{"id":"NHA000052","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000052","datePublished":"2017-05-18","dateModified":"2017-05-18","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":"心房細動患者8,180症例および対照者28,612名のGWAS","en":"GWAS for AF"}}],"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":"心房細動：8,180症例\n対照者：28,612名","en":"8180 atrial fibrillation patients and 28,612 controls"}},{"key":"participant-attributes","label":{"ja":"対象者属性","en":"Participant attribute"},"type":"text","text":{"ja":"性別、年齢","en":"Gender, Age"}},{"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":36792,"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":"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":"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, 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\nR square < 0.9","en":"Genotyping QC: sample call rate < 0.98, SNV call rate < 0.99,\nHWE P < 1 x 10^-6 in the control samples\nImputation QC: HWE P < 1 x 10^-6 or MAF < 0.01 in the reference panel\nDifferences of MAF between the GWAS dataset and the reference panel > 0.16\nR square < 0.9"}},{"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":5000000,"unit":null,"high":null,"suffix":{"ja":" SNVs (約)","en":" SNVs (Approx.)"}}]},{"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"}},{"code":"genotype-data","label":{"ja":"遺伝子型データ","en":"Genotype data"}}]},{"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":"txt","label":{"en":"TXT"}},{"code":"xlsx","label":{"en":"XLSX"}}]}