{"id":"NHA000086","research":"hum0166","url":"https://humandbs.dbcls.jp/dataset/NHA000086","datePublished":"2019-07-30","dateModified":"2019-07-30","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":"炎症性腸疾患1221症例に対するチオプリン製剤による副作用（白血球減少症、脱毛症）の有無に関するGWAS","en":"GWAS for 1221 patients of inflammatory bowel diseases with thiopurine-induced adverse events (leukopenia, alopecia)"}}],"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":"炎症性腸疾患：1221＋2680 症例\nクローン病（ICD10：K509）：516＋1175 症例\n潰瘍性大腸炎（ICD10：K519）：674＋1459 症例\n腸管ベーチェット病（ICD10：M352）：16＋43 症例\n炎症性腸疾患（分類不能）（ICD10：K523）：15＋3 症例","en":"inflammatory bowel diseases: 1221 + 2680 cases\nCrohn's disease (ICD10: K509): 516 + 1175 cases\nUlcerative Colitis (ICD10: K519): 674 + 1459 cases\nGastrointestinal Behçet's disease (ICD10: M352): 16 >+ 43 cases\nother inflammatory bowel diseases (ICD10: K523): 15 + 3 cases"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"K509","label":{"ja":"クローン＜Crohn＞病，詳細不明","en":"Crohn disease, unspecified"}}],"name":{"ja":"クローン病","en":"Crohn's disease"}},{"terms":[{"code":"K519","label":{"ja":"潰瘍性大腸炎，詳細不明","en":"Ulcerative colitis, unspecified"}}],"name":{"ja":"潰瘍性大腸炎","en":"Ulcerative Colitis"}},{"terms":[{"code":"M352","label":{"ja":"ベーチェット＜Behcet＞病","en":"Behçet disease"}}],"name":{"ja":"腸管ベーチェット病","en":"Gastrointestinal Behçet's disease"}},{"terms":[{"code":"K523","label":{"ja":"分類不能大腸炎","en":"Indeterminate colitis"}}],"name":{"ja":"炎症性腸疾患（分類不能）","en":"other inflammatory bowel diseases"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"affected","label":{"ja":"罹患","en":"Affected"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":3901,"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":"・SNVs with low imputation quality\n(with a posterior genotype probability of < 0.8 for each genotype or with info score < 0.5 for each variant)\n・call rate < 0.97\n・minor allele frequency (MAF) < 0.01 or 0.05\n(0.01 for GWASs of > 50 cases, 0.05 for GWASs of low-frequency adverse events or conditional GWASs on rs116855232)\n・Hardy-Weinberg equilibrium (HWE) p < 1 × 10^−6","en":"・SNVs with low imputation quality\n(with a posterior genotype probability of < 0.8 for each genotype or with info score < 0.5 for each variant)\n・call rate < 0.97\n・minor allele frequency (MAF) < 0.01 or 0.05\n(0.01 for GWASs of > 50 cases, 0.05 for GWASs of low-frequency adverse events or conditional GWASs on rs116855232)\n・Hardy-Weinberg equilibrium (HWE) p < 1 × 10^−6"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"・EAGLE (v 2.4) for prephasing\n・IMPUTE4 (v 1.0) ＋ 2KJPN (reference panel)","en":"・EAGLE (v 2.4) for prephasing\n・IMPUTE4 (v 1.0) ＋ 2KJPN (reference panel)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Affymetrix Power Tools (version 1.16.1, Affymetrix)","en":"Affymetrix Power Tools (version 1.16.1, Affymetrix)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":5831032,"unit":null,"high":null,"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"}}]}