{"id":"NHA000198","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000198","datePublished":"2024-12-18","dateModified":"2024-12-18","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":"視神経脊髄炎関連疾患のGWAS統計量","en":"Summary statistics of the genome-wide meta-analysis of NMOSD"}}],"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":"視神経脊髄炎関連疾患（NMOSD）（ICD10：G36.0）：240症例\n対照者：50,578名","en":"NMOSD (ICD10: G36.0): 240 cases\ncontrol participants: 50,578"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"G360","label":{"ja":"視神経脊髄炎［デビック＜Devic＞病］","en":"Neuromyelitis optica [Devic]"}}],"name":{"ja":"視神経脊髄炎関連疾患（NMOSD）","en":"NMOSD"}}]},{"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":50818,"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":"Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) or potential sex chromosome aneuploidy. We included only the individuals of the estimated East Asian ancestry using the principal component (PC) analysis, and then further restricted to those in Japanese Hondo (the main island of Japan) clusters.\nVariant QC: We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project and in-house reference panel.\nPost-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%.","en":"Sample QC: We excluded samples with low genotyping call rates (call rate < 98%) or potential sex chromosome aneuploidy. We included only the individuals of the estimated East Asian ancestry using the principal component (PC) analysis, and then further restricted to those in Japanese Hondo (the main island of Japan) clusters.\nVariant QC: We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project and in-house reference panel.\nPost-imputation QC: We 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: shapeit4\nインピュテーション: minimac4","en":"Haplotype phasing: shapeit4\nImputation: minimac4"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"遺伝子型決定: GenomeStudio\nSAIGE","en":"Genotyping: GenomeStudio\nSAIGE"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":8894915,"unit":null,"high":null,"suffix":{"ja":" variants","en":" variants"}}]},{"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"}}]}