Genomic prediction of coronary heart disease

Aims Genetics plays an important role in coronary heart disease (CHD) but the clinical utility of genomic risk scores (GRSs) relative to clinical risk scores, such as the Framingham Risk Score (FRS), is unclear. Our aim was to construct and externally validate a CHD GRS, in terms of lifetime CHD risk and relative to traditional clinical risk scores. Methods and results We generated a GRS of 49 310 SNPs based on a CARDIoGRAMplusC4D Consortium meta-analysis of CHD, then independently tested it using five prospective population cohorts (three FINRISK cohorts, combined n = 12 676, 757 incident CHD events; two Framingham Heart Study cohorts (FHS), combined n = 3406, 587 incident CHD events). The GRS was associated with incident CHD (FINRISK HR = 1.74, 95% confidence interval (CI) 1.61–1.86 per S.D. of GRS; Framingham HR = 1.28, 95% CI 1.18–1.38), and was largely unchanged by adjustment for known risk factors, including family history. Integration of the GRS with the FRS or ACC/AHA13 scores improved the 10 years risk prediction (meta-analysis C-index: +1.5–1.6%, P < 0.001), particularly for individuals ≥60 years old (meta-analysis C-index: +4.6–5.1%, P < 0.001). Importantly, the GRS captured substantially different trajectories of absolute risk, with men in the top 20% of attaining 10% cumulative CHD risk 12–18 y earlier than those in the bottom 20%. High genomic risk was partially compensated for by low systolic blood pressure, low cholesterol level, and non-smoking. Conclusions A GRS based on a large number of SNPs improves CHD risk prediction and encodes different trajectories of lifetime risk not captured by traditional clinical risk scores.National Health and Medical Research Council Early Career Fellowship (1090462 to G.A.); National Health and Medical Research Council and the National Heart Foundation of Australia (1061435 and 1062227 to M.I.); Finnish Foundation for Cardiovascular Research to V.S; British Heart Foundation and NIHR to N.J.S.; AP and SR are supported by the Academy of Finland (grant no. 251704, 286500, 293404 to AP, and 251217, 285380 to SR), Juselius Foundation, Finnish Foundation for Cardiovascular Research, NordForsk e-Science NIASC (grant no 62721) and Biocentrum Helsinki (to SR). The MI Genetics (MIGen) Consortium Study was funded by the National Heart, Lung, and Blood Institute of the United States National Institutes of Health (R01 HL087676). Genotyping was partially funded by The Broad Institute Center for Genotyping and Analysis, which was supported by grant U54 RR02027 from the National Center for Research Resources. This study makes use of data generated by the Wellcome Trust Case-Control Consortium. A full list of the investigators who contributed to the generation of the data is available from www.wtccc.org.uk. Funding for the project was provided by the Wellcome Trust under award 076113 and 085475. The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 261433 (Biobank Standardisation and Harmonisation for Research Excellence in the European Union—BioSHaRE-EU). We are grateful to the CARDIoGRAMplusC4D consortium for making their large-scale genetic data available. A list of members of the consortium and the contributing studies is available at www.cardiogramplusc4d.org