genome wide SNPs

材料と対象者

バイオバンク・ジャパン (179,000名) 形質数: 79

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 GWAS: For binary traits, SAIGE software was used with age, age2, sex, age×sex, age2×sex, and top 20 principal components as covariates. For quantitative traits (biomarkers) , BOLT-LMM was used with the same covariates. Fine-mapping: FINEMAP and SuSiE were used with GWAS summary statistics and in-sample dosage LD, allowing up to 10 causal variants per region.

フィルタリング

GWAS: We included imputed variants with Rsq > 0.7. For binary traits, variants with MAC < 10 were additionally excluded. Fine-mapping: We defined fine-mapping regions based on a 3 Mb window around each lead variant and merged regions if they overlapped. We excluded the major histocompatibility complex (MHC) region (chr 6: 25-36 Mb) from analysis due to extensive LD structure in the region. For each method, we only included variants from successfully fine-mapped regions while excluding those from failed regions (e.g., due to conversion failure or available memory restrictions) .

バリアント数

13,531,752 variants (ref: hg19)

NBDCデータセットAccession

hum0197.v5.gwas.v1 / hum0197.v5.finemap.v1 (データのダウンロードは上記データIDをクリックし、遷移先のサイトの各Dataset IDをクリックしてください) Dictionary file

総データ量

14 GB

利用ポリシー

NBDC policy