{"id":"NHA000188","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000188","datePublished":"2023-06-27","dateModified":"2023-06-27","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":"間質性膀胱炎ハンナ型のGWAS","en":"GWAS for Hunner-type interstitial cystitis"}}],"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":"間質性膀胱炎ハンナ型（ICD10：N301）：144症例\n対照者：41,516名","en":"Hunner-type interstitial cystitis cases (ICD10: N301): 144\nControl participants: 41,516"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"N301","label":{"ja":"間質性膀胱炎（慢性）","en":"Interstitial cystitis (chronic)"}}],"name":{"ja":"間質性膀胱炎ハンナ型","en":"Hunner-type interstitial cystitis 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":41660,"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":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Japanese ancestry using PCA.\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.\nPost-imputation QC: We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 0.5%.","en":"Sample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Japanese ancestry using PCA.\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.\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":"shapeit4 for haplotype phasing\nminimac4 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\nSAIGE","en":"GenomeStudio for genotyping\nSAIGE"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":7909790,"unit":null,"high":null,"suffix":{"ja":" variants","en":" 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":"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":"docx","label":{"en":"DOCX"}},{"code":"zip","label":{"en":"ZIP"}}]}