{"id":"JGAD000167","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000167","datePublished":"2020-09-28","dateModified":"2020-09-28","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"162,255名の58臨床検査値のPhenotypeデータ","en":"58 quantitative traits data for 200,849 individuals"}}],"experiments":[{"label":{"ja":"Genotyping by array","en":"Genotyping by array"},"values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"162,255名の58臨床検査値","en":"162,255 individuals for 58 quantitative traits"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":162255,"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":"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":"DNA 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":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"humanomniexpress-beadchip-kit","label":{"en":"HumanOmniExpress BeadChip Kit"}},{"code":"humanexome-beadchip-kit","label":{"en":"HumanExome BeadChip Kit"}},{"code":"humanomniexpressexome-beadchip-kit","label":{"en":"HumanOmniExpressExome BeadChip Kit"}}]},{"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":"GenotypingのQC：sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6\nImputation referenceのQC:\n以下の条件に該当するSNVはreferenceから除外:\n1) HWE P < 1 x 10^-6、2) MAF < 0.01\nImputation後のQC:\nImputation quality (Rsq) < 0.7 を除外。","en":"Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6\nQC for reference panel:\nAfter excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded.\nQC after imputation:\nVariants with imputation quality of Rsq < 0.7 were excluded."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"minimac [imputation（1000 genomes Phase I v3 ）]","en":"minimac [imputation (1000 genomes Phase I v3)]"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenCall software（GenomeStudio）","en":"GenCall software (GenomeStudio)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":5961600,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" SNVs","en":" SNVs"}},{"value":147353,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "},"suffix":{"ja":" SNVs","en":" SNVs"}}]},{"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":"data-summary","label":{"ja":"データ概要","en":"Data summary"},"type":"text","text":{"ja":"肝機能: アルカリフォスファターゼ","en":"Liver-related: Alkaline phosphatase"}},{"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)"}}]}]}],"dataVolume":2098640,"fileFormats":[{"code":"pheno","label":{"en":"PHENO"}}]}