{"id":"NHA000169","research":"hum0343","url":"https://humandbs.dbcls.jp/dataset/NHA000169","datePublished":"2022-05-26","dateModified":"2022-05-26","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":"COVID19感染者のGWAS集計情報","en":"GWAS for COVID-19"}}],"experiments":[{"label":"Genome wide SNPs","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"[GWAS-1]\nCOVID-19感染者 （ICD-10：U071）：2,393症例、対照者：3,289名\n[GWAS-2]\n[GWAS-1]のCOVID-19感染者の内、重症者：990症例、対照者：3,289名\n[GWAS-3]\n[GWAS-1] の対象者の内65歳未満の者（COVID-19感染者：1,484症例、対照者：2,377名）\n[GWAS-4]\n[GWAS-3]の65歳未満のCOVID19感染者の内、重症者：440症例、対照者：2,377名","en":"[GWAS-1]\nCOVID-19 (ICD-10: U071): 2,393 cases, Healthy controls: 3,289 individuals\n[GWAS-2]\nSevere COVID-19: 990 cases and 3,289 healthy controls from [GWAS-1]\n[GWAS-3]\nCOVID-19 under age 65: 1,484 cases and 2,377 healthy controls under age 65 from [GWAS-1]\n[GWAS-4]\nSevere COVID-19 under age 65: 440 cases and 2,377 healthy controls under age 65 from [GWAS-3]"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"U071","label":{"ja":"コロナウイルス感染症2019，ウイルスが同定されたもの","en":"COVID-19, virus identified"}}],"name":{"ja":"COVID-19感染者","en":"COVID-19"}}]},{"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":5682,"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":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"genotyping-by-array","label":{"en":"Genotyping by array"}}]},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"infinium-asian-screening-array-kit","label":{"en":"Infinium Asian Screening Array Kit"}}]},{"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"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"SampleのQC： We excluded samples with\n(1) sample call rate < 0.97\n(2) excess heterozygosity of genotypes > mean + 3SD\n(3) related samples with PI_HAT > 0.175\n(4) outlier samples from East Asian clusters in principal component analysis with 1000 Genomes Project samples.\nGenotypingのQC： We excluded variants with\n(1) variant call rate < 0.99\n(2) significant call rate differences between cases and controls with P < 5.0×10-8\n(3) deviation from Hardy-Weinberg equilibrium with P < 1.0×10-6\n(4) minor allele count < 5\nImputation後のQC： MAF ≥ 0.1% and imputation score (Rsq) > 0.5","en":"Sample QC: We excluded samples with\n(1) sample call rate < 0.97\n(2) excess heterozygosity of genotypes > mean + 3SD\n(3) related samples with PI_HAT > 0.175\n(4) outlier samples from East Asian clusters in principal component analysis with 1000 Genomes Project samples.\nGenotyping QC: We excluded variants with\n(1) variant call rate < 0.99\n(2) significant call rate differences between cases and controls with P < 5.0×10-8\n(3) deviation from Hardy-Weinberg equilibrium with P < 1.0×10-6\n(4) minor allele count < 5\nImputation QC: MAF ≥ 0.1% and imputation score (Rsq) > 0.5"}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"haplotype phasing: SHAPEIT4 (autosome) 、SHAPEIT2 (X-chromosome)\nimputation: Minimac4","en":"haplotype phasing: SHAPEIT4 (autosome), SHAPEIT2 (X-chromosome)\nimputation: Minimac4"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"genotyping: GenomeStudio\n関連解析: PLINK2","en":"genotyping: GenomeStudio\nAssociation Analysis: PLINK2"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":13484569,"unit":null,"high":null,"suffix":{"ja":" バリアント ([GWAS-1])","en":" variants ([GWAS-1])"}},{"value":13199053,"unit":null,"high":null,"suffix":{"ja":" バリアント ([GWAS-2])","en":" variants ([GWAS-2])"}},{"value":13241602,"unit":null,"high":null,"suffix":{"ja":" バリアント ([GWAS-3])","en":" variants ([GWAS-3])"}},{"value":12764136,"unit":null,"high":null,"suffix":{"ja":" バリアント ([GWAS-4])","en":" variants ([GWAS-4])"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"imputed-genotype-data","label":{"ja":"インピュテーション済み遺伝子型データ","en":"Imputed genotype data"}}]},{"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)"}}]}]}],"fileFormats":[{"code":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}