Validation of an integrated risk tool, including polygenic risk score, for atherosclerotic cardiovascular disease in multiple ethnicities and ancestries

Summary-level coronary artery disease (CAD) and ischaemic stroke (IS) GWAS data generated by Genomics plc as presented in:

Weale M. et al. Validation of an integrated risk tool, including polygenic risk score, for atherosclerotic cardiovascular disease in multiple ethnicities and ancestries. American Journal of Cardiology (in press). 

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NOTES
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These analyses were carried out using the full UK Biobank imputation data release (v3b). Analyses were restricted to a subset of UK Biobank, described as “PRS training” in the Supplementary Materials of the published paper. “PRS training” included 187,150 randomly sampled individuals from the White British unrelated (WBU) UK Biobank subset.

CAD and IS case phenotypes were defined as described in the “UK Biobank phenotype definitions” section of the paper’s Supplementary Materials, using both prevalent (pre-baseline) and incident (post-baseline) events.

All analyses included age-at-assessment, sex, genotyping chip, and 10 principal components as covariates. 

We used plink2.0 logistic regression. For chromosome X variants males were treated as having 0 or 2 alternative alleles. 

The results are not adjusted for genomic control.

DATA FILE CONTENT DESCRIPTION
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cpra: Variant ID in ‘CPRA’ format. Position reflects position in b37. 
chrom: Chromosome
pos: Position in base pairs (b37, 1-based)
alt: Alternative allele (effect allele)
beta: Effect size (log odds ratio)
standard_error: Standard error of beta 
minus_log10_p: Minus log(base 10) of P-value
ref: Reference allele (non-effect allele)
ncase: Number of cases
ncontrol: Number of controls