{"id":"hum0103","secondaryIds":[],"version":3,"url":"https://humandbs.dbcls.jp/research/hum0103/v3","datePublished":"2021-07-13","versions":[{"version":1,"datePublished":"2018-02-27"},{"version":2,"datePublished":"2019-06-21"},{"version":3,"datePublished":"2021-07-13"},{"version":4,"datePublished":"2022-01-18"}],"title":{"ja":"シークエンス解析によるがんゲノム研究：胆道がん","en":"Genome sequencing analysis for biliary tract cancer"},"summary":{"aims":{"ja":"日本人の胆道がんにおけるゲノム変異を探索する","en":"To investigate genomic alterations of Japanese biliary tract cancers"},"methods":{"ja":"胆道がん切除切片における非腫瘍組織（正常組織）および腫瘍組織より抽出したDNAを使用したNGSライブラリーを作成後、Illumina HiSeq 2000/2500、NovaSeq 6000にて塩基配列を決定する。","en":"DNAs were extracted from biliary tract cancer and paired non-cancer (normal) tissues. NGS libaraies were prepared by using TruSeq DNA Sample Prep kit (Illumina) for whole genome sequencing (WGS) and Nextera Rapid Capture kit (Illumina) / Agilent SureSelect Exome V5 kit for whole exome sequencing (WES). Sequencing was perfomred by Illumina HiSeq 2000/2500 or NovaSeq 6000."},"targets":{"ja":"胆道がん症例の腫瘍組織および非腫瘍組織のDNA","en":"WGS and WES data of Japanese biliary tract cancer patients."},"url":{"ja":null,"en":null}},"listingSummary":{},"releaseNote":{"ja":"JGAD000117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 JGAD000117 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":"Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations","doi":"https://doi.org/10.1016/j.jhep.2018.01.009","datasets":["JGAD000117","JGAD000118"]}],"datasets":["JGAD000117","JGAD000403","JGAD000118"],"controlledAccessUsers":[{"principalInvestigator":{"ja":"柴田 龍弘","en":"Tatsuhiro Shibata"},"affiliation":{"ja":"がんゲノミクス研究分野, 国立がん研究センター研究所","en":"Division of Cancer Genomics, National Cancer Center Research Institute"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"ゲノム異常解析に基づく､肝がん､膵がん､肺がん､胃がん､大腸がん､胆道がん､乳がん､食道がん､卵巣が\nん､子宮がん､膀胱がん､頭頸部がん､骨軟部肉腫の発生･進展の分子機構の解明","en":"Study the molecular mechanics of tumor development and progression with analysing genomic mutations of liver, pancreatic, lung, colorectal, biliary tract, breast,\nesophageal, ovarian, cervical, bladder, renal, head-and-neck and bone cancers."},"periodStart":"2018-09-11","periodEnd":"2018-11-28","datasets":["JGAD000117","JGAD000118"]},{"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":["JGAD000117"]},{"principalInvestigator":{"en":"Justo Lorenzo Bermejo"},"affiliation":{"en":"Statistical Genetics Research Group. Institute of Medical Biometry, Heidelberg University Hospital"},"country":{"ja":"ドイツ","en":"Germany"},"researchTitle":{"en":"Genomic characterization of gallbladder tumors from patients worldwide"},"periodStart":"2022-10-13","periodEnd":"2028-12-31","datasets":["JGAD000118","JGAD000505"]},{"principalInvestigator":{"ja":"山本 拓也","en":"Takuya Yamamoto"},"affiliation":{"ja":"プレシジョン免疫プロジェクト, 国立研究開発法人 医薬基盤・健康・栄養研究所","en":"Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"新規がん抗原の同定に基づく消化器がんおよび悪性黒色腫（メラノーマ）に対するワクチン開発基盤研究\r\n","en":"Basic research for vaccine development against gastrointestinal cancer and malignant melanoma based on the identification of novel cancer antigens\r\n"},"periodStart":"2024-11-12","periodEnd":"2026-03-31","datasets":["JGAD000117","JGAD000118","JGAD000504","JGAD000505","JGAD000506"]}]}