{"id":"NHA000200","research":"hum0496","url":"https://humandbs.dbcls.jp/dataset/NHA000200","datePublished":"2025-02-27","dateModified":"2025-02-27","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":"血清ALT値、AST値、GGT値のGWAS","en":"GWAS for serum levels of ALT, AST and GGT"}}],"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":"ALT：15,224名（OBi-Ryukyu 8,440名、BBJ-Ryukyu 6,784名）\nAST：15,203名（OBi-Ryukyu 8,406名、BBJ-Ryukyu 6,797名）\nGGT：14,496名（OBi-Ryukyu 8,434名、BBJ-Ryukyu 6,062名）","en":"ALT: n=15,224 (OBi-Ryukyu n=8,440, BBJ-Ryukyu n=6,784)\nAST: n=15,203 (OBi-Ryukyu n=8,406, BBJ-Ryukyu n=6,797)\nGGT: n=14,496 (OBi-Ryukyu n=8,434, BBJ-Ryukyu n=6,062)"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":15224,"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":"okinawa-biobank","label":{"en":"Okinawa Biobank"}},{"code":"biobank-japan","label":{"en":"BioBank Japan"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血または唾液から抽出したDNA","en":"DNAs extracted from peripheral blood cells or saliva"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"saliva","label":{"ja":"唾液","en":"Saliva"}}]},{"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":"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":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":null},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-infinium-asian-screening-array","label":{"en":"Illumina Infinium Asian Screening Array"}},{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"SampleのQC：sample call rate ≧0.98\nGenotypingのQC：SNP call rate ≧ 0.98、MAF ≧ 0.01、p-values for Hardy-Weinberg equilibrium (HWE) test > 1×10−6\nImputation後のQC：MAF ≧ 0.005、Rsq ≧ 0.7","en":"Sample QC: sample call rate ≧0.98\nGenotyping QC: SNP call rate ≧ 0.98, MAF ≧ 0.01, p-values for Hardy-Weinberg equilibrium (HWE) test > 1×10−6\nImputation QC: MAF ≧ 0.005, Rsq ≧ 0.7"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"minimac4\nImputation：reference 3,256 Japanese WGS from the BBJ and 2,504 individuals from the 1KGP (phase3v5)","en":"minimac4\nImputation: reference 3,256 Japanese WGS from the BBJ and 2,504 individuals from the 1KGP (phase3v5)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":9224376,"unit":null,"high":null,"prefix":{"ja":"ALT: ","en":"ALT: "},"suffix":{"ja":" variants","en":" variants"}},{"value":9222117,"unit":null,"high":null,"prefix":{"ja":"AST: ","en":"AST: "},"suffix":{"ja":" variants","en":" variants"}},{"value":9235975,"unit":null,"high":null,"prefix":{"ja":"GGT: ","en":"GGT: "},"suffix":{"ja":" variants","en":" variants"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"gwas-summary-statistics","label":{"ja":"GWAS 要約統計量","en":"GWAS summary statistics"}}]},{"key":"has-phenotype-data","label":{"ja":"表現型データの有無","en":"Phenotype data"},"type":"vocabulary","terms":[{"code":"included","label":{"ja":"あり","en":"Included"}}]},{"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":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}