{"id":"NHA000195","research":"hum0197","url":"https://humandbs.dbcls.jp/dataset/NHA000195","datePublished":"2024-10-28","dateModified":"2024-10-28","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":"eHHV-6B陽性/陰性を示す自己免疫疾患のGWAS統計量","en":"GWAS for autoimmune diseases"}}],"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":"自己免疫疾患（ICD10：L400、M0690、M329、J840、G35）：238症例\neHHV-6B陽性：22症例\neHHV-6B陰性：216症例","en":"Autoimmune diseases (ICD10: L400, M0690, M329, J840, G35): 238 cases\neHHV-6B-positive: 22 cases\neHHV-6B-negative: 216 cases"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"L400","label":{"ja":"尋常性乾せん＜癬＞","en":"Psoriasis vulgaris"}},{"code":"M069","label":{"ja":"関節リウマチ，詳細不明","en":"Rheumatoid arthritis, unspecified"}},{"code":"M329","label":{"ja":"全身性エリテマトーデス＜紅斑性狼瘡＞＜SLE＞，詳細不明","en":"Systemic lupus erythematosus, unspecified"}},{"code":"J840","label":{"ja":"肺胞性及び肺胞周囲性病態","en":"Alveolar and parietoalveolar conditions"}},{"code":"G35","label":{"ja":"多発性硬化症","en":"Multiple sclerosis"}}],"name":{"ja":"自己免疫疾患","en":"Autoimmune diseases"}}]},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"affected","label":{"ja":"罹患","en":"Affected"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":238,"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":"wgs","label":{"en":"WGS"}}]},{"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":"truseq-dna-pcr-free-library-prep-kit","label":{"en":"TruSeq DNA PCR-Free Library Prep Kit"}}]},{"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"}},{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"t2t-chm13","label":{"en":"T2T-CHM13"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"Sample QC: Individuals were excluded if they showed conflicting sex assignments between genetically inferred sex by variants and WGS coverage, deviating heterozygosity rate (±3 standard deviations), or cryptic relatedness (pi-hat > 0.2). We included samples of the estimated Japanese ancestry using PCA. Four cases were excluded.\nVariant QC: We excluded (1) non-autosomal variants, (2) multi-allelic sites and spanning deletions, and (3) variants with P-value for Hardy?Weinberg equilibrium < 1e-10 in cases and < 1e-6 in controls.","en":"Sample QC: Individuals were excluded if they showed conflicting sex assignments between genetically inferred sex by variants and WGS coverage, deviating heterozygosity rate (±3 standard deviations), or cryptic relatedness (pi-hat > 0.2). We included samples of the estimated Japanese ancestry using PCA. Four cases were excluded.\nVariant QC: We excluded (1) non-autosomal variants, (2) multi-allelic sites and spanning deletions, and (3) variants with P-value for Hardy?Weinberg equilibrium < 1e-10 in cases and < 1e-6 in controls."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"The FASTQ reads were aligned to T2T-CHM13v2.0 with BWA-MEM (v0.7.27), followed by GATK4 MarkDuplicates and Base Quality Score Recalibration (v4.2.6.1) according to the GATK Best Practice. Then, we performed per-sample SNP and indel calling using GATK4 HaplotypeCaller and joint genotyping using GATK4 GenomicsDBImport and GenotypeGVCF. We conducted LD-based genotype refinement for low-confidence genotypes and missing sites in WGS data using BEAGLE v5.4 with default settings.\nPLINK v2.0","en":"The FASTQ reads were aligned to T2T-CHM13v2.0 with BWA-MEM (v0.7.27), followed by GATK4 MarkDuplicates and Base Quality Score Recalibration (v4.2.6.1) according to the GATK Best Practice. Then, we performed per-sample SNP and indel calling using GATK4 HaplotypeCaller and joint genotyping using GATK4 GenomicsDBImport and GenotypeGVCF. We conducted LD-based genotype refinement for low-confidence genotypes and missing sites in WGS data using BEAGLE v5.4 with default settings.\nPLINK v2.0 software was used with top two principal components and sex as covariates."}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":6464509,"unit":null,"high":null,"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"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"}}]}