{"id":"NHA000154","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000154","datePublished":"2020-11-27","dateModified":"2020-11-27","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":"肺胞蛋白症のGWAS","en":"GWAS for autoimmune pulmonary alveolar proteinosis"}}],"experiments":[{"label":"genome wide SNPs","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"肺胞蛋白症（ICD10：J840）：198症例\n対照者：395名","en":"Autoimmune pulmonary alveolar proteinosis cases (ICD10: J840): 198\nControl participants: 395"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"J840","label":{"ja":"肺胞性及び肺胞周囲性病態","en":"Alveolar and parietoalveolar conditions"}}],"name":{"ja":"肺胞蛋白症","en":"Autoimmune pulmonary alveolar proteinosis cases"}}]},{"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":"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-infinium-asian-screening-array","label":{"en":"Illumina Infinium Asian Screening Array"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) and in close genetic relation (PI_HAT > 0.175). We included samples of the estimated East Asian ancestry.\nVariant QC: We excluded variants with (1) genotyping call rate < 98%, (2) P value for Hardy-Weinberg equilibrium < 1.0 × 10−6, and (3) minor allele count < 5, or (4) > 10% frequency difference with the imputation reference panel.","en":"Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) and in close genetic relation (PI_HAT > 0.175). We included samples of the estimated East Asian ancestry.\nVariant QC: We excluded variants with (1) genotyping call rate < 98%, (2) P value for Hardy-Weinberg equilibrium < 1.0 × 10−6, and (3) minor allele count < 5, or (4) > 10% frequency difference with the imputation reference panel."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenomeStudio for genotyping, shapeit2 for haplotype phasing, and minimac3 for imputation\nPLINK2","en":"GenomeStudio for genotyping, shapeit2 for haplotype phasing, and minimac3 for imputation\nPLINK2"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":12153232,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" variants (QC後)","en":" variants (After QC)"}},{"value":242876,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "},"suffix":{"ja":" variants (QC後)","en":" variants (After QC)"}}]},{"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"}}]}