{"id":"JGAD000137","research":"hum0119","url":"https://humandbs.dbcls.jp/dataset/JGAD000137","datePublished":"2020-09-28","dateModified":"2021-04-20","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"NAFLD264症例および対照7672名のGWAS\nNASH580症例および対照7672名のGWAS\nNASH-HCC58症例および対照7672名のGWAS","en":"GWAS for NAFLD, NASH, and NASH-HCC"}}],"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":"NAFLD（ICD10：K76.0）：264症例\nNASH（ICD10：K75.81）：580症例\nNASH-HCC（ICD10：C220）：58症例\n対照者：7672名","en":"NAFLD (ICD10: K76.0): 264 patients\nNASH (ICD10: K75.81): 580 patients\nNASH-HCC (ICD10: C220): 58 patients\n7672 healthy controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"K760","label":{"ja":"脂肪肝＜肝の脂肪化＞，他に分類されないもの","en":"Fatty (change of) liver, not elsewhere classified"}}],"name":{"ja":"NAFLD","en":"NAFLD"}},{"terms":[{"code":"K758","label":{"ja":"その他の明示された炎症性肝疾患","en":"Other specified inflammatory liver diseases"}}],"name":{"ja":"NASH","en":"NASH"}},{"terms":[{"code":"C220","label":{"ja":"肝細胞癌","en":"Malignant neoplasm: Liver cell carcinoma"}}],"name":{"ja":"NASH-HCC","en":"NASH-HCC"}}]},{"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":8574,"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":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"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":"human610-quad-beadchip-kit","label":{"en":"Human610-Quad BeadChip Kit"}},{"code":"humancoreexome-beadchip-kit","label":{"en":"HumanCoreExome BeadChip Kit"}},{"code":"humanomni2-5-beadchip-kit","label":{"en":"HumanOmni2.5 BeadChip Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-human610-quad","label":{"en":"Illumina Human610-Quad"}},{"code":"illumina-humancoreexome","label":{"en":"Illumina HumanCoreExome"}},{"code":"illumina-humanomni2-5","label":{"en":"Illumina HumanOmni2.5"}}]},{"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":"sample call-rate < 0.95、PCAにより日本人集団から逸脱、近縁（pihat > 0.38）\nSNP call-rate < 0.99、HWE-p < 1e-6、MAF < 0.01を除外","en":"Exclusion criteria : sample call-rate < 0.95, PCA outlier of Japanese population, encrypted relatedness (pihat > 0.38)\nSNP call-rate < 0.99, HWE-p < 1e-6, MAF< 0.01"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenomeStudio（Illumina）","en":"GenomeStudio (Illumina)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":93606,"unit":null,"high":null,"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"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)"}}]}]}],"dataVolume":14131824,"fileFormats":[{"code":"xlsx","label":{"en":"XLSX"}}]}