{"id":"NHA000183","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000183","datePublished":"2023-04-05","dateModified":"2023-04-05","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"unrestricted-access","label":{"ja":"非制限公開","en":"Unrestricted-access"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"BBJ第1コホート4,880名のmobile element多型頻度情報","en":"mobile element variations in 4,880 individuals from BBJ 1st cohort"}}],"experiments":[{"label":"Mobile element variations (WGS)","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"BBJ第1コホート4880名のWGSデータ（下記データを含む）\n・1,026名のWGSデータ（JGAD000220）\n・心筋梗塞症例1,765名および認知症症例199名のWGSデータ（JGAD000495）\n・胃がん症例255名のWGSデータ（AGDD_000005）\n・アジアゲノムプロジェクトの1007名\n・大腸・直腸がん症例の617名\n・AGDD_000005のQCで除かれた1名\n・JGAD000220のQCで除かれた10名","en":"WGS data of 4,880 individuals from BBJ 1st cohort\n- WGS data (JGAD000220) of the biobank Japan project (N=1,037)\n- WGS data (JGAD000495) of 1,765 myocardial infarction patients and 199 dementia patients\n- WGS data (AGDD_000005) of 225 gastric cancer patients\n- 1,007 individuals from Asian Genome Project\n- 617 colorectal cancer patients\n- One individual excluded from AGDD_000005 by QC\n- 10 individuals excluded from JGAD000220 by QC"}},{"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gDNA","en":"gDNA 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":"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":"wgs","label":{"en":"WGS"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":null,"en":null}},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"超音波断片化","en":"Ultrasonic fragmentation"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}},{"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":151,"unit":"bp","high":null,"suffix":{"ja":" (HiSeq X)","en":" (HiSeq X)"}},{"value":126,"unit":"bp","high":null,"suffix":{"ja":" (HiSeq 2500)","en":" (HiSeq 2500)"}}]},{"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-MEM","en":"BWA-MEM"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":null,"en":null}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":null,"en":null}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"MEGAnE *2","en":"MEGAnE *2"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":15,"unit":"x","high":null,"suffix":{"ja":" (以上)","en":" (Or more)"}},{"value":25,"unit":"x","high":null,"prefix":{"ja":"1235名: ","en":"1235 subjects: "},"suffix":{"ja":" (以上)","en":" (Or more)"}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":24933,"unit":null,"high":null,"suffix":{"ja":" (4880名)","en":" (4880 subjects)"}},{"value":10997,"unit":null,"high":null,"suffix":{"ja":" (1235名)","en":" (1235 subjects)"}}]},{"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)"}}]}]}],"fileFormats":[{"code":"txt","label":{"en":"TXT"}},{"code":"zip","label":{"en":"ZIP"}}]}