{"id":"hum0158","version":3,"url":"https://humandbs.dbcls.jp/research/hum0158/v3","datePublished":"2021-07-13","versions":[{"version":1,"datePublished":"2018-10-22"},{"version":2,"datePublished":"2019-06-21"},{"version":3,"datePublished":"2021-07-13"}],"title":{"ja":"シークエンス解析によるがんゲノム研究：肝臓がん","en":"Genome sequencing analysis for liver cancer"},"summary":{"aims":{"ja":"日本人の肝臓がんにおけるゲノム変異を探索する","en":"To investigate genomic alterations of Japanese liver cancers"},"methods":{"ja":"肝臓がん切除切片における腫瘍組織および非腫瘍組織または末梢血より抽出したDNAもしくはRNAを使用したNGSライブラリーを作成後、Illumina HiSeqまたは Genome Analyzerにて塩基配列を決定する。","en":"DNAs and RNAs were extracted from liver cancer tissues and paired non-cancer (normal) tissues or blood samples. NGS libaraies were prepared for whole genome sequencing (WGS) and RNA-seq. Sequencing was perfomred by Illumina HiSeq or Genome Analyzer."},"targets":{"ja":"肝臓がん（肝細胞がん、肝内胆管がん、混合型肝がん）患者の非腫瘍組織および腫瘍組織のDNA・RNA","en":"DNAs and RNAs extracted from cancer tissues and normal tissues of Japanese liver cancer patients."},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列決定\n発現","en":"Sequencing, Expression profiling"},"targets":{"ja":"肝臓癌：263症例\n（日本人）","en":"263 liver cancers\n(Japanese)"},"typeOfData":{"ja":"NGS\n（WGS、RNA-seq）","en":"NGS\n(WGS, RNA-seq)"}},"releaseNote":{"ja":"JGAD000228に含まれるwhole genome sequencing解析データに対し、GEnome Medical alliance Japan（GEM Japan, GEM-J）の取り組みとして、GATK Best Practicesに準拠した方法により、GRCh37の参照ゲノム配列へのマッピングおよびバリアント検知を実施した際のbam/gvcfデータを追加した。","en":"Whole genome sequencing analyzed data included in the JGAD000228 were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. Bam files and gvcf files were added. This project is an initiative of the GEnome Medical alliance Japan (GEM Japan, GEM-J)."},"dataProviders":[{"name":{"ja":"中川 英刀","en":"Hidewaki Nakagawa"},"organization":{"name":{"ja":"理化学研究所 生命医科学研究センター","en":"RIKEN Center for Integrative Medical Sciences"}}}],"researchProjects":[],"grants":[],"relatedPublications":[{"title":"Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.","doi":"https://doi.org/10.1038/ng.3547","datasets":["JGAD000228","JGAD000229"]},{"title":"Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes.","doi":"https://doi.org/10.1016/j.ccell.2019.04.007","datasets":["JGAD000228","JGAD000229"]}],"datasets":["JGAD000228","JGAD000404","JGAD000229"],"controlledAccessUsers":[{"principalInvestigator":{"ja":"山本 雅之","en":"Masayuki Yamamoto"},"affiliation":{"ja":"東北メディカル・メガバンク機構, 東北大学","en":"Tohoku Medical Megabank Organization"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"日本人全ゲノムデータベースの構築","en":"Construction of Japanese whole genome database"},"periodStart":"2019-06-24","periodEnd":"2022-04-15","datasets":["JGAD000228"]},{"principalInvestigator":{"ja":"寶珍 輝尚","en":"Teruhisa Hochin"},"affiliation":{"ja":"情報工学・人間科学系, 京都工芸繊維大学","en":"Faculty of Information and Human Sciences, Kyoto Institute of Technology"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"機械学習によるヒトゲノム変異の解析","en":"Analysis of mutation of human genome using Machine Learning"},"periodStart":"2019-07-09","periodEnd":"2022-03-23","datasets":["JGAD000228","JGAD000229"]},{"principalInvestigator":{"ja":"白石 航也","en":"Kouya Shiraishi"},"affiliation":{"ja":"ゲノム生物学研究分野, 国立研究開発法人国立がん研究センター研究所","en":"Division of Genome Biology, National Cancer Research Institute"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"ゲノム解析に基づく宿主並びに腫瘍における免疫応答ネットワーク機構の解明","en":"Elucidation of immune-system networks between host and tumor based on genomic analysis"},"periodStart":"2019-08-05","periodEnd":"2029-03-31","datasets":["JGAD000228","JGAD000229"]},{"principalInvestigator":{"ja":"小笠原 理","en":"Osamu Ogasawara"},"affiliation":{"ja":"生命情報・DDBJセンター, 国立遺伝学研究所","en":"Bioinformation and DDBJ Center, National Institute of Genetics"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"JGA/AGD ゲノムデータを利用したヒトゲノム解析ワークフローの評価","en":"Evaluation of human genome analysis workflow using JGA/AGD genome data."},"periodStart":"2019-10-11","periodEnd":"2024-07-05","datasets":["JGAD000228","JGAD000229"]},{"principalInvestigator":{"en":"Robert Tsai"},"affiliation":{"en":"Institute of Biosciences & Technology, Texas A&M Health Science Center"},"country":{"ja":"アメリカ合衆国 (テキサス州)","en":"Texas, United States"},"researchTitle":{"en":"Genome-wide Discovery of new Plasma DNA Methylation Markers for Tracking the Progression of NAFLD to NASH and HCC"},"periodStart":"2020-11-09","periodEnd":"2023-07-25","datasets":["JGAD000229"]},{"principalInvestigator":{"en":"Kichoon Lee"},"affiliation":{},"country":{"ja":"アメリカ合衆国","en":"United States"},"researchTitle":{"en":"Access to the National Bioscience Database Center"},"periodStart":"2021-05-31","periodEnd":"2024-12-31","datasets":["JGAD000228","JGAD000229"]},{"principalInvestigator":{"en":"Jinyan Huang"},"affiliation":{"en":"Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China. Biomedical big data center, the First Affiliated Hospital, Zhejiang University"},"country":{"ja":"中国","en":"China"},"researchTitle":{"en":"Comprehensive analysis of alternative splicing in malignant tumors"},"periodStart":"2022-03-15","periodEnd":"2024-01-01","datasets":["JGAD000228"]},{"principalInvestigator":{"ja":"浜田 道昭","en":"Michiaki Hamada"},"affiliation":{"ja":"浜田研究室, 理工学術院, 早稲田大学","en":"Hamada Laboratory, Faculty of Science and Engineering, Waseda University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"RNA標的創薬データベースの構築","en":"Construction of RNA-targeted Drug Discovery Database"},"periodStart":"2023-01-05","periodEnd":"2027-10-31","datasets":["JGAD000229"]}]}