{"id":"NHA000201","research":"hum0505","url":"https://humandbs.dbcls.jp/dataset/NHA000201","datePublished":"2025-05-30","dateModified":"2025-05-30","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":"9歳時のImmunoCAP ISACによる特異的IgE検査を実施済みの成育コホート研究参加者564名のGWAS集計情報","en":"GWAS for 564 children who participated in the adult cohort study"}}],"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":"9歳時のImmunoCAP ISACによる特異的IgE検査を実施済みの成育コホート研究参加者564名\n総IgE値データは562名","en":"564 children who participated in T-child study (a birth cohort study) with ImmunoCAP ISAC sIgE 112 data available at age 9 years\n562 children for total serum IgE data"}},{"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":564,"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":"age-group","label":{"ja":"年齢層","en":"Age group"},"type":"vocabulary","terms":[{"code":"child","label":{"ja":"小児","en":"Child"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血もしくは唾液から抽出したDNA","en":"DNAs extracted from peripheral blood cells or saliva"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"saliva","label":{"ja":"唾液","en":"Saliva"}}]},{"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"}}]},{"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のQC：以下の基準に基づき、サンプルを除外した\n(1) コール率が98％未満\n(2) 1000 Genomes Project Phase 3 を用いた主成分分析（principal component analysis）により推定された日本人集団からの外れ値\n(3) 推定された親族関係がPI_HAT＞0.1875の近親者\n(4) 表現型と遺伝子型による性別の不一致\nGenotypingのQC：以下の基準に基づき、ジェノタイピングされたバリアントを選定した\n(1) Gentrainスコア≧0.7\n(2) マイナーアレル頻度＞1％\n(3) ジェノタイピングコール率＞95％\n(4) Hardy-Weinberg平衡検定のP値＞1.0 × 10⁻⁵\nImputation後のQC：Rsq＞0.7、かつ、マイナーアレルカウント≧20","en":"Sample QC: We excluded samples based on the following criteria\n(1) a call rate of < 98%\n(2) outliers from the Japanese ancestry estimated by use of principal-component (PC) analysis using the 1000 Genome Project Phase 3\n(3) PI_HAT > 0.1875\n(4) phenotype-genotype sex discordance\nGenotyping QC: We selected the genotyped variants based on the following criteria\n(1) Gentrain score of >= 0.7\n(2) minor allele frequency > 1%\n(3) variant genotyping call rate > 95%\n(4) Hardy-Weinberg-equilibrium P value > 1.0 × 10^-5.\nImputation QC: Rsq > 0.7 and minor allele count >= 20."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"SHAPEIT2 software and Minimac4 software\nImputation reference：JGAS000114 reference panel （GRCh37）","en":"SHAPEIT2 software and Minimac4 software\nImputation reference: JGAS000114 reference panel (GRCh37)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":7099279,"unit":null,"high":null,"prefix":{"ja":"総IgE: ","en":"Total IgE: "},"suffix":{"ja":" variants","en":" variants"}},{"value":6471740,"unit":null,"high":null,"prefix":{"ja":"総IgE以外: ","en":"Excluding total IgE: "},"suffix":{"ja":" variants","en":" variants"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"gwas-summary-statistics","label":{"ja":"GWAS 要約統計量","en":"GWAS summary statistics"}}]},{"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":"txt","label":{"en":"TXT"}},{"code":"docx","label":{"en":"DOCX"}}]}