genome wide SNPs

材料と対象者

バイオバンク・ジャパン第1コホート: 171,287名

実験方法

genome wide SNPs

プラットフォーム

Illumina [HumanOmniExpressExome BeadChip、HumanOmniExpress BeadChip、HumanExome BeadChip]

試料説明

末梢血から抽出したDNA

試薬

HumanOmniExpressExome BeadChip、HumanOmniExpress BeadChip、HumanExome BeadChip

解析方法

Eagle、Minimac3 1) GCTA-fastGWA with the adjustment of covariates: age, age2, sex, the top 20 PCs, 45 disease status, geographic regions, and PCA clusters. 2) Fixed-effect meta-analysis of Mainland summary data including individuals from the Mainland and EA_admix clusters (n = 151,075) and of Ryukyu summary data including individuals from the Ryukyu, Ryukyu admix, and Hokkaido_sub clusters (n = 10,080) using METAL

フィルタリング

Sample QC: We excluded (i) individuals with lower call rates (< 99%) , (ii) closely related individuals with genetic relatedness ≥ 0.178 calculated from a genetic related matrix (GRM) by GCTA (version 1.93.3beta2) . We included samples of the estimated Japanese ancestry using PCA. Variant QC: We excluded variants with (i) call rate < 99%, (ii) P value for Hardy-Weinberg equilibrium (HWE) < 1.0 × 10-6, (iii) number of heterozygotes < 5, and (iv) a concordance rate < 99.5% or a non-reference concordance rate between GWAS array and whole genome sequencing. after association test: Double genomic control correction method using METAL was conducted. Computing Z score for each variant by considering the sign of the beta coefficient and the associated p-value, we left the variants with positive Z score.

バリアント数

3,454,970 SNPs

NBDCデータセットAccession

hum0197.v21.gwas-jomon.v1 (データのダウンロードは上記Data IDをクリックしてください) Dictionary file

総データ量

65 MB (txt)

利用ポリシー

NBDC policy