{"id":"NHA000080","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/NHA000080","datePublished":"2019-03-26","dateModified":"2019-03-26","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":"日本人集団165,436名における喫煙習慣のGWAS","en":"GWAS for smoking behaviour"}}],"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":"165,436名の喫煙習慣データ","en":"165,436 individuals whose smoking status is available"}},{"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, 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 and MAF < 0.01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 and MAF < 0.01 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":5961480,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" SNVs","en":" SNVs"}},{"value":163412,"unit":null,"high":null,"prefix":{"ja":"男性X染色体(喫煙開始年齢): ","en":"Male X chromosome (age started smoking): "},"suffix":{"ja":" SNVs","en":" SNVs"}},{"value":146130,"unit":null,"high":null,"prefix":{"ja":"女性X染色体(喫煙開始年齢): ","en":"Female X chromosome (age started smoking): "},"suffix":{"ja":" SNVs","en":" SNVs"}}]},{"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"}}]}