{"id":"JGAD000660","research":"hum0311","url":"https://humandbs.dbcls.jp/dataset/JGAD000660","datePublished":"2022-08-12","dateModified":"2022-08-12","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"BBJ第一コホート180,882名を男女別に7つのバッチに分けて実施したImputationデータならびにindexデータ","en":"Imputation data and index data for 180,882 patients from BBJ 1st cohort"}}],"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":"BBJ第一コホート（47疾患）：180,882名\nICD10：A15-A16、B16-B17.0、B18.0-B18.1、B17.1、B18.2、C15、C16、C18、C22、C23-C24、C25、C33-C34、C50、C53、C54、C56、C61、C81、D25、E05、E10、E78.0-E78.5、G12、G40-G41、H25-H26、H40-H42、I20、I21-I22、I44-I49、I50、I60、I69.0、I63、I69.3、I70、J30、J41-J44、J45-J46、J80-J84、K05、K74.3-K74.6、L00-L99、L20、M05-M06、M80-M82、N04、N20-N23、N80、R00-R9","en":"180,882 patients from BBJ 1st cohort\nICD10: A15-A16, B16-B17.0, B18.0-B18.1, B17.1, B18.2, C15, C16, C18, C22, C23-C24, C25, C33-C34, C50, C53, C54, C56, C61, C81, D25, E05, E10, E78.0-E78.5, G12, G40-G41, H25-H26, H40-H42, I20, I21-I22, I44-I49, I50, I60, I69.0, I63, I69.3, I70, J30, J41-J44, J45-J46, J80-J84, K05, K74.3-K74.6, L00-L99, L20, M05-M06, M80-M82, N04, N20-N23, N80, R00-R9"}},{"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":180882,"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":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"east-asian","label":{"ja":"東アジア人","en":"East Asian"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血（一部唾液）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":[{"code":"humanomniexpressexome-beadchip-kit","label":{"en":"HumanOmniExpressExome BeadChip Kit"}},{"code":"humanomniexpress-beadchip-kit","label":{"en":"HumanOmniExpress BeadChip Kit"}},{"code":"humanexome-beadchip-kit","label":{"en":"HumanExome BeadChip Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-humanomniexpressexome","label":{"en":"Illumina HumanOmniExpressExome"}},{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch38","label":{"en":"GRCh38"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"imputation前のQC:\nBefore imputation, we excluded SNPs using the following criteria:\n\nHeterozygosity count for each chip < 5\nP-value for Hardy-Weinberg equilibrium (HWE) for each chip < 1.0 x 10^-6\n*- Genotype concordance rate with whole-genome sequencing (WGS) for 939 samples < 99.5% and its non-reference discordance rate >= 0.5%\nLower call rate SNPs if the position was the same when merging datasets\nCall rate < 99%*\nP-values for chrX SNPs were calculated by using female samples\n\nWe also excluded samples using the following criteria:\n\nCall Rate < 98%\nSamples whose inferred sex was not matched with the clinical information\nLower call rate samples for duplicated or monozygotic twin in the dataset\nOutliers from East Asian clusters from principal component analysis with 1KGp3v5 samples.","en":"Before imputation, we excluded SNPs using the following criteria:\n\nHeterozygosity count for each chip < 5\nP-value for Hardy-Weinberg equilibrium (HWE) for each chip < 1.0 x 10^-6\n*- Genotype concordance rate with whole-genome sequencing (WGS) for 939 samples < 99.5% and its non-reference discordance rate >= 0.5%\nLower call rate SNPs if the position was the same when merging datasets\nCall rate < 99%*\nP-values for chrX SNPs were calculated by using female samples\n\nWe also excluded samples using the following criteria:\n\nCall Rate < 98%\nSamples whose inferred sex was not matched with the clinical information\nLower call rate samples for duplicated or monozygotic twin in the dataset\nOutliers from East Asian clusters from principal component analysis with 1KGp3v5 samples."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"Eagle software (v2.4.1) without a reference panel\nMinimac4 software (v1.0.2)","en":"Eagle software (v2.4.1) without a reference panel\nMinimac4 software (v1.0.2)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenomeStudio Software","en":"GenomeStudio Software"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":515587,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" SNVs","en":" SNVs"}},{"value":11140,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "},"suffix":{"ja":" SNVs","en":" SNVs"}}]},{"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)"}}]}]}],"dataVolume":11130036776095,"fileFormats":[{"code":"vcf","label":{"en":"VCF"}},{"code":"tbi","label":{"en":"TBI"}}]}