{"id":"NHA000068","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000068","datePublished":"2018-04-04","dateModified":"2018-04-04","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":"開放隅角緑内障3,980症例および\n対照者18,815名のGWAS","en":"GWAS for POAG"}}],"experiments":[{"label":"Genotyping by array","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"開放隅角緑内障（ICD10：H401）：3,980症例（男性：1,997、女性：1,983）\n対照者：18,815名（男性：7,817、女性：10,998）","en":"3980 POAG patients (Male: 1,997, Female: 1,983)\n18,815 controls (Male: 7,817, Female: 10,998)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"H401","label":{"ja":"原発開放隅角緑内障","en":"Primary open-angle glaucoma"}}],"name":{"ja":"開放隅角緑内障","en":"POAG patients"}}]},{"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":"GenotypingのQC：sample call rate < 0.98, SNV call rate < 0.99, MAF < 0.5%,\n対照者群で HWE P < 1 x 10^-6\nImputationのQC：リファレンスパネルで HWE P < 1 x 10^-6 もしくは MAF < 0.01\nGWASデータセットとリファレンスパネルのアレル頻度差 > 0.16\nImputation後のQC：Imputation quality (Rsq) < 0.7を除外。\nさらに、ベータが4未満もしくは4を超えるものは公開用に除外。","en":"Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99, HWE P < 1 x 10^-6\nQC for reference panel: After excluding 11 closely related individuals, variants with HWE P < 1.0 x 10^-6, MAF < 0.01 were excluded.\nQC after imputation: Variants with imputation quality of Rsq < 0.7 were excluded. We also excluded variants with |beta| > 4 in the uploaded files."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"minimac（ver. 0.1.1）[imputation（1000 genomes Phase I v3 ）]","en":"minimac (ver. 0.1.1) [imputation (1000 genomes Phase I v3)]"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":5961428,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" SNPs","en":" SNPs"}},{"value":147351,"unit":null,"high":null,"prefix":{"ja":"男性X染色体: ","en":"Male X chromosome: "},"suffix":{"ja":" SNPs","en":" SNPs"}},{"value":147353,"unit":null,"high":null,"prefix":{"ja":"女性X染色体: ","en":"Female X chromosome: "},"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":"html","label":{"en":"HTML"}},{"code":"zip","label":{"en":"ZIP"}}]}