{"id":"JGAD000777","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000777","datePublished":"2023-11-09","dateModified":"2023-11-09","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":"BBJ第1コホート1,007名のWGSデータ","en":"WGS for 1,007 individuals"}}],"experiments":[{"label":{"ja":"WGS","en":"WGS"},"values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"2003年から2007年度にバイオバンク・ジャパンに登録された47疾患患者：1,007名","en":"1,007 individuals from BBJ 1st cohort"}},{"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":1007,"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":"cohort","label":{"ja":"コホート","en":"Cohort"},"type":"vocabulary","terms":[{"code":"biobank-japan","label":{"en":"BioBank Japan"}}]},{"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":"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":"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-nano-dna-library-prep-kit","label":{"en":"TruSeq Nano DNA Library Prep Kit"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"超音波断片化","en":"Ultrasonic fragmentation"}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-hiseq-x","label":{"en":"Illumina HiSeq X"}}]},{"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":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch37","label":{"en":"GRCh37"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"BWA-MEM（version 0.7.13）","en":"BWA-MEM (version 0.7.13)"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"Picard 2.10.10","en":"Picard 2.10.10"}},{"key":"calibration-for-re-alignment-and-base-quality","label":{"ja":"再アライメント・塩基品質補正","en":"Realignment and base quality recalibration"},"type":"text","text":{"ja":"GATK 3.8","en":"GATK 3.8"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"GATK 3.8 HaplotypeCallerで変異コール時にMAPQ<20のリードを除外","en":"Reads with MAPQ<20 were excluded at variant calling with GATK 3.8 HaplotypeCaller"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"・常染色体，X PAR，X NonPAR 女性\nDP < 2 または GQ < 20 の genotype を missing に設定，call rate < 90% を除外\n・X NonPAR 男性，Y\nDP < 1 または GQ < 20 の genotype を missing に設定，call rate < 90% を除外\n・X NomPAR\n女性の HWE_P","en":"- Autosomal Chromosomes, X PAR, X NonPAR female\n- Set missing genotypes with DP < 2 or GQ < 20\n- call rate < 90% were excluded\n- X NonPAR male, Y\n- Set missing genotypes with DP < 1 or GQ < 20\n- call rate < 90% were excluded\n- X NomPAR\nHWE_P of female"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK Haplotype Caller（version 3.8）","en":"GATK Haplotype Caller (version 3.8)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":19.93455,"unit":"x","high":null}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":71643487,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "},"suffix":{"ja":" (AC=0を含むレコード数)","en":" (Record numbers including AC=0)"}},{"value":82997,"unit":null,"high":null,"prefix":{"ja":"X PAR: ","en":"X PAR: "},"suffix":{"ja":" (AC=0を含むレコード数)","en":" (Record numbers including AC=0)"}},{"value":2618495,"unit":null,"high":null,"prefix":{"ja":"X nonPAR: ","en":"X nonPAR: "},"suffix":{"ja":" (AC=0を含むレコード数)","en":" (Record numbers including AC=0)"}},{"value":171271,"unit":null,"high":null,"prefix":{"ja":"Y染色体: ","en":"Y chromosome: "},"suffix":{"ja":" (AC=0を含むレコード数)","en":" (Record numbers including AC=0)"}}]},{"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)"}}]}]}],"dataVolume":41586833299152,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"vcf","label":{"en":"VCF"}}]}