{"id":"NHA000190","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000190","datePublished":"2023-10-02","dateModified":"2023-10-02","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":"腸内微生物叢のGWAS\n血中代謝物のGWAS\nKEGG Gene OrthologおよびKEGG PathwayのGWAS","en":"GWAS for gut microbiome\nGWAS for plasma metabolite\nGWAS for KEGG Gene Ortholog and KEGG Pathway"}}],"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":"日本人集団：524名（423種の微生物）\n日本人集団：362名（306種の代謝物）\n日本人集団：524名（KEGG Gene OrthologおよびKEGG Pathway）","en":"524 Japanese individuals (423 species in the gut microbiome)\n306 Japanese individuals (306 plasma metabolites)\n524 Japanese individuals (KEGG Gene Ortholog and KEGG Pathway)"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":524,"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":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"japanese","label":{"ja":"日本人","en":"Japanese"}}]},{"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":"experimental-method","label":{"ja":"実験方法","en":"Experimental method"},"type":"vocabulary","terms":[{"code":"genotyping-by-array","label":{"en":"Genotyping by array"}},{"code":"wgs","label":{"en":"WGS"}}]},{"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"}},{"code":"truseq-dna-pcr-free-library-prep-kit","label":{"en":"TruSeq DNA PCR-Free Library Prep Kit"}},{"code":"kapa-hyper-prep-kit","label":{"en":"KAPA Hyper Prep 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"}},{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}},{"code":"illumina-hiseq-2500","label":{"en":"Illumina HiSeq 2500"}},{"code":"illumina-hiseq-3000","label":{"en":"Illumina HiSeq 3000"}},{"code":"illumina-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}}]},{"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":"・SNP array data：\nサンプル QC：We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian ancestry using PCA.\nバリアント 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.\nインピュテーション後のQC：We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 1%.\n・WGS：\nWe excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10\nAfter imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%.","en":"SNP array data:\nSample QC: We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian 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 < 1%.\nWGS:\nWe excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10\nAfter imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%."}},{"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":"・SNP array:\n遺伝子型決定: GenomeStudio\n・WGS:\nWA-MEM v0.7.13、GATK v3.8-0\nPLINK2","en":"SNP array:\nGenotyping: GenomeStudio\nWGS:\nWA-MEM v0.7.13 + GATK v3.8-0\nPLINK2"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":7213470,"unit":null,"high":null,"prefix":{"ja":"腸内微生物叢/KEGG (SNP array): ","en":"Gut microbiota/KEGG (SNP array): "},"suffix":{"ja":" variants","en":" variants"}},{"value":6840258,"unit":null,"high":null,"prefix":{"ja":"血中代謝物 (WGS): ","en":"Blood metabolites (WGS): "},"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":"tsv","label":{"en":"TSV"}},{"code":"docx","label":{"en":"DOCX"}}]}