{"id":"NHA000158","research":"hum0261","url":"https://humandbs.dbcls.jp/dataset/NHA000158","datePublished":"2021-01-19","dateModified":"2021-01-19","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":"PBC1,920症例および健常対照者1,770名のGWAS","en":"GWAS for 1,920 PBCs and 1,770 healthy controls"}}],"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":"PBC（ICD10：K743）：1,920症例\n健常対照者：1,770名","en":"1,920 PBCs (ICD10: K743) and 1,770 healthy controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"K743","label":{"ja":"原発性胆汁性肝硬変","en":"Primary biliary cirrhosis"}}],"name":{"ja":"PBC","en":"PBCs"}}]},{"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":3690,"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-axiom-genome-wide-asi-1-array","label":{"en":"Affymetrix Axiom Genome-Wide ASI 1 Array"}},{"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":"Sample QCs: sample call rate < 0.97, closely related samples by PRIMUS (PI_HAT > 0.09375), outlier from Japanese cluster by PCA (Smirnov-Grubbs test with a Bonferroni corrected P < 0.05)\nSNP QCs: SNP call rate < 0.99, HWE P < 0.0001, MAF < 0.05","en":"Sample QCs: sample call rate < 0.97, closely related samples by PRIMUS (PI_HAT > 0.09375), outlier from Japanese cluster by PCA (Smirnov-Grubbs test with a Bonferroni corrected P < 0.05)\nSNP QCs: SNP call rate < 0.99, HWE P < 0.0001, MAF < 0.05"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"Eagle v2.3.2 for haplotype phasing","en":"Eagle v2.3.2 for haplotype phasing"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"ASI: Genotyping Console ver. 4.2.0.26\nJaponica: Affymetrix Power Tools ver. 1.18.2\nIMPUTE4 v1.0 for genotype imputation with 2KJPN reference panel","en":"ASI: Genotyping Console ver. 4.2.0.26\nJaponica: Affymetrix Power Tools ver. 1.18.2\nIMPUTE4 v1.0 for genotype imputation with 2KJPN reference panel"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":4902084,"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"}}]}