{"id":"hum0068","version":8,"url":"https://humandbs.dbcls.jp/research/hum0068/v8","datePublished":"2023-09-22","versions":[{"version":1,"datePublished":"2017-07-10"},{"version":2,"datePublished":"2020-10-19"},{"version":3,"datePublished":"2021-12-14"},{"version":4,"datePublished":"2022-03-23"},{"version":5,"datePublished":"2022-12-27"},{"version":6,"datePublished":"2023-02-10"},{"version":7,"datePublished":"2023-06-19"},{"version":8,"datePublished":"2023-09-22"},{"version":9,"datePublished":"2024-04-10"}],"title":{"ja":"ゲノム解析に基づく肺がんの発生・進展の分子機構の解明","en":"Cancer genomics for elucidation of molecular mechanisms of carcinogenecis and progression in lung cancer"},"summary":{"aims":{"ja":"ナノポアシークエンサーMinIONを用いた肺腺がんの変異検出手法の確立","en":"Establishing a method for detecting variations of lung adenocarcinoma"},"methods":{"ja":"【PCR amplicon Seq】ナノポアシークエンサーMinIONによるアンプリコンシークエンス\n【WGS】NovaSeqおよびナノポアシークエンサーPromethIONによるwhole-genomeシークエンスデータを用いた新規構造異常の同定と評価\n【RNA-seq】NovaSeq、HiSeqおよびナノポアシークエンサーPromethIONによるRNAシークエンス\n【scDNA-seq】NovaSeqによるsingle cellのwhole-genomeシークエンス\n【Target Capture】NovaSeqによるTarget Captureシークエンス\n【Visium Spatial Gene Expression】Illuminaによる空間トランスクリプトームVisiumシークエンス\n【Multiplex Fluorescence Immunostaining】PhenoCyclerシステムによる多重蛍光免疫染色\n【Xenium In Situ Gene Expression】10xによる高性能in situ遺伝子発現マッピング","en":"[PCR amplicon Seq] Amplicon sequencing by using of MinION (Nanopore)\n[WGS] Whole-genome sequencing for identification and characterization of a novel class of structual aberrations in cancers by using of NovaSeq and PromethION.\n[RNA-seq] RNA sequencing by using of NovaSeq, HiSeq and PromethION.\n[scDNA-seq] Single cell DNA sequencing by using of NovaSeq.\n[Target Capture] Target capture sequencing by using of NovaSeq.\n[Visium Spatial Gene Expression] Spatial transcriptome sequencing Visium (10x Genomics)\n[Multiplex Fluorescence Immunostaining] Multiplex fluorescence immunostaining by PhenoCycler (Akoya Biosciences)\n[Xenium In Situ Gene Expression] High-performance in situ gene expression mapping Xenium (10x Genomics)"},"targets":{"ja":"肺腺がん8症例＋21症例＋74症例＋20症例","en":"Lung adenocarcinoma"},"url":{"ja":[{"url":"https://kero.hgc.jp/","text":"https://kero.hgc.jp/"}],"en":[{"url":"https://kero.hgc.jp/","text":"https://kero.hgc.jp/"}]}},"listingSummary":{},"releaseNote":{"ja":"肺腺がん1症例の腫瘍組織に対して実施した10xによるXenium高性能in situ遺伝子発現マッピングデータをcsv、h5、html、json、mtx、tiff、parquet、tsv、xenium、zarrファイルにて提供する。","en":"Tumor tissue of a lung adenocarcinoma patient was used for Xenium In Situ Gene Expression Assay. Csv, h5, html, json, mtx, tiff, parquet, tsv, xenium, and zarr files are provided."},"dataProviders":[{"name":{"ja":"河野 隆志","en":"Takashi Kono"},"organization":{"name":{"ja":"国立がん研究センター ゲノム生物学研究分野","en":"Division of Genome Biology, National Cancer Center Research Institute"}}}],"researchProjects":[],"grants":[{"title":{"ja":"先進ゲノム解析研究推進プラットフォーム","en":"Platform for Advanced Genome Science"},"agency":{"ja":"科学研究費助成事業 新学術領域研究","en":"KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas"},"grantIds":["16H06279"]},{"title":{"ja":"がんシステムの新次元俯瞰と攻略; ナノポアシークエンサーによるがん細胞の変異検出およびフェーズ情報解析手法の確立","en":"Conquering cancer through neo-dimensional systems understanding; Sequencing and phasing cancer mutations using a nanopore sequencer MinION"},"agency":{"ja":"科学研究費助成事業 新学術領域研究","en":"KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas"},"grantIds":["16H01582"]},{"title":{"ja":"ナノポア型長鎖シークエンサーを駆使したがんゲノム異常における新規概念の創出および患者層別化手法の開発","en":"Stratification of cancer patients by novel genomic aberrations using long-read sequencing technologies"},"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":["JP19cm0106539"]},{"title":{"ja":"ロングリード技術を駆使した非小細胞肺癌におけるがんゲノム多様性・進化に関する研究","en":"Study of genomic evolution of non-small cell lung cancers using long read sequencing technologies"},"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":["JP21cm0106582"]},{"title":{"ja":"ロングリード技術による肺がんゲノム・エピゲノム不均一性と微小環境ストレスの関係性解明に関する研究開発","en":"Study of heterogeneity of genomic and epigenomic aberrations and association with microenvironment in lung cancer tissues"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療加速化研究事業（P-PROMOTE）","en":"Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP23ama221522"]}],"relatedPublications":[{"title":"Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer.","doi":"https://doi.org/10.1093/dnares/dsx027","datasets":["JGAD000065"]},{"title":"Long-read sequencing for non-small-cell lung cancer genomes","doi":"https://doi.org/10.1101/gr.261941.120","datasets":["JGAD000252","JGAD000253"]},{"title":"Phasing analysis of lung cancer genomes using a long read sequencer","doi":"https://doi.org/10.1038/s41467-022-31133-6","datasets":["JGAD000252","JGAD000253","JGAD000463"]},{"title":"Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma","doi":"https://doi.org/10.1038/s41467-023-43732-y","datasets":["JGAD000252","JGAD000253","JGAD000463","JGAD000696"]}],"datasets":["JGAD000065","JGAD000670","JGAD000252","JGAD000696","JGAD000253","JGAD000463"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Youping Deng"},"affiliation":{"en":"Department of Complementary & Integrative Medicine, University of Hawaii Manoa"},"country":{"ja":"アメリカ合衆国 (ハワイ州)","en":"Hawaii, United States"},"researchTitle":{"ja":"Identification of driver genes and somatic mutations for lung cancer diagnosis and prognosis","en":"Identification of driver genes and somatic mutations for lung cancer diagnosis and prognosis"},"periodStart":"2018-10-04","periodEnd":"2029-07-10","datasets":["JGAD000252"]},{"principalInvestigator":{"ja":"有田 正規","en":"Masanori Arita"},"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":"DDBJ センターと NBDC による JGA 解析データの提供","en":"Provision of processed JGA data analyzed by DDBJ Center and NBDC"},"periodStart":"2021-10-07","periodEnd":"2030-03-31","datasets":["JGAD000065","JGAD000252","JGAD000253","JGAD000463","JGAD000696"]},{"principalInvestigator":{"ja":"中岡 博史","en":"Hirofumi Nakaoka"},"affiliation":{"ja":"腫瘍ゲノム研究部, 公益財団法人佐々木研究所","en":"Department of Cancer Genome Research, Sasaki Institute"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"肺がん遺伝子解析研究","en":"Genetic analysis of lung cancer"},"periodStart":"2022-08-17","periodEnd":"2026-07-23","datasets":["JGAD000252"]},{"principalInvestigator":{"en":"Gang Fang"},"affiliation":{"en":"Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai"},"country":{"ja":"アメリカ合衆国","en":"United States"},"researchTitle":{"en":"NBDC data 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lung cancer"},"periodStart":"2025-05-20","periodEnd":"2028-03-31","datasets":["JGAD000252","JGAD000253","JGAD000463","JGAD000696"]},{"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、卵巣がん、子宮がん、膀胱がん、腎臓がん、頭頚部がん、骨軟部肉腫、悪性黒色腫の発生・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, gastric, colorectal, biliary tract, breast, esophageal, ovarian, cervical, bladder, renal, head-and-neck and bone cancers."},"periodStart":"2025-01-27","periodEnd":"2026-03-31","datasets":["JGAD000252","JGAD000696"]},{"principalInvestigator":{"ja":"唐崎 隆弘","en":"TAKAHIRO KARASAKI"},"affiliation":{"ja":"呼吸器外科, 東京大学医学部附属病院","en":"Department of Thoracic Surgery, The University of Tokyo Hospital"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"高感度な循環腫瘍シグナル検出法の開発","en":"Development of a high-sensitivity assay for enhanced detection of circulating tumor signal"},"periodStart":"2026-02-12","periodEnd":"2030-11-30","datasets":["JGAD000252","JGAD000253","JGAD000463","JGAD000670","JGAD000696","JGAD000887"]}]}