{"id":"NHA000207","research":"hum0496","url":"https://humandbs.dbcls.jp/dataset/NHA000207","datePublished":"2026-02-27","dateModified":"2026-02-27","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":"SNP-chipを用いて決定したHondoクラスター、Ryukyuクラスターごとのアレルカウントおよびアレル頻度データ","en":"allele counts and frequencies of 526,270 SNPs about general population living in Okinawa Prefecture"}}],"experiments":[{"label":"Genotyping by array","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"OBiに登録された沖縄県在住の一般集団 合計10,135名\nRyukyuクラスター 8,715名\nHondoクラスター 1,420名","en":"General Population living in Okinawa Prefecture n=10,135\nRyukyu Cluster (n = 8,715)\nHondo Cluster (n = 1,420)"}},{"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":10135,"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":"okinawa-biobank","label":{"en":"Okinawa Biobank"}}]},{"key":"population","label":{"ja":"対象集団","en":"Population"},"type":"vocabulary","terms":[{"code":"ryukyu","label":{"ja":"琉球","en":"Ryukyu"}},{"code":"hondo","label":{"ja":"本土","en":"Hondo"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"末梢血または唾液から抽出したDNA","en":"DNAs extracted from peripheral blood or saliva"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"peripheral-blood","label":{"ja":"末梢血","en":"Peripheral blood"}},{"code":"saliva","label":{"ja":"唾液","en":"Saliva"}}]},{"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":"genotyping-by-array","label":{"en":"Genotyping by array"}}]},{"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":"infinium-asian-screening-array-kit","label":{"en":"Infinium Asian Screening Array Kit"}}]},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"illumina-infinium-asian-screening-array","label":{"en":"Illumina Infinium Asian Screening Array"}}]},{"key":"reference-sequence","label":{"ja":"参照ゲノム","en":"Reference genome"},"type":"vocabulary","terms":[{"code":"grch38","label":{"en":"GRCh38"}}]},{"key":"filtering","label":{"ja":"QC・フィルタリング","en":"QC and filtering"},"type":"text","text":{"ja":"【Genotyping QC（除外基準）】\nSNP call rate < 0.98\npHWE < 1×10−6\nsample call rate < 0.98\n最新の Manifest ファイル（ASA-24v1-0_E2.csv） に無いSNP\n【Blast QC】\nIllumina Manifestファイルに記載されているすべてのTop Genomic Seq配列をGRCh38データベースに対してblastし、複数箇所にマップされるSNPを除外\n【その他の除外基準】\n① 独自のWGS（158サンプル）による遺伝子型との比較において、遺伝子型ミスマッチが3サンプル以上のSNP\n② Ryukyuクラスターと独自WGSデータ（273サンプル）との比較において、アレル頻度の差が0.1以上のSNP\n③ HondoクラスターとToMMo 54kとの比較において、アレル頻度の差が0.05以上のSNP\n④ Hondoクラスターと1KG30xJPTとの比較において、アレル頻度の差が0.1以上のSNP\n注1) ③は、①と②で除外されなかったSNPに適用。④は、①、②、③で除外されなかったSNPに適用\n注2) ①～④に存在しないためフィルタリングを適用できなかった22,635 SNPについては、「NoCheck」と表示","en":"QC1. Genotyping QC (Exclusion Criteria)\nSNP call rate < 0.98\npHWE < 1×10−6\nSample call rate < 0.98\nSNPs not included in the latest manifest file (ASA-24v1-0_E2.csv)\nQC2. Blast QC\nAll Top Genomic Seq sequences listed in the Illumina Manifest file were blasted against the GRCh38 database, and non-single map SNPs were excluded.\nQC3. Other Exclusion Criteria\n(i) SNPs with ≥3 genotype mismatches, based on comparison with WGS (in-house) genotypes for 158 samples.\n(ii) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Ryukyu cluster and in-house WGS data (n = 273).\n(iii) SNPs with an allele frequency difference ≥ 0.05, based on comparison between the Hondo cluster and ToMMo 54k.\n(iv) SNPs with an allele frequency difference ≥ 0.1, based on comparison between the Hondo cluster and 1KG30xJPT\nNote 1) (iii) was applied to SNPs that were not assessed in (i) and (ii).\n(iv) was applied to SNPs that were not assessed in (i), (ii), and (iii).\nNote 2) SNPs not applied in (i) through (iv) due to absence of genotype data of in-house WGS data or allele frequency data in external database, are flagged as \"NoCheck\" in the table."}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"GenCall software（GenomeStudio）","en":"GenCall software (GenomeStudio)"}},{"key":"variant-number","label":{"ja":"バリアント数","en":"Variant count"},"type":"number","numbers":[{"value":526270,"unit":null,"high":null,"suffix":{"ja":" SNPs (上記その他の除外基準で「NoCheck」と表示された22,635 SNPsを含む場合、ファイル名；OBi_FreqTable_20251226_QC_relaxed.tsv)","en":" SNPs (When including the 22,635 SNPs marked \"NoCheck\" by the other exclusion criteria above, file name: OBi_FreqTable_20251226_QC_relaxed.tsv)"}},{"value":503635,"unit":null,"high":null,"suffix":{"ja":" SNPs (上記その他の除外基準で「NoCheck」と表示された22,635 SNPsを含まない場合、ファイル名；OBi_FreqTable_20251226_QC_default.tsv)","en":" SNPs (When excluding the 22,635 SNPs marked \"NoCheck\" by the other exclusion criteria above, file name: OBi_FreqTable_20251226_QC_default.tsv)"}}]},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"allele-frequency","label":{"ja":"アレル頻度","en":"Allele frequency"}}]},{"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":"xlsx","label":{"en":"XLSX"}},{"code":"zip","label":{"en":"ZIP"}}]}