{"id":"NHA000199","research":"hum0495","url":"https://humandbs.dbcls.jp/dataset/NHA000199","datePublished":"2025-02-13","dateModified":"2025-02-13","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":"発作性心房細動のExomeデータを元にしたGWAS統計情報","en":"GWAS for PAF using whole exome sequencing data"}}],"experiments":[{"label":"WES + Genotyping by array","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"PAF（ICD10：I48.0）：1,176症例\n非PAF（対照）：1,172名","en":"PAF (ICD10: I48.0): 1,176 cases\nnon-PAF (control) : 1,172 individuals"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"I480","label":{"ja":"発作性心房細動","en":"Paroxysmal atrial fibrillation"}}],"name":{"ja":"PAF","en":"PAF"}}]},{"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":2348,"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":"DNA 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":"wes","label":{"en":"WES"}},{"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":"sureselect-xt-reagent-kit","label":{"en":"SureSelect XT Reagent Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"超音波断片化（Covaris）","en":"Ultrasonic fragmentation (Covaris)"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}}]},{"key":"read-type","label":{"ja":"リードタイプ","en":"Read type"},"type":"vocabulary","terms":[{"code":"paired-end","label":{"ja":"ペアエンド","en":"Paired-end"}}]},{"key":"read-length","label":{"ja":"リード長","en":"Read length"},"type":"number","numbers":[{"value":150,"unit":"bp","high":null}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC：以下のサンプルを除外\n（1） Sample call rate < 0.97\n（2） 性別の不一致\n（3） 血縁関係者（親族係数0.088を超える二親等以上のサンプル）\n（4） 挿入/欠失比、データ量、ヘテロ接合性/ホモ接合性比に基づき外れた値のサンプル\nVariant QC：以下のバリアントを除外\n（1） genotype quality < 20\n（2） depth < 10\n（3） Allele imbalance\n（4） variant call rate < 0.97\n（5） Hardy-Weinberg equilibrium P-values =< 1 × 10−8\n（6） PCA\nImputation QC：-","en":"Sample QC: We excluded samples with\n(1) Sample call rate < 0.97\n(2) Samples with sex mismatches\n(3) One sample for each pair of second degree or closer relatives (kinship coefficient >0.088)\n(4) Samples with outliers in sample size, heterozygosity and missing rates\nVariant QC: We excluded variants with\n(1) genotype quality < 2\n(2) depth < 10\n(3) allele imbalance\n(4) variant call rate < 0.97\n(5) Hardy-Weinberg equilibrium P-values =< 1 × 10−8\n(6) PCA"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK HaplotypeCaller","en":"GATK HaplotypeCaller"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":518621,"unit":null,"high":null}]},{"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"}}]}