{"id":"JGAD000410","research":"hum0014","url":"https://humandbs.dbcls.jp/dataset/JGAD000410","datePublished":"2021-06-21","dateModified":"2021-08-25","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":"JGAD000220のWGSデータのbam/gvcfデータ","en":"bam/gvcf data of WGS (JGAD000220)"}}],"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：1,026名","en":"1,026 individuals"}},{"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":1026,"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":"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":"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"}}]},{"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.\nAlignment:\nData matched for the following conditions 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 include 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.\n\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":31.8,"unit":"x","high":null}]},{"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":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"alignment","label":{"ja":"アライメント","en":"Alignment"}},{"code":"variant-calls","label":{"ja":"変異コール","en":"Variant calls"}}]},{"key":"data-summary","label":{"ja":"データ概要","en":"Data summary"},"type":"text","text":{"ja":"GEnome Medical alliance Japan（GEM Japan, GEM-J）の取り組みとして、GATK Best Practicesに準拠した方法により、GRCh37の参照ゲノム配列へのマッピングおよびバリアント検知を実施した際のデータです。詳しくはこちらをご覧ください。","en":"Whole genome sequencing analyzed data included in the JGAD000220 were mapped to the GRCh37 reference genome sequence, and variant detection was carried out using the GATK (Genome Analysis Toolkit) standards. This project is an initiative of the GEnome Medical Alliance Japan (GEM Japan, GEM-J). Learn more"}},{"key":"processed-data-dataset-id","label":{"ja":"加工データのデータセットID","en":"Dataset ID of processed data"},"type":"text","text":{"ja":"JGAD000690\nJGAD000758（joint call）","en":"JGAD000690\nJGAD000758 (joint call)"}},{"key":"processing-method","label":{"ja":"加工方法","en":"Processing method"},"type":"text","text":{"ja":"加工済みデータ一覧（Whole Genome Sequencing解析）","en":"List of processed data (Whole Genome Sequencing Analysis)"}},{"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":53314226509310,"fileFormats":[{"code":"bam","label":{"en":"BAM"}},{"code":"bai","label":{"en":"BAI"}},{"code":"vcf","label":{"en":"VCF"}},{"code":"tbi","label":{"en":"TBI"}}]}