- Here, we provide summary statistics of trans-ethnic meta-analysis. These results are meta-analysis of either (i) BBJ + UKB + FinnFen, (ii) BBJ + UKB, or (iii) BBJ + FinnGen.
- Genotyping array: BBJ: the Illumina HumanOmniExpressExome BeadChip or a combination of the Illumina HumanOmniExpress and HumanExome BeadChips. UK Biobank: either the Applied Biosystems UK BiLEVE Axiom Array or the Applied Biosystems UK Biobank Axiom Array. FinnGen: the FinnGen1 ThermoFisher array or other genotyping arrays in previous cohorts.
- Sample population: BBJ: We included samples of the estimated East Asian ancestry using PCA. UK Biobank: We analyzed individuals of white British genetic ancestry as determined by the PCA-based sample selection criteria. FinnGen: We excluded population outliers via PCA.
- Phenotyping: BBJ GWAS was conducted based on the phenotype name in Japanese. UKB GWAS was conducted based on UKB ICD10/9 mapped to Phecode, and FinnGen GWAS was conducted based on FinnGen endpoint.
- Phasing and imputation: BBJ: Eagle and Minimac3 software. UK Biobank: IMPUTE4 software. FinnGen: beagle4.1 software.
- Imputation reference: BBJ: Combined panel of WGS data from the BioBank Japan project (N=1,037) and 1KGP p3v5 ALL (N=2,504). UK Biobank: A combination of the Haplotype Reference Consortium, UK10K, and 1000 Genomes Phase 3 reference panels. FinnGen: A panel with whole-genome sequencing data from 3,775 Finnish individuals.
- Post-imputation QC: BBJ: We included imputed variants with Rsq > 0.7. UK Biobank: We excluded the variants with (i) INFO score ≤ 0.8, (ii) MAF ≤ 0.0001 (except for missense and protein-truncating variants annotated by VEP, which were excluded if MAF ≤ 1 × 10-6), and (iii) PHWE ≤ 1 × 10-10. FinnGen: We excluded variants with an imputation INFO score < 0.8 or MAF < 0.0001.
- Association test: For binary traits (disease endpoints and medications), 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 or plink software was used with the same covariates.
- Meta-analysis: METAL software was used to conduct meta-analysis by the inverse-variance method.
Uploaded files
| File name |
Descriptions |
| GWASsummary_{TRAITNAME}_META_SakaueKanai2020.auto.txt.gz |
Summary results for autosomal variants |
| GWASsummary_{TRAITNAME}_META_SakaueKanai2020.chrX.txt.gz |
Summary results for X-chromosomal variants |
Please always be aware that UKB GWAS was conducted based on UKB ICD10/9 mapped to Phecode, and FinnGen GWAS was conducted based on FinnGen endpoint. We strongly recommend you to check the phenotype codings before using these summary statistics.
Columns
We provide the summary statitics of trans-ethnic meta-analysis (using METAL software) and allele frequency data from each of the cohorts. Please always carefully check the header before using the summary statistics. Column numbers are different according to the phenotypes!
| # |
column name |
Descriptions |
| 1 |
v |
marker name (CHR:POS:REF:ALT) |
| 2 |
CHR |
chromosome |
| 3 |
POS |
position (hg19) |
| 4 |
Allele1 |
REF allele |
| 5 |
Allele2 |
ALT allele (This allele is the effect allele.) |
| 6 |
AF_Allele2_BBJ |
allele frequency of Allele2 (ALT) in BBJ |
| X |
AF_Allele2_UKB |
allele frequency of Allele2 (ALT) in UK Biobank |
| X |
AF_Allele2_FG |
allele frequency of Allele2 (ALT) in FinnGen |
| X |
Direction |
the signs of betas in each of the cohorts in the order of BBJ, UK Biobank and FinnGen* |
| X |
BETA |
effect size of Allele2 in meta-analysis |
| X |
SE |
standard error of BETA in meta-analysis |
| X |
p.value |
P value in meta-analysis |
* The directions are consisted of the meta-analyzed cohorts only (either (i) BBJ + UKB + FinnFen, (ii) BBJ + UKB, or (iii) BBJ + FinnGen).
X; the column number can be different according to the combination of the cohorts where the meta-analysis has been performed.
Reference
If you use these summary statistics, please cite the following paper;
Sakaue S and Kanai M et al. A global atlas of genetic associations of 220 deep phenotypes. medRxiv 2020.