{"id":"NHA000187","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000187","datePublished":"2023-06-06","dateModified":"2023-06-06","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":"15形質のGWAS","en":"GWAS for 15 phenotypes"}}],"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":"バイオバンク・ジャパン（180,215名）、UKバイオバンク（377,441名）\nFinnGen、BCAC、PRACTICALの要約統計量を含めたメタ解析（乳がん：648,746名、前立腺がん：482,080名）\n疾患群：胆道がん（ICD10：C22.1、23-24）、乳がん（ICD10：C50）、子宮頸がん（ICD10：C53）、大腸がん（ICD10：C18-20）、子宮体がん（ICD10：C54）、食道がん（ICD10：C15）、胃がん（ICD10：C16）、肝細胞がん（ICD10：C22.0）、肺がん（ICD10：C34）、非ホジキンリンパ腫（ICD10：C82-83）、卵巣がん（ICD10：C56）、膵がん（ICD10：C25）、前立腺がん（ICD10：C61）\n対照群：がんに罹患していない登録者\n（各コホート内で疾患群間にはサンプルオーバーラップあり）\n形質数：15","en":"BioBank Japan (n=180,215), UK Biobank (n=377,441)\nlarge-scale meta-analysis including the summary statistics of other cohorts (FinnGen, BCAC, and PRACTICAL) for breast and prostate cancer (n=648,746 and 482,080)\nno. Phenotypes: 15\nPatients: biliary tract (ICD10: C22.1, 23-24), breast (ICD10: C509), cervical (ICD10: C53), colorectal (ICD10: C18-20), endometrial (ICD10: C54), esophageal (ICD10: C15), gastric (ICD10: C16), hepatocellular (ICD10: C22.0), lung (ICD10: C34), non-Hodgkin's lymphoma (ICD10: C82-83), ovarian (ICD10: C56), pancreatic (ICD10: C25), and prostate (ICD10: C61) cancer\nControls: without cancer individuals\n(There is overlap among patients in each disease category)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C221","label":{"ja":"肝内胆管癌","en":"Malignant neoplasm: Intrahepatic bile duct carcinoma"}},{"code":"C23","label":{"ja":"胆のう＜嚢＞の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of gallbladder"}},{"code":"C24","label":{"ja":"その他及び部位不明の胆道の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of other and unspecified parts of biliary tract"}}],"name":{"ja":"胆道がん","en":"biliary tract"}},{"terms":[{"code":"C509","label":{"ja":"乳房，部位不明","en":"Malignant neoplasm: Breast, unspecified"}}],"name":{"ja":"乳がん","en":"breast"}},{"terms":[{"code":"C53","label":{"ja":"子宮頚部の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of cervix uteri"}}],"name":{"ja":"子宮頸がん","en":"cervical"}},{"terms":[{"code":"C18","label":{"ja":"結腸の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of colon"}},{"code":"C19","label":{"ja":"直腸S状結腸移行部の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of rectosigmoid junction"}},{"code":"C20","label":{"ja":"直腸の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of rectum"}}],"name":{"ja":"大腸がん","en":"colorectal"}},{"terms":[{"code":"C54","label":{"ja":"子宮体部の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of corpus uteri"}}],"name":{"ja":"子宮体がん","en":"endometrial"}},{"terms":[{"code":"C15","label":{"ja":"食道の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of oesophagus"}}],"name":{"ja":"食道がん","en":"esophageal"}},{"terms":[{"code":"C16","label":{"ja":"胃の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of stomach"}}],"name":{"ja":"胃がん","en":"gastric"}},{"terms":[{"code":"C220","label":{"ja":"肝細胞癌","en":"Malignant neoplasm: Liver cell carcinoma"}}],"name":{"ja":"肝細胞がん","en":"hepatocellular"}},{"terms":[{"code":"C34","label":{"ja":"気管支及び肺の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of bronchus and lung"}}],"name":{"ja":"肺がん","en":"lung"}},{"terms":[{"code":"C82","label":{"ja":"ろ＜濾＞胞性リンパ腫","en":"Follicular lymphoma"}},{"code":"C83","label":{"ja":"非ろ＜濾＞胞性リンパ腫","en":"Non-follicular lymphoma"}}],"name":{"ja":"非ホジキンリンパ腫","en":"non-Hodgkin's lymphoma"}},{"terms":[{"code":"C56","label":{"ja":"卵巣の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of ovary"}}],"name":{"ja":"卵巣がん","en":"ovarian"}},{"terms":[{"code":"C25","label":{"ja":"膵の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of pancreas"}}],"name":{"ja":"膵がん","en":"pancreatic"}},{"terms":[{"code":"C61","label":{"ja":"前立腺の悪性新生物＜腫瘍＞","en":"Malignant neoplasm of prostate"}}],"name":{"ja":"前立腺がん","en":"prostate"}}]},{"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-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":"uk-biobank","label":{"en":"UK Biobank"}},{"code":"finngen","label":{"en":"FinnGen"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}},{"code":"european","label":{"ja":"ヨーロッパ人","en":"European"}},{"code":"finnish","label":{"ja":"フィンランド人","en":"Finnish"}}]},{"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"}},{"code":"uk-bileve-axiom-array","label":{"en":"UK BiLEVE Axiom Array"}},{"code":"uk-biobank-axiom-array","label":{"en":"UK Biobank Axiom Array"}},{"code":"finngen1-thermofisher-array","label":{"en":"FinnGen1 ThermoFisher Array"}},{"code":"infinium-oncoarray-500k-v1-0-beadchip-kit","label":{"en":"Infinium OncoArray-500K v1.0 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":"applied-biosystems-uk-bileve-axiom-array","label":{"en":"Applied Biosystems UK BiLEVE Axiom Array"}},{"code":"applied-biosystems-uk-biobank-axiom-array","label":{"en":"Applied Biosystems UK Biobank Axiom Array"}},{"code":"thermo-fisher-scientific-finngen1-thermofisher-array","label":{"en":"Thermo Fisher Scientific FinnGen1 ThermoFisher Array"}},{"code":"illumina-icogs","label":{"en":"Illumina iCOGS"}},{"code":"illumina-oncoarray","label":{"en":"Illumina OncoArray"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"各データセットのsample QCとVariant QC：Read meファイルをご参照ください。\nRsq < 0.7 および MAF < 0.01 のバリアントを除外","en":"Sample QC and Variant QC for each dataset: refer to ReadMe file\nWe excluded the variants with Rsq < 0.7 and MAF < 0.01."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"BBJ：Eagle、Minimac3\nUK Biobank：IMPUTE4\nFinnGen：beagle4.1\nBCAC：IMPUTE2\nPRACTICAL：IMPUTE2","en":"BBJ: Eagle, Minimac3\nUK Biobank: IMPUTE4\nFinnGen: beagle4.1\nBCAC: IMPUTE2\nPRACTICAL: IMPUTE2"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"SAIGE software was used with age, sex, and top five principal components as covariates\nRE2C software was used for the multi-trait meta-analysis adjusting for sample overlap between GWAS summary data","en":"SAIGE software was used with age, sex, and top five principal components as covariates.\nRE2C software was used for the multi-trait meta-analysis adjusting for sample overlap between GWAS summary data."}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":7398798,"unit":null,"high":null,"prefix":{"ja":"BBJ 13MN: ","en":"BBJ 13MN: "}},{"value":7442557,"unit":null,"high":null,"prefix":{"ja":"BBJ 各がん種: ","en":"BBJ each cancer: "},"suffix":{"ja":" (平均)","en":" (Mean)"}},{"value":7420485,"unit":null,"high":7444681,"prefix":{"ja":"BBJ 各がん種: ","en":"BBJ each cancer: "},"suffix":{"ja":" (範囲)","en":" (Range)"}},{"value":9602853,"unit":null,"high":null,"prefix":{"ja":"UK Biobank 13MN: ","en":"UK Biobank 13MN: "}},{"value":9620786,"unit":null,"high":null,"prefix":{"ja":"UK Biobank 各がん種: ","en":"UK Biobank each cancer: "},"suffix":{"ja":" (平均)","en":" (Mean)"}},{"value":9620343,"unit":null,"high":9620935,"prefix":{"ja":"UK Biobank 各がん種: ","en":"UK Biobank each cancer: "},"suffix":{"ja":" (範囲)","en":" (Range)"}},{"value":5374018,"unit":null,"high":null,"prefix":{"ja":"BBJ＋UK Biobank 13MN: ","en":"BBJ+UK Biobank 13MN: "}},{"value":5696155,"unit":null,"high":null,"prefix":{"ja":"BBJ＋UK Biobank 各がん種: ","en":"BBJ+UK Biobank each cancer: "},"suffix":{"ja":" (平均)","en":" (Mean)"}},{"value":5677934,"unit":null,"high":5698357,"prefix":{"ja":"BBJ＋UK Biobank 各がん種: ","en":"BBJ+UK Biobank each cancer: "},"suffix":{"ja":" (範囲)","en":" (Range)"}},{"value":5104756,"unit":null,"high":null,"prefix":{"ja":"BBJ＋UK Biobank＋FinnGen＋BCAC (乳がん): ","en":"BBJ+UK Biobank+FinnGen+BCAC (breast cancer): "}},{"value":5105796,"unit":null,"high":null,"prefix":{"ja":"BBJ＋UK Biobank＋FinnGen＋PRACTICAL (前立腺がん): ","en":"BBJ+UK Biobank+FinnGen+PRACTICAL (prostate cancer): "}},{"value":5100089,"unit":null,"high":null,"prefix":{"ja":"BBJ＋UK Biobank＋FinnGen＋BCAC＋PRACTICAL (乳がん＋前立腺がん): ","en":"BBJ+UK Biobank+FinnGen+BCAC+PRACTICAL (breast cancer+prostate cancer): "}}]},{"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"}}]}