{"id":"NHA000204","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000204","datePublished":"2025-12-02","dateModified":"2025-12-02","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":"Y染色体欠失のGWAS統計量","en":"GWAS for loss of the Y chromosome"}}],"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":"日本人男性：161,026名\nバイオバンク・ジャパン（BBJ）：120,522名\nJapan COVID-19 Task Force（JCTF）：3,161名\n東北メディカル・メガバンク（TMM）：26,544名\nワクチン接種者コホート（COVC）*1：888名\n愛知県がんセンター病院疫学研究（HERPACC）：6,636名\n次世代多目的コホート（JPHC）：3,275名","en":"161,026 Japanese males\nBioBank Japan (BBJ): 120,522\nJapan COVID-19 Task Force (JCTF): 3,161\nTohoku Medical Megabank (TMM): 26,544\nCohort of COVID-19 vaccine recipients (COVC)*1: 888\nHospital-based Epidemiologic Research Program at Aichi Cancer Center (HERPACC): 6,636\nThe Japan Public Health Center-based Prospective Study for the Next Generation (JPHC): 3,275"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":161026,"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":"tohoku-medical-megabank","label":{"en":"Tohoku Medical Megabank"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}}]},{"key":"sex","label":{"ja":"性別","en":"Sex"},"type":"vocabulary","terms":[{"code":"male","label":{"ja":"男性","en":"Male"}}]},{"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":"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"}},{"code":"illumina-infinium-asian-screening-array","label":{"en":"Illumina Infinium Asian Screening Array"}},{"code":"affymetrix-japonica-array","label":{"en":"Affymetrix Japonica Array"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"サンプル QC：We excluded individuals with a low call rate (< 0.95) and outliers from the PCA-based East Asian cluster.\nバリアント QC：Quality control of the variants was conducted using the following criteria: (i) with a low call rate (< 0.99); (ii) with low minor allele counts (< 5); and (iii) with Hardy-Weinberg equilibrium test P value < 1.0 × 10−10.\nインピュテーション後のQC：Variants with imputation quality Rsq < 0.3 or minor allele frequency (MAF) < 0.005 were excluded.","en":"Sample QC: We excluded individuals with a low call rate (< 0.95) and outliers from the PCA-based East Asian cluster.\nVariant QC: Quality control of the variants was conducted using the following criteria: (i) with a low call rate (< 0.99); (ii) with low minor allele counts (< 5); and (iii) with Hardy-Weinberg equilibrium test P value < 1.0 × 10−10.\nPost-imputation QC: Variants with imputation quality Rsq < 0.3 or minor allele frequency (MAF) < 0.005 were excluded."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"BBJ：Eagle、Minimac3\nJCTF、COVC、HERPACC、JPHC：SHAPEIT4、Minimac4\nTMM：SHAPEIT2、IMPUTE4","en":"BBJ: Eagle, Minimac3\nJCTF, COVC, HERPACC, JPHC: SHAPEIT4, Minimac4\nTMM: SHAPEIT2, IMPUTE4"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"BBJ：SAIGE\nJCTF、COVC、HERPACC、JPHC：SAIGE\nTMM：regenie\nメタ解析：METAL","en":"BBJ: SAIGE\nJCTF, COVC, HERPACC, JPHC: SAIGE\nTMM: regenie\nmeta-analysis: METAL"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":9062001,"unit":null,"high":null,"suffix":{"ja":" variant (参照：全ゲノム配列データ n = 11,754 例からなる自家製の日本人特異的参照パネル)","en":" variant (reference: In-house Japanese-specific reference panel composed of n = 11,754 whole-genome sequence 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":"txt","label":{"en":"TXT"}},{"code":"docx","label":{"en":"DOCX"}}]}