Genomics Approach to orofacial clefts focusing theubiquitin-proteasome system

2013 Fiscal Year Final Research Report

• 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
• 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

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
• [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] 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
• [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
• [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
• [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
  • Year and Date: 20120715-17
• [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
  • Year and Date: 20120713-14
• [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
  • Year and Date: 20120713-14
• [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
  • Year and Date: 20120523-25
• [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
• [Remarks]
  • URL: https://github.com/misshie/bioruby-ucsc-api