{"id":"NHA000171","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000171","datePublished":"2022-06-10","dateModified":"2022-06-10","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":"頭蓋内胚細胞腫瘍のGWAS","en":"GWAS for intracranial germ cell tumors"}}],"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":"頭蓋内胚細胞腫瘍（ICD10：C719）：133症例\n対照者：762名","en":"Intracranial germ cell tumors cases (ICD10: C719): 133\nControl participants: 762"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C719","label":{"ja":"脳，部位不明","en":"Malignant neoplasm: Brain, unspecified"}}],"name":{"ja":"頭蓋内胚細胞腫瘍","en":"Intracranial germ cell tumors cases"}}]},{"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":895,"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":"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":"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":"サンプルQC：\n① 検体毎のgenotyping call rate < 0.97、② PI_HAT > 0.17、③ 非東アジア系、に該当する場合除外\nバリアントQC：\n① genotyping call rate < 0.99、② minor allele count < 5、③ P-value for Hardy-Weinberg equilibrium in controls < 1.0 × 10^−5 、④ > 10% allele frequency difference with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project、に該当する場合除外\nインピュテーション後のQC：\n① Rsq < 0.7、② minor allele frequency < 0.5%、に該当する場合除外","en":"Sample QC:\nWe excluded individuals (i) with genotyping call rate < 0.97, (ii) in close kinship (PI_HAT > 0.17), and (iii) estimated of non-East Asian ancestry were excluded.\nVariant QC:\nWe excluded variants with (i) genotyping call rate < 0.99, (ii) minor allele count < 5, (iii) P value for Hardy-Weinberg equilibrium < 1.0 × 10−5 in controls, and (iv) > 10% allele frequency difference with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project.\nPost-imputation QC:\nWe excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"ハプロタイプフェージング: shapeit2 for haplotype phasing\nインピュテーション: minimac3","en":"shapeit2 for haplotype phasing\nminimac3 for imputation"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"遺伝子型決定: GenomeStudio\nPLINK2","en":"GenomeStudio for genotyping\nPLINK2"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":7803874,"unit":null,"high":null,"suffix":{"ja":" (常染色体のバリアント)","en":" (autosomal variants)"}},{"value":181867,"unit":null,"high":null,"suffix":{"ja":" (X染色体のバリアント)","en":" (X-chromosomal 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":"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":"docx","label":{"en":"DOCX"}},{"code":"zip","label":{"en":"ZIP"}}]}