{"id":"JGAD000985","research":"hum0533","url":"https://humandbs.dbcls.jp/dataset/JGAD000985","datePublished":"2025-10-17","dateModified":"2025-10-17","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（Exome、RNA-seq）","en":"NGS (Exome, RNA-seq)"}}],"experiments":[{"label":"WES","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"GAPPS（ICD10：D139）：7症例\n61検体（胃腫瘍組織：14検体、胃ポリープ：13検体、正常胃粘膜：27検体、末梢血：7検体）","en":"GAPPS (ICD10: D139): 7 cases\n61 samples (14 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa, 7 peripheral blood)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"D139","label":{"ja":"消化器系，部位不明確","en":"Benign neoplasm: Ill-defined sites within the digestive system"}}],"name":{"ja":"GAPPS","en":"GAPPS"}}]},{"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":7,"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":"腫瘍組織および非腫瘍組織から抽出したDNA","en":"DNA extracted from tumor tissues or non-tumor tissues"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"stomach","label":{"ja":"胃","en":"Stomach"}},{"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":"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":"wes","label":{"en":"WES"}}]},{"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":"sureselect-human-all-exon-v6","label":{"en":"SureSelect Human All Exon V6"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"酵素反応","en":"Enzymatic 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-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"Median MAPQ ≥ 60","en":"Median MAPQ ≥ 60"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"FastQC（v0.11.9）\nHard-filter（GATK推奨値）\nSNP： QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0\nINDEL： QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0","en":"FastQC (v0.11.9)\nHard-filter (GATK recommendation)\nSNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0\nINDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GATK（v4.2.6.1）、Picard MarkDuplicates（v2.27.5）、Samtools （v1.14）、ANNOVAR （2020-06-08 release）","en":"GATK (v4.2.6.1), Picard MarkDuplicates (v2.27.5), Samtools (v1.14), ANNOVAR (2020-06-08 release)"}},{"key":"coverage-depth","label":{"ja":"カバレッジ (深度)","en":"Coverage (depth)"},"type":"number","numbers":[{"value":175,"unit":"x","high":null},{"value":144,"unit":"x","high":236,"suffix":{"ja":" (範囲)","en":" (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":"GAPPS（ICD10：D139）：7症例\n53検体（胃腫瘍組織：13検体、胃ポリープ：13検体、正常胃粘膜：27検体）","en":"GAPPS (ICD10: D139): 7 cases\n53 samples (13 gastric carcinoma, 13 gastric polyp, 27 normal gastric mucosa)"}},{"key":"disease","label":{"ja":"疾患","en":"Disease"},"type":"disease","diseases":[{"terms":[{"code":"D139","label":{"ja":"消化器系，部位不明確","en":"Benign neoplasm: Ill-defined sites within the digestive system"}}],"name":{"ja":"GAPPS","en":"GAPPS"}}]},{"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":7,"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":"腫瘍組織および非腫瘍組織から抽出したRNA","en":"RNA extracted from tumor tissues or non-tumor tissues"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"stomach","label":{"ja":"胃","en":"Stomach"}}]},{"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-rna-library-prep-kit-for-illumina","label":{"en":"NEBNext Ultra II RNA Library Prep Kit for Illumina"}}]},{"key":"fragmentation","label":{"ja":"断片化","en":"Fragmentation"},"type":"text","text":{"ja":"酵素反応","en":"Enzymatic 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-quality","label":{"ja":"マッピング品質","en":"Mapping quality"},"type":"text","text":{"ja":"Median MAPQ ≥ 60","en":"Median MAPQ ≥ 60"}},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"FastQC（v0.11.9）\nHard-filter（GATK推奨値）\nSNP： QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0\nINDEL： QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0","en":"FastQC (v0.11.9)\nHard-filter (GATK recommendation)\nSNP: QD < 2.0, FS > 60.0, MQ < 40.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, SOR > 3.0\nINDEL: QD < 2.0, FS > 200.0, ReadPosRankSum < -20.0, SOR > 10.0"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"STAR（v2.7.10a）、RSEM（v1.3.3）、Samtools（v1.14）、DESeq2 （v1.38.3）","en":"STAR (v2.7.10a), RSEM (v1.3.3), Samtools (v1.14), DESeq2 (v1.38.3)"}},{"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":653902040830,"fileFormats":[{"code":"bam","label":{"en":"BAM"}},{"code":"bai","label":{"en":"BAI"}},{"code":"csv","label":{"en":"CSV"}}]}