{"id":"hum0068","version":1,"url":"https://humandbs.dbcls.jp/research/hum0068/v1","datePublished":"2017-07-10","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8症例の腫瘍組織から抽出したRNAを対象とし、逆転写反応の後にPCRによって目的領域を増幅した。Nanopore Sequencing Kitにてライブラリを作製し、MinION（Oxford Nanopore Technologies社）を用いたシークエンスの結果をFastqファイルにて提供する。","en":"RNAs were extracted from 8 lung adenocarcinoma patients. After reverse transcription reaction, target regions were amplified by PCR. Libraries were prepared using Nanopore Sequencing Kit and DNA sequencing was performed by using of MinION (Oxford Nanopore Technologies). Fastq files are provided (single-end)."},"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","JGAD000252","JGAD000253","JGAD000670","JGAD000887"],"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 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