{"id":"NHA000175","research":"hum0347","url":"https://humandbs.dbcls.jp/dataset/NHA000175","datePublished":"2022-07-15","dateModified":"2022-07-15","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":"AESD症例のGWAS統計情報","en":"GWAS for AESD"}}],"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":"けいれん重積型急性脳症 （ICD-10：G934）：254症例\n対照健常者：799名","en":"AESD (ICD-10: G934): 254 cases\nhealthy adult controls: 799 individuals"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"G934","label":{"ja":"脳症＜エンセファロパチ＜シ＞ー＞，詳細不明","en":"Encephalopathy, unspecified"}}],"name":{"ja":"けいれん重積型急性脳症","en":"AESD"}}]},{"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":1053,"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":[{"code":"axiom-2-0-reagent-kit","label":{"en":"Axiom 2.0 Reagent Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"affymetrix-japonica-array","label":{"en":"Affymetrix Japonica Array"}}]},{"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":"以下の条件のものを除外：\nサンプルQC：\n（1） Sample Call rate < 0.97\n（2） 血縁関係者（PI_HAT > 0.1875）\n（3） サンプル集団中主成分分析により、見かけ上外れ値となったサンプル\nSNP QC：\n（1） SNP call rate < 0.99\n（2） HWE P < 0.0001\n（3） MAF < 0.05\n（4） 性染色体とミトコンドリア上に位置しているSNP","en":"Exclude the following conditions:\nSample QCs:\n(1) overall call rates < 0.97\n(2) relatives (PI_HAT > 0.1875)\n(3) outliers from Japanese cluster by principal component analysis\nSNP QCs:\n(1) SNP call rate < 0.99\n(2) HWE P < 0.0001\n(3) MAF < 0.05\n(4) located in sex chromosomes or mitochondria"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Affymetrix Power Tools ver. 1.18.2","en":"Affymetrix Power Tools ver. 1.18.2"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":445917,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"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":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}