{"id":"NHA000194","research":"hum0467","url":"https://humandbs.dbcls.jp/dataset/NHA000194","datePublished":"2024-10-02","dateModified":"2024-10-02","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":"骨盤臓器脱と診断された女性のGWAS集計情報","en":"GWAS for POP"}}],"experiments":[{"label":"Genotyping by array (GWAS)","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"[GWAS-1]\nPOP（ICD10：N81）：BBJ_Hondo 418症例、対照：BBJ_Hondo 68,040名\n[GWAS-2]\nPOP：POP_Hondo 128症例、対照：OBi_Hondo 387名\n[GWAS-3]\nPOP：BBJ_Ryukyu 29症例、対照：BBJ_Ryukyu 5,852名\n[GWAS-4]\nPOP：POP_Ryukyu 196症例、対照：OBi_Ryukyu 2,346名","en":"[GWAS-1]\nPOP (ICD-10: N81): BBJ_Hondo n = 418, Controls: BBJ_Hondo n = 68,040\n[GWAS-2]\nPOP: POP_Hondo n = 128, Controls: OBi_Hondo n = 387\n[GWAS-3]\nPOP: BBJ_Ryukyu n = 29, Controls: BBJ_Ryukyu n = 5,852\n[GWAS-4]\nPOP: POP_Ryukyu n = 196, Controls: OBi_Ryukyu n = 2,346"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"N81","label":{"ja":"女性性器脱","en":"Female genital prolapse"}}],"name":{"ja":"POP","en":"POP"}}]},{"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":77396,"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":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"biobank-japan","label":{"en":"BioBank Japan"}},{"code":"okinawa-biobank","label":{"en":"Okinawa Biobank"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"hondo","label":{"ja":"本土","en":"Hondo"}},{"code":"ryukyu","label":{"ja":"琉球","en":"Ryukyu"}}]},{"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":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"}},{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"SampleのQC： sample call rates ≧ 0.98\nGenotypingのQC：SNP call rate ≧ 0.98 (OBi, POP) or 0.99 (BBJ) , MAF ≧ 0.01, p-values for Hardy-Weinberg equilibrium (HWE) test ≧ 1×10⁻⁶\nImputation後のQC：MAF ≧ 0.005, Rsq ≧ 0.7","en":"Sample QC: sample call rates ≧ 0.98\nGenotyping QC: SNP call rate ≧ 0.98 (OBi, POP) or 0.99 (BBJ), MAF ≧ 0.01, p-values for Hardy-Weinberg equilibrium (HWE) test ≧ 1×10⁻⁶\nImputation QC: MAF ≥ 0.005 and imputation score (Rsq) ≥ 0.7"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"minimac4\nImputation：reference 1KGP3+JEWEL_3K","en":"minimac4\nImputation: reference 1KGP3+JEWEL_3K"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":9862117,"unit":null,"high":null,"suffix":{"ja":" variants","en":" variants"}}]},{"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"}}]}