{"id":"hum0017","version":1,"url":"https://humandbs.dbcls.jp/research/hum0017/v1","datePublished":"2016-02-22","versions":[{"version":1,"datePublished":"2016-02-22"}],"title":{"ja":"中枢神経原発悪性リンパ腫のエクソーム解析","en":"Exome sequencing of primary central nervous system lymphoma"},"summary":{"aims":{"ja":"中枢神経原発悪性リンパ腫（primary central nervous system lymphoma: PCNSL）は原因不明な脳内リンパ腫であり、有効な治療に乏しい。全エクソン配列解析を行うことでタンパクコード遺伝子の体細胞変異を発見し、PCNSLのがん化機構の解明を目指す。","en":"Primary central nervous system lymphoma (PCNSL) is a rare type lymphoma confined to the central nervous system. Effective therapies against PCNSL are severely limited. By conducting whole exome sequencing of PCNSL specimens, we aimed to reveal molecular mechanism underlying PCNSL carcinogenesis."},"methods":{"ja":"脳外科手術によって摘出されたPCNSL試料と、同一患者より得られた末梢血単核球（計41ペア）よりゲノムDNAおよびRNAを抽出し、Exome解析、RNA-seq解析を行った。","en":"Genomic DNA was extracted from surgically resected PCNSL tissues and paired peripheral blood, and subjected to Exome analysis. RNA extracted from surgically resected PCNSL tissues was subjected to RNA-seq analysis."},"targets":{"ja":"PCNSL患者：41症例","en":"Forty-one cases diagnosed to have PCNSL"},"url":{"ja":[{"url":"https://www.ncc.go.jp/jp/ri/division/genetics/index.html","text":"https://www.ncc.go.jp/jp/ri/division/genetics/index.html"}],"en":[{"url":"https://www.ncc.go.jp/en/ri/division/genetics/index.html","text":"https://www.ncc.go.jp/en/ri/division/genetics/index.html"}]}},"listingSummary":{"methods":{"ja":"配列決定\n発現","en":"Sequencing, expression profiling"},"targets":{"ja":"PCNSL：41症例\n（日本人）","en":"41 PCNSLs\n(Japanese)"},"typeOfData":{"ja":"NGS\n（Exome、RNA-seq）","en":"NGS\n(Exome, RNA-seq)"}},"releaseNote":{"ja":"このバージョンでは、脳外科手術によって摘出されたPCNSL試料と、同一患者より得られた末梢血単核球のペアから抽出したゲノムDNAおよびPCNSL試料から抽出したRNAを対象とし、以下の解析を行った。\n• Exome（41症例）\nSureSelect ver. 5（Agilent）によりエクソン領域を絞り込み、HiSeq 2000（Illumina）のPaired-end modeにより両端100-105塩基の配列を決定、bam file形式にて提供する。\n• RNA-seq（30症例）\nNEBNext Ultra Directional RNA Library Prep KitによるRNAライブラリ作製後、HiSeq 2000（Illumina）のPaired-end modeにより平均長100塩基を解読した（fastq file形式にて提供）。","en":"• Exome: 41 samples\nGenomic DNAs were extracted from surgically resected PCNSL tissues and paired peripheral blood cells, and subjected to the enrichment of exon fragments by using SureSelect system (Agilent). They were sequenced 100-105 bases from both ends with a HiSeq 2000 system (Illumina) with paired-end mode (bam files).\n• RNA-seq: 30 samples\nRNAs extracted from surgically resected PCNSL tissues were used for RNA-seq (fastq).\nRNA liberally builded using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and read by Illumina HiSeq 2000 (paired-end: 100 bp)."},"dataProviders":[{"name":{"ja":"間野 博行","en":"Hiroyuki Mano"},"organization":{"name":{"ja":"国立がん研究センター研究所 細胞情報学分野","en":"Division of Cellular Signaling, National Cancer Center Research Institute"}}}],"researchProjects":[{"name":{"ja":"PCNSL Genomic Analysis","en":"PCNSL Genomic Analysis"},"url":{"ja":[{"url":"https://www.ncc.go.jp/jp/ri/division/genetics/index.html","text":"https://www.ncc.go.jp/jp/ri/division/genetics/index.html"}],"en":[{"url":"https://www.ncc.go.jp/en/ri/division/genetics/index.html","text":"https://www.ncc.go.jp/en/ri/division/genetics/index.html"}]}}],"grants":[{"title":{"ja":"がん治療標的探索プロジェクト","en":"Project for novel therapeutic targets in cancer"},"agency":{"ja":"日本医療研究開発機構 革新的先端研究開発支援事業インキュベートタイプ（AMED-LEAP）","en":"Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP)"},"grantIds":null}],"relatedPublications":[{"title":"Genomic characterization of primary central nervous system lymphoma","doi":"https://doi.org/10.1007/s00401-016-1536-2","datasets":["JGAD000021"]}],"datasets":["JGAD000021"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Li WEI"},"affiliation":{"en":"National Key Laboratory of Birth Defects 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Fudan University"},"country":{"ja":"中国","en":"China"},"researchTitle":{"en":"Genomic and molecular characterization of primary central\r\nnervous system lymphoma"},"periodStart":"2022-06-13","periodEnd":"2023-10-11","datasets":["JGAD000021"]},{"principalInvestigator":{"ja":"齋藤 竜太","en":"Ryuta Saito"},"affiliation":{"ja":"脳神経外科学, 名古屋大学大学院医学系研究科","en":"Neurosurgery, Nagoya University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"脳腫瘍の発生、進展に関わる遺伝子異常と腫瘍微小環境の形成に関する研究\r\n","en":"Genetic analysis during the progression of brain tumors and its impact on tumor microenvironment formation"},"periodStart":"2022-10-13","periodEnd":"2027-03-31","datasets":["JGAD000021"]},{"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 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lymphoma"},"periodStart":"2025-09-02","periodEnd":"2027-12-31","datasets":["JGAD000021"]}]}