{"id":"hum0182","version":4,"url":"https://humandbs.dbcls.jp/research/hum0182/v4","datePublished":"2021-11-12","versions":[{"version":1,"datePublished":"2019-06-20"},{"version":2,"datePublished":"2020-05-12"},{"version":3,"datePublished":"2021-01-06"},{"version":4,"datePublished":"2021-11-12"},{"version":5,"datePublished":"2022-05-27"}],"title":{"ja":"全ゲノムシークエンスデータの解析による変異と遺伝的多様性の包括的解析","en":"Comprehansive analysis of somatic mutations and genetic variations with whole genome sequencing"},"summary":{"aims":{"ja":"全ゲノムシークエンスによる構造異常の包括的解析","en":"Indetification of stractural variations by using of long read whole genome sequencing data"},"methods":{"ja":"長鎖一分子シークエンサー（nanopore）およびHiSeq 2000、Genome Analyzer IIx（Illumina）による全ゲノムシークエンス","en":"Whole genome sequencing with Nanopore sequencer, HiSeq 2000 and Genome Analyzer IIx (Illumina)"},"targets":{"ja":"① 国際がんゲノムコンソーシアム（ICGC）の際に収集した日本人肝臓がん1症例（RK067）（hum0158）の末梢血（正常細胞）由来DNA\n② HapMap日本人（NA18943）のDNA\n③ 国際がんゲノムコンソーシアム（ICGC）の際に収集した日本人肝臓がん174症例（RK001～RK338）（hum0158）の末梢血（正常細胞）由来DNA\n④ 国際がんゲノムコンソーシアム（ICGC）の際に収集した日本人肝臓がん11症例（RK014、RK019、RK020、RK067、RK085、RK0143、RK147、RK156、RK157、RK167、RK281）（hum0158）の末梢血（正常細胞）および腫瘍組織由来DNA\n⑤ ICGCの際に収集した日本人肝臓がん42症例の腫瘍組織および腫瘍組織周辺の非腫瘍組織由来RNA 、ならびに、乳がん細胞株のRNA","en":"DNA samples from 2 Japanese individuals.\n1) DNA extracted from normal blood cell of a liver cancer patient (ICGC: RK067 [hum0158])\n2) HapMap sample (NA18943)\n3) DNA extracted from normal blood cell of 174 liver cancer patients (ICGC: RK001-RK338 [hum0158])\n4) DNA extracted from tumor tissues and normal blood cell of 11 liver cancer patients (ICGC: RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281 [hum0158])\n5) RNAs derived from 42 Japanese HCCs and 42 matched non-tumor liver tissues collected by ICGC\nRNA from breast cancer cell line MCF-7"},"url":{"ja":null,"en":null}},"listingSummary":{},"releaseNote":{"ja":"国際がんゲノムコンソーシアム（ICGC）の際に収集した日本人肝臓がん11症例の末梢血（正常細胞）および腫瘍組織由来DNA（RK014、RK019、RK020、RK067、RK085、RK0143、RK147、RK156、RK157、RK167、RK281）を対象とし、長鎖シークエンサー（nanopore）による全ゲノムシークエンスを行った際のfast5ファイルを提供する。","en":"Oxford Nanopore long-reads fast5 sequencing data from DNA of 11 Japanese liver cancer patients' (RK014, RK019, RK020, RK067, RK085, RK0143, RK147, RK156, RK157, RK167, RK281) samples and matched normal samples are provided."},"dataProviders":[{"name":{"ja":"藤本 明洋","en":"Akihiro Fujimoto"},"organization":{"name":{"ja":"東京大学大学院 医学系研究科 人類遺伝学教室","en":"Department of Human Genetics, Graduate School of Medicine,The University of Tokyo"}}}],"researchProjects":[{"name":{"ja":"国立研究開発法人日本医療研究開発機構 ゲノム医療実現推進プラットフォーム事業「先端ゲノム研究開発」プロジェクト","en":"Japan Agency for Medical Research and Development (AMED)"},"url":{"ja":null,"en":null}}],"grants":[{"title":{"ja":"先進的シークエンス情報解析技術基盤の開発","en":"Development of advanced data analysis methods for genome sequencing"},"agency":{"ja":"日本医療研究開発機構（AMED） ゲノム医療実現推進プラットフォーム事業","en":"Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP18km0405207"]},{"title":{"ja":"長鎖シークエンス技術を用いた肝癌の転写異常の包括的解析","en":"Comprehensive analysis of full-length transcriptome of liver cancer with a long-reads sequencing technology"},"agency":{"ja":"科学研究費助成事業 基盤研究（B）","en":"KAKENHI Grant-in-Aid for Scientific Research (B)"},"grantIds":["18H02680"]},{"title":{"ja":"ゲノム配列を核としたヤポネシア人の起源と成立の解明","en":"Yaponesian genome"},"agency":{"ja":"科学研究費助成事業 新学術領域研究（研究領域提案型）","en":"KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)"},"grantIds":["18H05511"]},{"title":{"ja":"B型肝炎に関する統合的臨床ゲノムデータベースの構築を目指す研究","en":"Construction of integrated clinical genome database regarding hepatitis B related diseases"},"agency":{"ja":"日本医療研究開発機構（AMED） 臨床ゲノム情報統合データベース整備事業","en":"Program for Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP18kk0205007"]}],"relatedPublications":[{"title":"Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population.","doi":"https://doi.org/10.1186/s13073-019-0656-4","datasets":["JGAD000261","DRA008482"]},{"title":"Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer","doi":"https://doi.org/10.1186/s13073-021-00883-1","datasets":["JGAD000261"]}],"datasets":["JGAD000261","DRA008482"],"controlledAccessUsers":[{"principalInvestigator":{"en":"Shuaicheng Li"},"affiliation":{},"country":{"ja":"香港","en":"Hong Kong"},"researchTitle":{"en":" A new method to construct the haplotypes of viral integration regions based on multiple sequencing data."},"periodStart":"2021-12-13","periodEnd":"2023-01-05","datasets":["JGAD000261"]},{"principalInvestigator":{"en":"zeng tianfu"},"affiliation":{"en":"Laboratory of Omics Technology and Bioinformatics, Sichuan University"},"country":{"ja":"中国","en":"China"},"researchTitle":{"en":"Study on Heterogeneity of Hepatocellular Carcinoma Based on Nanopore Sequencing Technology"},"periodStart":"2023-10-30","periodEnd":"2024-09-18","datasets":["JGAD000635"]}]}