{"id":"hum0160","version":2,"url":"https://humandbs.dbcls.jp/research/hum0160/v2","datePublished":"2021-07-13","versions":[{"version":1,"datePublished":"2019-05-28"},{"version":2,"datePublished":"2021-07-13"}],"title":{"ja":"シークエンス解析によるがんゲノム研究：食道がん","en":"Genome sequencing analysis for esophageal squamous cell carcinoma"},"summary":{"aims":{"ja":"日本人の食道がんにおけるゲノム変異を探索する","en":"To investigate genomic alterations of Japanese esophageal squamous cell carcinomas"},"methods":{"ja":"食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/X Fiveにて塩基配列を決定する。","en":"DNAs were extracted from esophageal squamous cell carcinoma tissues and paired non-cancer (normal) tissues. NGS libaraies were prepared by using TruSeq Nano DNA Low Throughput Library Prep Kit for whole genome sequencing (WGS). Sequencing was perfomred by Illumina HiSeq 2000/2500/X Five."},"targets":{"ja":"食道がん患者の非腫瘍組織および腫瘍組織のDNA","en":"DNAs extracted from cancer tissues and non-cancer tissues of Japanese esophageal squamous cell carcinoma patients."},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列決定","en":"Sequencing"},"targets":{"ja":"食道癌：20症例\n（日本人）","en":"20 esophageal squamous cell carcinomas\n(Japanese)"},"typeOfData":{"ja":"NGS\n（WGS）","en":"NGS\n(WGS)"}},"releaseNote":{"ja":"JGAD000233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 JGAD000233 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":[],"datasets":["JGAD000233","JGAD000405"],"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":["JGAD000233"]},{"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":["JGAD000233"]}]}