{"id":"JGAD000893","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000893","datePublished":"2024-10-18","dateModified":"2024-10-18","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":"JGAD000495（BBJ1,964名のWGS）の加工データ（ミトコンドリアのバリアントコール）","en":"Processed data of JGAD000495 (WGS for 1,964 individuals) by JGA (mitochondrial variant calls)"}}],"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2017年度にバイオバンク・ジャパンに登録された症例：1,964名\n心筋梗塞（ICD10：I21）：1,765症例\n認知症（ICD10：F00-03）：199症例","en":"1,765 myocardial infarction patients (ICD10: I21) and 199 dementia patients (ICD10: F00-03)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"I21","label":{"ja":"急性心筋梗塞","en":"Acute myocardial infarction"}}],"name":{"ja":"心筋梗塞","en":"myocardial infarction patients"}},{"terms":[{"code":"F00","label":{"ja":"アルツハイマー＜Alzheimer＞病の認知症（G30.-†）","en":"Dementia in Alzheimer disease"}},{"code":"F01","label":{"ja":"血管性認知症","en":"Vascular dementia"}},{"code":"F02","label":{"ja":"他に分類されるその他の疾患の認知症","en":"Dementia in other diseases classified elsewhere"}},{"code":"F03","label":{"ja":"詳細不明の認知症","en":"Unspecified dementia"}}],"name":{"ja":"認知症","en":"dementia patients"}}]},{"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":1964,"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-dna-pcr-free-library-prep-kit","label":{"en":"TruSeq DNA PCR-Free 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":151,"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 0.7.12","en":"BWA mem 0.7.12"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"Picard 2.10.6","en":"Picard 2.10.6"}},{"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 3.7","en":"GATK 3.7"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"GATK 3.7 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 3.7 HaplotypeCaller"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"リードのbase qualityが全体的に悪い検体、リード毎の%GCの結果にて異常を示した検体を除去。\nAlignment後、Low mapping rate検体、Insert sizeがおかしい検体、メタデータの性別情報とalingment結果より推定される性別情報が不一致な検体、性染色体異常疑いの検体を除去。\nGenotyping時に、VQSR、DP/GP filter (DP < 5, GQ < 20, DP > 60 && GQ < 95を除去)、heterozygosity filter (F>=0.05 を除去)、HWE filter (p < 10-6を除去)、Repeat & Low Complexity filterを実施。\n1000 genomes projectと合わせたPCAを実施し、日本人クラスタから大きく外れる検体を除外。\nその後、Genome-In-A-Bottleプロジェクトから公開されているHighConfidenceRegionリストに記載のある領域のバリアントにフラグを付与。","en":"Data with bad base quality and high %GC content were removed.\nAligment:\nData matched for the following condition were removed.\n- Low mapping rate\n- Different insert size\n- Gender information mismatch between meta-data and genotype data\n- Suspected sex chromosome aberration\nGenotyping:\nGATK's best practices includes a variant filtering step following Variant Quality Score Recalibration (VQSR)\n- DP/GP (DP < 5, GQ < 20, DP > 60, GQ < 95)\n- Heterozygosity (F>=0.05)\n- Hardy-Weinberg equilibrium (p < 10^-6)\n- Repeat & Low Complexity\nPrincipal Component Analysis (PCA):\nPCA was performed with individuals included in the 1000 genomes project and outliers from Japanese cluster were removed.\nAfter these filtering steps, variants located in the regions listed as the HighConfidenceRegion (Genome-In-A-Bottle project) were flagged."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK 3.7 HaplotypeCaller","en":"GATK 3.7 HaplotypeCaller"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":15,"unit":"x","high":null,"prefix":{"ja":"心筋梗塞: ","en":"Myocardial infarction: "}},{"value":30,"unit":"x","high":null,"prefix":{"ja":"認知症: ","en":"Dementia: "}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":10202908,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}},{"value":410435,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "}},{"value":76768387,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}},{"value":2898518,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "}}]},{"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":70872921,"fileFormats":[{"code":"vcf","label":{"en":"VCF"}},{"code":"idx","label":{"en":"IDX"}}]}