{"id":"NHA000182","research":"hum0331","url":"https://humandbs.dbcls.jp/dataset/NHA000182","datePublished":"2023-02-01","dateModified":"2023-02-01","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"unrestricted-access","label":{"ja":"非制限公開","en":"Unrestricted-access"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"NGS（WGS）","en":"NGS (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":"健常者（難病やがんを罹患していない生活習慣病を持つ人を含む）（ICD10：Z006）：9290名","en":"Healthy individuals without any cancers or rare diseases (ICD10: Z006): 9290 individuals"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"Z006","label":{"ja":"臨床研究計画における対照者の検査","en":"Examination for normal comparison and control in clinical research programme"}}],"name":{"ja":"健常者（難病やがんを罹患していない生活習慣病を持つ人を含む）","en":"Healthy individuals without any cancers or rare diseases"}}]},{"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":9290,"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":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"各バイオバンクから選定した健常者の末梢血から抽出したDNA","en":"DNAs 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-novaseq-6000","label":{"en":"Illumina NovaSeq 6000"}}]},{"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":"grch38","label":{"en":"GRCh38"}}]},{"key":"mapping","label":{"ja":"マッピング","en":"Mapping"},"type":"text","text":{"ja":"bwa mem（v0.7.15）互換アルゴリズム（Parabricks 3.1.0 fq2bam）","en":"bwa mem (v0.7.15) compatible algorithm (Parabricks 3.1.0 fq2bam)"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"MarkDuplicates（GATK4.1.0）互換アルゴリズム（Parabricks 3.1.0 fq2bam）","en":"MarkDuplicates (GATK4.1.0) compatible algorithm (Parabricks 3.1.0 fq2bam)"}},{"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":null,"en":null}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"MQによるハードフィルタリングは未実施","en":"No hard filtering was performaed by mapping quality."}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"以下の条件で全ゲノムシークエンス解析を実施\n- ライブラリサイズが400bp-750bpであることを確認\n- QV30以上の塩基の割合が75%以上\n- FASTQCによる重複リード除去後の総塩基数が900億塩基以上\n\nアライメントとバリアントコール後に以下のサンプルを解析から除外した\n- Depthおよびマップ率が異常値を示すサンプル\n- 性染色体のDepthが臨床情報の性別と矛盾するサンプル\n- KINGプログラムで2親等以内と判定されたサンプルのいずれか\n\nバリアントコールの結果は以下のフィルタリングを実行した\n- GQ<20またはDP<11またはDP>64またはヘテロ接合体コールにおいてマイナーアリルの割合が25%未満のジェノタイプはno callに設定\n- VQSRの結果をVCFのFILTERフィールドにセット\n- コール率95%未満のバリアントにはFILTERにLowCRをセット\n- Hardy-Weinberg平衡検定のP値が10-6未満のバリアントにはFILTERにHWEをセット","en":"Whole genome sequencing analysis was performed under the following conditions.\n- Confirm library size is 400bp-750bp.\n- At least 75% of the bases are QV30 or better.\n- Total number of bases after removal of duplicate reads by FASTQC is more than 90 GBase.\n\nAfter alignment and variant calling, the following samples were excluded from the analysis.\n- Samples with abnormal values for depth and mapping rate.\n- Samples where the depth of the sex chromosome is inconsistent with the clinical information.\n- Any of the samples determined to be within the second degree of kinship in the KING program.\n\nVariant call results were filtered for the following\n- Genotypes with GQ64 or with less than 25% minor alleles in heterozygous calls are set to no call\n- Set VQSR results to FILTER field in VCF\n- Set LowCR in FILTER field for variants with less than 95% call rate\n- Variants with a Hardy-Weinberg equilibrium test P-value less than 10-6 have HWE set in FILTER field"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"HaplotypeCaller（GATK4.1.0）互換アルゴリズム（Parabricks 3.1.0 haplotypecaller）","en":"HaplotypeCaller (GATK 4.1.0) compatible algorithm (Parabricks 3.1.0 haplotypecaller)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":34,"unit":"x","high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":18899392,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}},{"value":836126,"unit":null,"high":null,"prefix":{"ja":"X染色体: ","en":"X chromosome: "}},{"value":153554029,"unit":null,"high":null,"prefix":{"ja":"常染色体: ","en":"Autosomes: "}},{"value":6325046,"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)"}}]}]}],"fileFormats":[{"code":"vcf","label":{"en":"VCF"}},{"code":"markdown","label":{"en":"Markdown"}}]}