{"id":"JGAD000018","research":"hum0028","url":"https://humandbs.dbcls.jp/dataset/JGAD000018","datePublished":"2020-09-28","dateModified":"2024-10-08","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"HLA領域（7座位）の遺伝子型情報およびHLAアリル情報","en":"HLA alleles and SNPs\nin HLA region (7 loci)"}}],"experiments":[{"label":"Targeted DNA sequencing","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"日本人健常者：908名","en":"908 Japanese healthy controls"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":908,"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gDNA","en":"gDNAs 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":"targeted-dna-sequencing","label":{"en":"Targeted DNA sequencing"}}]},{"key":"targets","label":{"ja":"測定対象","en":"Target"},"type":"text","text":{"ja":"HLA領域（chr6:29,000,000-34,000,000, GRCh37）\n対象変異数：8817個\n（SNP：7149個, HLA 2-digit/4-digit：226個, HLA amino acid polymorphisms：1442個）\nHLA座位：HLA-A, -C, -B, -DRB1, -DQA1, -DQB1, -DPA1, -DPB1","en":"HLA region (chr6:29,000,000-34,000,000, GRCh37)\n8817 polymorphisms\n(7149 SNPs, HLA 2-digit/4-digit polymorphisms: 226, HLA amino acid polymorphisms: 1442)"}},{"key":"reagents","label":{"ja":"試薬キット","en":"Reagent kit"},"type":"vocabulary","terms":[{"code":"humanomniexpress-beadchip-kit","label":{"en":"HumanOmniExpress BeadChip Kit"}},{"code":"humanexome-beadchip-kit","label":{"en":"HumanExome BeadChip Kit"}},{"code":"immunochip","label":{"en":"Immunochip"}},{"code":"humanhap550-beadchip-kit","label":{"en":"HumanHap550 BeadChip Kit"}},{"code":"wakflow-hla-typing-kit","label":{"en":"WAKFlow HLA Typing Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-humanomniexpress","label":{"en":"Illumina HumanOmniExpress"}},{"code":"illumina-humanexome","label":{"en":"Illumina HumanExome"}},{"code":"illumina-immunochip","label":{"en":"Illumina Immunochip"}},{"code":"illumina-humanhap550","label":{"en":"Illumina HumanHap550"}}]},{"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 Call rate < 0.98, SNP call rate < 0.99, HWE-P < 1x10^-6","en":"Sample Call Rate < 0.98, SNP Call Rate < 0.99, HWE-P < 1x10^-6"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenCall software（GenomeStudio）","en":"GenCall software (GenomeStudio)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":8817,"unit":null,"high":null,"suffix":{"ja":" SNPs","en":" SNPs"}}]},{"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)"}}]}]}],"dataVolume":35360304,"fileFormats":[{"code":"bed","label":{"en":"BED"}},{"code":"bim","label":{"en":"BIM"}},{"code":"fam","label":{"en":"FAM"}},{"code":"txt","label":{"en":"TXT"}}]}