{"id":"NHA000161","research":"hum0237","url":"https://humandbs.dbcls.jp/dataset/NHA000161","datePublished":"2021-03-05","dateModified":"2021-03-05","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":"アルツハイマー病のGWAS","en":"GWAS for Alzheimer's disease"}}],"experiments":[{"label":"Genotyping by array","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"アルツハイマー病（ICD10：F00）：3,962症例\n非アルツハイマー病：4,074名","en":"Alzheimer's disease (ICD10: F00): 3,962 cases\n4,074 controls"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"F00","label":{"ja":"アルツハイマー＜Alzheimer＞病の認知症（G30.-†）","en":"Dementia in Alzheimer disease"}}],"name":{"ja":"アルツハイマー病","en":"Alzheimer's disease"}}]},{"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":8036,"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":"axiom-2-0-reagent-kit","label":{"en":"Axiom 2.0 Reagent Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"affymetrix-japonica-array","label":{"en":"Affymetrix Japonica Array"}},{"code":"affymetrix-genome-wide-human-snp-array-6-0","label":{"en":"Affymetrix Genome-Wide Human SNP Array 6.0"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"サンプルQCs：\n（1）性情報とX染色体近交係数から予測される性の不一致\n（2）近交係数：ヘテロ接合度 < 0.1\n（3）サンプル内genotypeコール率 < 0.95\n（4）血縁係数 > 0.2\n（5）主成分分析によって東アジア集団（1000 Genomes Phase 3）クラスターから外れた検体\nマーカー (SNPs・Indels) QCs：\n（1）マーカー内genotypingコール率 < 0.95\n（2）マイナーアリル頻度（MAF） < 0.001\n（3）HWE P < 0.001","en":"Sample QCs: (1) sex inconsistencies (--check-sex), (2) inbreeding coefficient (--het 0.1), (3) genotype missingness (--missing 0.05), (4) kinship coefficient (--genome 0.2) and (5) exclusion of outliers from the clusters of East Asian populations in principal component analysis that was conducted together with 1000 Genomes Phase 3 data.\nMarker (SNPs and Indels) QCs: (1) genotyping efficiency or call rate (--geno 0.95), (2) minor allele frequency (--freq 0.001), (3) Hardy-Weinberg equilibrium (--hwe 0.001)."}},{"key":"imputation","label":{"ja":"インピュテーション","en":"Imputation"},"type":"text","text":{"ja":"IMPUTE2 with 3.5KJPN (ToMMo)\nIMPUTE2 with 1000 Genomes Project reference panel（1000 Genomes Phase 3）","en":"IMPUTE2 with 3.5K Japanese reference panel\nIMPUTE2 with 1000 Genomes Project reference panel (1000 Genomes Phase 3)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"Axiom Analysis suite 1.1.1.66","en":"Axiom Analysis suite 1.1.1.66"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":4852957,"unit":null,"high":null,"suffix":{"ja":" SNVs","en":" SNVs"}}]},{"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"}}]}