{"id":"NHA000196","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000196","datePublished":"2024-10-28","dateModified":"2024-10-28","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":"縄文割合のGWAS","en":"GWAS for the individual Jomon proportions"}}],"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・ジャパン第1コホート：171,287名","en":"The first cohort of Biobank Japan (n = 171,287)"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":171287,"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":"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"}}]},{"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"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC: We excluded (i) individuals with lower call rates (< 99%), (ii) closely related individuals with genetic relatedness ≥ 0.178 calculated from a genetic related matrix (GRM) by GCTA (version 1.93.3beta2). We included samples of the estimated Japanese ancestry using PCA.\nVariant QC: We excluded variants with (i) call rate < 99%, (ii) P value for Hardy-Weinberg equilibrium (HWE) < 1.0 × 10-6, (iii) number of heterozygotes < 5, and (iv) a concordance rate < 99.5% or a non-reference concordance rate between GWAS array and whole genome sequencing.\nafter association test: Double genomic control correction method using METAL was conducted. Computing Z score for each variant by considering the sign of the beta coefficient and the associated p-value, we left the variants with positive Z score.","en":"Sample QC: We excluded (i) individuals with lower call rates (< 99%), (ii) closely related individuals with genetic relatedness ≥ 0.178 calculated from a genetic related matrix (GRM) by GCTA (version 1.93.3beta2). We included samples of the estimated Japanese ancestry using PCA.\nVariant QC: We excluded variants with (i) call rate < 99%, (ii) P value for Hardy-Weinberg equilibrium (HWE) < 1.0 × 10-6, (iii) number of heterozygotes < 5, and (iv) a concordance rate < 99.5% or a non-reference concordance rate between GWAS array and whole genome sequencing.\nafter association test: Double genomic control correction method using METAL was conducted. Computing Z score for each variant by considering the sign of the beta coefficient and the associated p-value, we left the variants with positive Z score."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"Eagle、Minimac3","en":"Eagle, Minimac3"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"1) GCTA-fastGWA with the adjustment of covariates: age, age2, sex, the top 20 PCs, 45 disease status, geographic regions, and PCA clusters.\n2) Fixed-effect meta-analysis of Mainland summary data including individuals from the Mainland and EA_admix clusters (n = 151,075) and of Ryukyu summary data including individuals from the Ryukyu, Ryukyu admix, and Hokkaido_sub clusters (n = 10,080) using METAL","en":"1) GCTA-fastGWA with the adjustment of covariates: age, age2, sex, the top 20 PCs, 45 disease status, geographic regions, and PCA clusters.\n2) Fixed-effect meta-analysis of Mainland summary data including individuals from the Mainland and EA_admix clusters (n = 151,075) and of Ryukyu summary data including individuals from the Ryukyu, Ryukyu admix, and Hokkaido_sub clusters (n = 10,080) using METAL."}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":3454970,"unit":null,"high":null,"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"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":"docx","label":{"en":"DOCX"}},{"code":"zip","label":{"en":"ZIP"}}]}