformatics Open Source Conference
  • Place of Presentation: Long Beach Convention Center, Long Beach, CA, USA
• [Presentation] Hiroyuki Mishima, Raoul J.P. Bonnal, Naohisa Goto, Francesco Strozzi, Toshiaki Katayama, Pjotr Prins (2012)
  • Author(s): Hiroyuki Mishima, Raoul J.P. Bonnal, Naohisa Goto, Francesco Strozzi, Toshiaki Katayama, Pjotr Prins
  • Organizer: The 13th Annual Bioinformatics Open Source Conference
  • Place of Presentation: Long Beach Convention Center, Long Beach, CA, USA
• [Presentation] The Ruby UCSC API: accessing the UCSC Genome Database using Ruby (2012)
  • Author(s): Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul J.P. Bonnal, Koh-ichiro Yoshiura
  • Organizer: 20th Annual International Conference on Intelligent Systems for Molecular Biology
  • Place of Presentation: Long Beach Convention Center, Long Beach, CA, USA
• [Presentation] 5500 SOLiD を使ったヒトエクソーム解析データ処理の実際 (2012)
  • Author(s): 三嶋博之
  • Organizer: NGS現場の会第二回研究会
  • Place of Presentation: 大阪市ホテル阪急エキスポパーク
• [Presentation] ヒトゲノム変異解析ワークフローにおける公共データベース活用 (2012)
  • Author(s): 三嶋博之
  • Organizer: 第３５回日本分子生物学会年会
  • Place of Presentation: 福岡市福岡国際会議場・マリンメッセ福岡
• [Presentation] (教育講演６）次世代シークエンサーを用いたDisease Gene Hunting (2012)
  • Author(s): 三嶋博之
  • Organizer: 第２４回日本小児口腔外科学会総会・学術大会
  • Place of Presentation: 名古屋市愛知学院大学
  • Invited
• [Presentation] 5500 SOLiDを使ったヒトエクソーム解析データ処理の実際 (2012)
  • Author(s): 三嶋博之
  • Organizer: NGS現場の会第二回研究会
  • Place of Presentation: 大阪市ホテル阪急エキスポパーク
• [Presentation] Pwrakeを使ったヒト変異解析ワークフロー管理 (2011)
  • Author(s): 三嶋博之
  • Organizer: 次世代シークエンサ現場の会第一回研究会
  • Place of Presentation: 熱海市
• [Presentation] SNPマイクロアレイを用いたホモザイゴシティマッピング (2011)
  • Author(s): 三嶋博之, 黒滝直弘, 木下晃, 金澤伸雄, 井田弘明, 吉浦孝一郎
  • Organizer: 日本人類遺伝学会第56回大会
  • Place of Presentation: 千葉市幕張メッセ
• [Presentation] The Ruby UCSC API: accessing the UCSC Genome Database using Ruby (2011)
  • Author(s): Mishima H, Aerts J, Yoshiura K
  • 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
• [Remarks]
  • URL: https://github.com/misshie/bioruby-ucsc-api
• [Remarks] The Ruby UCSC API
  • URL: https://github.com/misshie/bioruby-ucsc-api
• [Remarks]
  • URL: https://github.com/misshie