{"id":"JGAD000340","research":"hum0238","url":"https://humandbs.dbcls.jp/dataset/JGAD000340","datePublished":"2020-09-28","dateModified":"2020-11-18","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":"NGS（WGS）に内在するHHV-6配列","en":"NGS (HHV-6 sequences in WGS)"}}],"experiments":[{"label":"WGS","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"JGAD000220 / AGDD_000005に含まれる全ゲノムシーケンスデータの内、HHV-6のゲノム挿入が確認された検体：10検体","en":"BBJ participants (WGS are included in JGAD000220 / AGDD_000005) whose DNA sequences contain germline integration of HHV-6 sequences: 10 samples"}},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":10,"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":"sample","label":{"ja":"検体数","en":"Sample"}}]},{"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-2500","label":{"en":"Illumina HiSeq 2500"}}]},{"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":160,"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"}},{"code":"hhv-6a","label":{"en":"HHV-6A"}}]},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"BWA-MEMを使用して、日本人のNA18999(GenBankアクセッション番号: KY316047.1)から得られたiciHHV-6Aゲノムに対してHHV-6リードをアライメントした。\nアラインメントに基づいて、freebayes(バージョン: v1.2.0-2-g29c4002)を使用してバリアントコールを行った(パラメーターploidy = 1およびmin-alternate-fraction = 0.8)。\nその後、Genome Analysis Toolkit(GATK)v3.7のFastaAlternateReferenceMakerツールを使用して、結果として得られたバリアントをKY316047.1リファレンスゲノムにパッチすることにより、個人サンプルのiciHHV-6ウイルス配列を生成した。\nヒトゲノムのリファレンスゲノム(hg19)にマッピングされないリードを使用し、HHV-6リファレンスに再度アライメントを行った。\nHHV-6カバレッジ高く、ヒトゲノムにおける内在化が疑われる10サンプルを選択した。","en":"We aligned HHV-6 reads against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM.\nBased on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8.\nWe generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7.\nWe used reads that are unmappable to the human reference genome (hg19) and realign such reads against a HHV-6 reference.\nTen subjects with high depth of coverage of HHV-6 were selected."}},{"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":1497248,"fileFormats":[{"code":"fasta","label":{"en":"FASTA"}}]}