{"id":"NHA000088","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000088","datePublished":"2019-09-27","dateModified":"2019-09-27","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":"159,095名の身長のGWAS","en":"GWAS for height"}}],"experiments":[{"label":"Genotyping by array (GWAS)","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"バイオバンクジャパンに参加した159,095名\n（男性：86,257名、女性：72,838名）","en":"159,095 individuals (Male: 86,257, Female: 72,838)"}},{"key":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"biobank-japan","label":{"en":"BioBank Japan"}}]},{"key":"sex","label":{"ja":"性別","en":"Sex"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"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":"genotyping-by-array","label":{"en":"Genotyping by array"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"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-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QCs：1) call rate < 98%、2) closely related samples (PI_HAT > 0.175)、3) outlier from Japanese cluster determined by PCA using GCTA を除外。\nImputation後のQC：Imputation quality (Rsq) < 0.3 を除外。","en":"Sample QCs: Exclusion criteria:\n1) call rate < 98%,\n2) closely related samples (PI_HAT > 0.175), and\n3) outlier from Japanese cluster determined by PCA using GCTA.\nQC after imputation: Variants with imputation quality of Rsq < 0.3 were excluded."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"Minimac3 [imputation reference panel using WGS data of the biobank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504)]","en":"Minimac3 [imputation reference panel using WGS data of the biobank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504)]"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":27211524,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" variants","en":" variants"}},{"value":684533,"unit":null,"high":null,"prefix":{"ja":"男性X染色体: ","en":"Male X chromosome: "},"suffix":{"ja":" variants","en":" variants"}},{"value":684533,"unit":null,"high":null,"prefix":{"ja":"女性X染色体: ","en":"Female X chromosome: "},"suffix":{"ja":" variants","en":" variants"}}]},{"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":"html","label":{"en":"HTML"}},{"code":"zip","label":{"en":"ZIP"}}]}