{"id":"JGAD000399","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000399","datePublished":"2021-05-21","dateModified":"2022-12-20","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"2003年から2007年度にバイオバンク・ジャパンに登録されたサンプル（約20万例）から抽出された11,234名の23遺伝子における全てのエクソン領域のTarget Capture Sequencingn解析より得られた体細胞変異データおよびSNPアレイにより得られた染色体変異データ","en":"target sequencing of 23 genes related to clonal hematopoiesis and SNP array in 11,234 subjects extracted from approximately 200,000 subjects registered in Biobank Japan between fiscal years 2003 to 2007"}}],"experiments":[{"label":{"ja":"Targeted DNA sequencing","en":"Targeted DNA sequencing"},"values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"2003年から2007年度にバイオバンク・ジャパンに登録されたサンプル（約20万例）から抽出された11,234名","en":"11,234 subjects extracted from approximately 200,000 subjects registered in Biobank Japan between fiscal years 2003 to 2007"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":11234,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"individual","label":{"ja":"人数","en":"Individual"}}]},{"key":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"biobank-japan","label":{"en":"BioBank Japan"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血から抽出したDNA","en":"DNA extracted from peripheral blood cells"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"normal","label":{"ja":"非腫瘍","en":"Normal"}}]},{"key":"sample-provider","label":{"ja":"試料の入手元","en":"Sample provider"},"type":"text","text":{"ja":null,"en":null}},{"key":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"targeted-dna-sequencing","label":{"en":"Targeted DNA sequencing"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":"下記の23遺伝子における全てのエクソン領域\nASXL1, CBL, CEBPA, DDX41, DNMT3A, ETV6, EZH2, GATA2, GNAS, GNB1, IDH1, IDH2, JAK2, KRAS, MYD88, NRAS, PPM1D, RUNX1, SF3B1, SRSF2, TET2, TP53, U2AF1","en":"23 genes related to clonal hematopoiesis\nASXL1, CBL, CEBPA, DDX41, DNMT3A, ETV6, EZH2, GATA2, GNAS, GNB1, IDH1, IDH2, JAK2, KRAS, MYD88, NRAS, PPM1D, RUNX1, SF3B1, SRSF2, TET2, TP53, U2AF1"}},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":null,"en":null}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq-2500","label":{"en":"Illumina HiSeq 2500"}}]},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":[{"code":"paired-end","label":{"ja":"ペアエンド","en":"Paired-end"}}]},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":[{"value":150,"unit":"bp","high":null}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"bwa","en":"bwa"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"≥40","en":"≥40"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Depth 20以上の領域が98%以上のサンプルを解析対象とした。","en":"We selected samples in which ≥20 depth was achieved in ≥98% regions."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Genomon pipeline","en":"Genomon pipeline"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":800,"unit":"x","high":null}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"somatic-variant-calls","label":{"ja":"体細胞変異コール","en":"Somatic variant calls"}}]},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"dataVolume":4563366,"fileFormats":[{"code":"txt","label":{"en":"TXT"}}]}