{"id":"hum0153","version":1,"url":"https://humandbs.dbcls.jp/research/hum0153/v1","datePublished":"2019-09-20","versions":[{"version":1,"datePublished":"2019-09-20"}],"title":{"ja":"希少腫瘍の発症・予後に関する遺伝子の網羅的解析研究","en":"Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis"},"summary":{"aims":{"ja":"脱分化型脂肪肉腫および腱鞘巨細胞種の疾患発症・予後に関連する遺伝子の探索","en":"Identification of genetics alterations of dedifferentiated liposarcoma and tendon sheath giant cell tumors (TSGCT)"},"methods":{"ja":"腫瘍組織および同一患者の非腫瘍組織（血液もしくは周辺正常組織）より抽出したDNA・RNAを用いたWhole Exome Sequencing（WES）、RNA-seq、ならびにTarget Capture Sequencing","en":"DNAs and RNAs were extracted from tumor and paired non-tumor tissues (peripheral blood or adjacent normal tissues). Whole exome sequencing (WES), RNA sequencing, and target capture sequencing were performed by HiSeq 2500 or MiSeq (Illumina)."},"targets":{"ja":"脱分化型脂肪肉腫 29症例\n・腫瘍組織：脱分化型成分29検体、高分化型成分8検体（WES+RNA seq）\n・非腫瘍組織（末梢血）：29検体（WES）\n腱鞘巨細胞種 36症例\n・腫瘍組織：10検体（WES）、18検体（RNA seq）、34検体（Target seq）\n・非腫瘍組織：10検体（WES）、34検体（Target seq）","en":"29 dedifferentiated liposarcoma and 36 TSGCT patients"},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列決定\n発現","en":"Sequencing, Expression profiling"},"targets":{"ja":"脱分化型脂肪肉腫：28症例\n腱鞘巨細胞種：36症例\n（日本人）","en":"28 Dedifferentiated liposarcoma patients\n36 Tendon sheath giant cell tumor patient\n(Japanese)"},"typeOfData":{"ja":"NGS\n（Exome、RNA-seq、Target Capture）","en":"NGS\n(Exome, RNA-seq, Target Capture)"}},"releaseNote":{"ja":"脱分化型脂肪肉腫および腱鞘巨細胞種の腫瘍組織及び非腫瘍組織（末梢血もしくは周辺正常組織）から抽出したDNA・RNAを用いた全エクソン解析、全トランスクリプトーム解析およびターゲットキャプチャーシークエンス解析結果をfastqおよびbamファイルにて提供する。\n脱分化型脂肪肉腫および同一患者の末梢血よりDNA・RNAを抽出後、Agilent SureSelect XT Human All Exon V5 + IncRNA kit（WES）、TruSeq Stranded mRNA Prep kit または TruSeq RNA Access Library Prep kit (RNA seq)にてライブラリを作成し、Illumina HiSeq 2500にて配列解読を行った。\n腱鞘巨細胞種および同一患者の非腫瘍組織（周辺正常組織）よりDNA・RNAを抽出後、Agilent SureSelect Exome V5 kit（WES）、TruSeq Stranded mRNA Prep kitもしくはTruSeq RNA Access Library Prep kit (RNA seq)にてライブラリを作成しIllumina HiSeq 2500にてシークエンスを行った。Target sequenceはCBL遺伝子の全エクソン領域をPCRにて増幅後、TruSeq Nano DNA Library Prepkitにてライブラリーを作成、MiSeqにて配列解読を行った。","en":"DNAs and RNAs were extracted from tumor and paired non-tumor (or peripheral blood) tissues of dedifferentiated liposarcoma and Tendon sheath giant cell tumors (TSGCT). Data are provided as bam and fastq files.\n[dedifferentiated liposarcoma / well-dediffirentiated liposarcoma]\nNGS libaraies were prepared by using of Agilent SureSelect XT Human All Exon V5 + IncRNA kit for DNA and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit for RNA. Whole exome sequencing (WES) and RNA Sequencing were perfomred by Illumina HiSeq 2500.\n[TSGCT]\nNGS libaraies were prepared by using of Agilent SureSelect Exome V5 kit for DNA and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit for RNA, and PCR + TruSeq Nano DNA Library Prepkit for DNA. WES, RNA-seq, and Target Capture Sequencing were perfomred by Illumina HiSeq 2500 or MiSeq."},"dataProviders":[{"name":{"ja":"松田 浩一","en":"Koichi Matsuda"},"organization":{"name":{"ja":"東京大学 大学院新領域創成科学研究科","en":"Graduate School of Frontier Sciences, The University of Tokyo"}}},{"name":{"ja":"平田 真","en":"Makoto Hirata"},"organization":{"name":{"ja":"東京大学 医科学研究所 ヒトゲノム解析センター","en":"Institute of Medical Science, The University of Tokyo"}}}],"researchProjects":[{"name":{"ja":"骨軟部腫瘍ゲノムコンソーシアム","en":"Japan Sarcome genome consortium"},"url":{"ja":null,"en":null}}],"grants":[{"title":{"ja":"ゲノム解析による骨軟部腫瘍の多様性の解明と治療標的・バイオマーカーの探索","en":"Genomic analysis of bone and soft tissue tumors and screening of their therapeutic targets and biomarkers"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療創生研究事業（P-CREATE）","en":"Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP17cm0106520"]},{"title":{"ja":"ゲノム解析による骨軟部腫瘍の多様性の解明と治療標的・バイオマーカーの探索","en":"Genomic analysis of bone and soft tissue tumors and screening of their therapeutic targets and biomarkers"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療創生研究事業（P-CREATE）","en":"Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP18cm0106535"]},{"title":{"ja":"軟部肉腫に対するゲノム解析による新規治療標的分子の探索","en":"Identification of novel therapeutic target of soft tissue tumors by genomic analysis."},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん研究シーズ戦略的育成プログラム（P-DIRECT）","en":"Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP15cm0106141"]},{"title":{"ja":"骨軟部腫瘍における診断マーカーの同定と腫瘍概念の再構築を目指した融合遺伝子の探索","en":"Analysis of fusion transcripts in bone and soft tissue tumors for indentification of novel disease biomarker and reorganization of disease classification."},"agency":{"ja":"科学研究費助成事業 基盤研究（A）","en":"KAKENHI Grant-in-Aid for Scientific Research (A)"},"grantIds":["16H02676"]}],"relatedPublications":[{"title":"Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations","doi":"https://doi.org/10.1002/ijc.32421","datasets":["JGAD000257","JGAD000258"]}],"datasets":["JGAD000257","JGAD000258"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Valerie Brunton"},"affiliation":{"en":"Edinburgh Cancer Research UK Centre, University of Edinburgh"},"country":{"ja":"イギリス","en":"United Kingdom"},"researchTitle":{"en":"Genomic analysis of soft tissue sarcoma"},"periodStart":"2021-07-09","periodEnd":"2025-04-17","datasets":["JGAD000257","JGAD000258"]},{"principalInvestigator":{"en":"William Tapper"},"affiliation":{"en":"Human development and health, University of Southampton"},"country":{"ja":"イギリス","en":"United Kingdom"},"researchTitle":{"en":"Utilising sarcoma omic information to identify disease gene networks and associated novel therapies for patients"},"periodStart":"2022-11-14","periodEnd":"2025-10-20","datasets":["JGAD000257"]},{"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":["JGAD000257","JGAD000258"]}]}