{"id":"NHA000162","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000162","datePublished":"2021-03-22","dateModified":"2021-03-22","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":"215形質のGWAS","en":"GWAS for 215 phenotypes"}}],"experiments":[{"label":"genome wide SNPs","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（179,000名）、UKバイオバンク（361,000名）、FinnGen（136,000名）\n形質数：220","en":"Biobank Japan (n = 179,000), UK biobank (n = 361,000), FinnGen (n = 136,000), no. Phenotypes: 220"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":676000,"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"}},{"code":"uk-biobank","label":{"en":"UK Biobank"}},{"code":"finngen","label":{"en":"FinnGen"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}},{"code":"british","label":{"ja":"イギリス人","en":"British"}},{"code":"finnish","label":{"ja":"フィンランド人","en":"Finnish"}}]},{"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":"DNAs 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":"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":[{"code":"humanomniexpressexome-beadchip-kit","label":{"en":"HumanOmniExpressExome BeadChip Kit"}},{"code":"humanomniexpress-beadchip-kit","label":{"en":"HumanOmniExpress BeadChip Kit"}},{"code":"humanexome-beadchip-kit","label":{"en":"HumanExome BeadChip Kit"}},{"code":"uk-bileve-axiom-array","label":{"en":"UK BiLEVE Axiom Array"}},{"code":"uk-biobank-axiom-array","label":{"en":"UK Biobank Axiom Array"}},{"code":"finngen1-thermofisher-array","label":{"en":"FinnGen1 ThermoFisher Array"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}},{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"applied-biosystems-uk-bileve-axiom-array","label":{"en":"Applied Biosystems UK BiLEVE Axiom Array"}},{"code":"applied-biosystems-uk-biobank-axiom-array","label":{"en":"Applied Biosystems UK Biobank Axiom Array"}},{"code":"thermo-fisher-scientific-finngen1-thermofisher-array","label":{"en":"Thermo Fisher Scientific FinnGen1 ThermoFisher Array"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"BBJ：We included imputed variants with Rsq > 0.7.\nUK Biobank：We excluded the variants with (i) INFO score ≤ 0.8, (ii) MAF ≤ 0.0001 (except for missense and protein-truncating variants annotated by VEP, which were excluded if MAF ≤ 1 × 10-6), and (iii) PHWE ≤ 1 × 10-10.\nFinnGen：We excluded variants with an imputation INFO score < 0.8 or MAF < 0.0001.","en":"BBJ: We included imputed variants with Rsq > 0.7.\nUK Biobank: We excluded the variants with (i) INFO score ≤ 0.8, (ii) MAF ≤ 0.0001 (except for missense and protein-truncating variants annotated by VEP, which were excluded if MAF ≤ 1 × 10-6), and (iii) PHWE ≤ 1 × 10-10.\nFinnGen: We excluded variants with an imputation INFO score < 0.8 or MAF < 0.0001."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"BBJ：Eagle、Minimac3\nUK Biobank：IMPUTE4\nFinnGen：beagle4.1","en":"BBJ: Eagle, Minimac3\nUK Biobank: IMPUTE4\nFinnGen: beagle4.1"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"For binary traits, SAIGE software was used with age, age2, sex, age×sex, age2×sex, and top 20 principal components as covariates. For quantitative traits (biomarkers), BOLT-LMM or plink software was used with the same covariates.","en":"For binary traits, SAIGE software was used with age, age2, sex, age×sex, age2×sex, and top 20 principal components as covariates. For quantitative traits (biomarkers), BOLT-LMM or plink software was used with the same covariates."}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":13530797,"unit":null,"high":null,"prefix":{"ja":"BBJ: ","en":"BBJ: "},"suffix":{"ja":" variants","en":" variants"}},{"value":13791467,"unit":null,"high":null,"prefix":{"ja":"UK Biobank: ","en":"UK Biobank: "},"suffix":{"ja":" variants","en":" variants"}},{"value":16859359,"unit":null,"high":null,"prefix":{"ja":"FinnGen: ","en":"FinnGen: "},"suffix":{"ja":" variants","en":" variants"}}]},{"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":"html","label":{"en":"HTML"}},{"code":"zip","label":{"en":"ZIP"}}]}