{"id":"NHA000197","research":"hum0466","url":"https://humandbs.dbcls.jp/dataset/NHA000197","datePublished":"2024-11-20","dateModified":"2024-11-20","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":"JPSC-AD研究参加者のGWAS集計情報","en":"GWAS for JPSC-AD study"}}],"experiments":[{"label":"Genotyping by array (GWAS)","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"JPSC-AD研究（ICD10：R90.8）参加者： 9,479名","en":"JPSC-AD study participants (ICD10: R90.8): 9,479 individuals"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"R908","label":{"ja":"中枢神経系の画像診断におけるその他の異常所見","en":"Other abnormal findings on diagnostic imaging of central nervous system"}}],"name":{"ja":"JPSC-AD研究","en":"JPSC-AD study participants"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":9479,"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":null},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-japanese-screening-array","label":{"en":"Illumina Japanese Screening Array"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC： Gender discrepancy, sample call rate <98%, close relatives, and outliers (distance > 10sd short, 11sd long) were excluded.\nGenotyping QC：Hardy-Weinberg equilibrium >1.0x10⁻⁶, call rate >99%, monomorphic, minor allele count <5, and frequency difference >6% with reference panel were excluded.\nImputation後 QC：Variants with minor allele frequency (MAF) <0.5% and Rsq <0.7 were excluded.","en":"Sample QC: Gender discrepancy, sample call rate <98%, close relatives, and outliers (distance > 10sd short, 11sd long) were excluded.\nGenotyping QC: Hardy-Weinberg equilibrium >1.0x10⁻⁶, call rate >99%, monomorphic, minor allele count <5, and frequency difference >6% with reference panel were excluded.\nPost-imputation QC: Variants with minor allele frequency (MAF) <0.5% and Rsq <0.7 were excluded."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"Imputation reference panel: BioBank Japan(1,037名)＋1000ゲノムプロジェクト(2,504名)(hum0014)","en":"Imputation reference panel: whole genome sequences of 1,037 (BioBank Japan) and 2,504 (1000 Genomes Project (Phase 3v5)) (hum0014)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Genotype call: GenomeStudio\nGenotype imputation: Minimac4 v1.0.0","en":"Genotype call: GenomeStudio\nGenotype imputation: Minimac4 v1.0.0"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":8495153,"unit":null,"high":null,"suffix":{"ja":" variants","en":" variants"}}]},{"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":"markdown","label":{"en":"Markdown"}},{"code":"zip","label":{"en":"ZIP"}}]}