{"id":"JGAD001048","research":"hum0567","url":"https://humandbs.dbcls.jp/dataset/JGAD001048","datePublished":"2026-09-24","dateModified":"2026-09-24","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、RNA-seq）","en":"NGS (WGS, RNA-seq)"}}],"experiments":[{"label":"WGS","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"稀な肝希少疾患、特にFALDを背景に発症した肝がん（ICD10：C220）：13 症例\n腫瘍組織：13検体\n非腫瘍肝組織：13検体","en":"liver cancer caused by rare liver diseases, especially FALD (ICD10: C220): 13 cases\ntumor tissue: 13 samples\nnon-tumor tissue: 13 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C220","label":{"ja":"肝細胞癌","en":"Malignant neoplasm: Liver cell carcinoma"}}],"name":{"ja":"稀な肝希少疾患、特にFALDを背景に発症した肝がん","en":"liver cancer caused by rare liver diseases, especially FALD"}}]},{"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":13,"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":"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":"腫瘍組織および非腫瘍組織から抽出したDNA","en":"DNAs extracted from tumor and non-tumor tissues"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"liver","label":{"ja":"肝臓","en":"Liver"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"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（Covaris）","en":"Ultrasonic fragmentation (Covaris)"}},{"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"}},{"code":"illumina-novaseq-x-plus","label":{"en":"Illumina NovaSeq X Plus"}}]},{"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","en":"BWA-MEM"}},{"key":"read-deduplication","label":{"ja":"リード重複除去","en":"Read deduplication"},"type":"text","text":{"ja":"Picard MarkDuplicates (Duplication rate: approx. 15%)","en":"Picard MarkDuplicates (Duplication rate: approx. 15%)"}},{"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 BQSR","en":"GATK BQSR"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"MAPQ >= 20","en":"MAPQ >= 20"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"・MarkIlluminaAdapters および SamToFastq を用いて、クリッピングパラメータを設定し、アダプターをトリミング\n・MergeBamAlignment (-CLIP_OVERLAPPING_READS true) により重複リードをクリッピング\n・GATK MarkDuplicatesを用いて重複リードをフィルタリング\n・dbSNPおよび既知のindelリソースに基づく塩基品質スコアの再校正（BQSR）\n・GATK FilterMutectCallsのデフォルトパイプラインを用いてアーティファクトおよびコンタミネーションをフィルタリング\n・Funcotatorにより機能アノテーション中のフィルタリング済みバリアントを除去\n*パイプラインの詳細な設定およびパラメータについては、DOI: 10.1097/HEP.0000000000001693のSupplementary Methodsを参照","en":"- Adapter trimming via MarkIlluminaAdapters and SamToFastq with clipping parameters.\n- Overlapping read clipping performed by MergeBamAlignment (-CLIP_OVERLAPPING_READS true).\n- Duplicate read filtering using GATK MarkDuplicates.\n- Base quality score recalibration (BQSR) against dbSNP and known indel resources.\n- Artifact and contamination filtering using GATK FilterMutectCalls default pipeline.\n- Filtered variant removal during functional annotation via Funcotator.\ncf. Supplementary Methods of DOI: 10.1097/HEP.0000000000001693 for detailed pipeline configurations and parameters"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK Mutect2 (v4.6.2.0) + Funcotator\nNextflow oncoanalyser (v2.1.0) / PURPLE\nNextflow oncoanalyser (v2.1.0) + R (StructuralVariantAnnotation / VariantAnnotation)","en":"GATK Mutect2 (v4.6.2.0) + Funcotator\nNextflow oncoanalyser (v2.1.0) / PURPLE\nNextflow oncoanalyser (v2.1.0) + R (StructuralVariantAnnotation / VariantAnnotation)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":100,"unit":"x","high":null}]},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":1010,"unit":null,"high":null,"suffix":{"ja":" Indels (中央値)","en":" Indels (Median)"}},{"value":189,"unit":null,"high":2786,"suffix":{"ja":" Indels (範囲)","en":" Indels (Range)"}},{"value":64,"unit":null,"high":null,"suffix":{"ja":" SVs (中央値)","en":" SVs (Median)"}},{"value":2,"unit":null,"high":160,"suffix":{"ja":" SVs (範囲)","en":" SVs (Range)"}},{"value":5373,"unit":null,"high":null,"suffix":{"ja":" SNVs (中央値)","en":" SNVs (Median)"}},{"value":2000,"unit":null,"high":12634,"suffix":{"ja":" SNVs (範囲)","en":" SNVs (Range)"}}]},{"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)"}}]}]},{"label":"RNA-seq","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"稀な肝希少疾患、特にFALDを背景に発症した肝がん（ICD10：C220）：13 症例\n腫瘍組織：13検体\n非腫瘍肝組織：13検体","en":"liver cancer caused by rare liver diseases, especially FALD (ICD10: C220): 13 cases\ntumor tissue: 13 samples\nnon-tumor tissue: 13 samples"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"C220","label":{"ja":"肝細胞癌","en":"Malignant neoplasm: Liver cell carcinoma"}}],"name":{"ja":"稀な肝希少疾患、特にFALDを背景に発症した肝がん","en":"liver cancer caused by rare liver diseases, especially FALD"}}]},{"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":13,"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":"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":"腫瘍組織および非腫瘍組織から抽出したRNA","en":"RNAs extracted from tumor and non-tumor tissues"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"liver","label":{"ja":"肝臓","en":"Liver"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"mixed","label":{"ja":"混在","en":"Mixed"}}]},{"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":"rna-seq","label":{"en":"RNA-seq"}}]},{"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":"nebnext-ultra-ii-directional-rna-library-prep-kit-for-illumina","label":{"en":"NEBNext Ultra II Directional RNA Library Prep Kit for Illumina"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"化学的断片化（二価カチオン、熱処理）","en":"Chemical fragmentation [divalent cations, heat treatment]"}},{"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"}},{"code":"illumina-novaseq-x-plus","label":{"en":"Illumina NovaSeq X Plus"}}]},{"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":"STAR (v2.7.10a)","en":"STAR (v2.7.10a)"}},{"key":"mapping-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":">91%","en":">91%"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"None (RSEM internally handles multi-mapping reads using EM algorithm)","en":"None (RSEM internally handles multi-mapping reads using EM algorithm)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"STAR (v2.7.10a) + RSEM (v1.3.3)","en":"STAR (v2.7.10a) + RSEM (v1.3.3)"}},{"key":"gene-number","label":{"ja":"遺伝子数","en":"Gene count"},"type":"number","numbers":[{"value":61552,"unit":null,"high":null}]},{"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":4643846600967,"fileFormats":[{"code":"fastq","label":{"en":"FASTQ"}},{"code":"maf","label":{"en":"MAF"}},{"code":"csv","label":{"en":"CSV"}}]}