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Polygenic and clinical risk scores and their impact on age at onset of cardiometabolic diseases and common cancers

By Nina J. Mars, Jukka T. Koskela, Pietari Ripatti, Tuomo T.J. Kiiskinen, Aki S Havulinna, Joni V. Lindbohm, Ari Ahola-Olli, Mitja Kurki, Juha Karjalainen, Priit Palta, FinnGen, Benjamin M Neale, Mark Daly, Veikko Salomaa, Aarno Palotie, Elisabeth Widén, Samuli Ripatti

Posted 06 Aug 2019
bioRxiv DOI: 10.1101/727057

Background Polygenic risk scores (PRS) have shown promise in predicting susceptibility to common diseases. However, the extent to which PRS and clinical risk factors act jointly and identify high-risk individuals for early onset of disease is unknown. Methods We used large-scale biobank data (the FinnGen study; n=135,300), with up to 46 years of prospective follow-up, and the FINRISK study with standardized clinical risk factor measurements to build genome-wide PRSs with >6M variants for coronary heart disease (CHD), type 2 diabetes (T2D), atrial fibrillation (AF), and breast and prostate cancer. We evaluated their associations with first disease events, age at disease onset, and impact together with routinely used clinical risk scores for predicting future disease. Results Compared to the 20-80th percentiles, a PRS in the top 2.5% translated into hazard ratios (HRs) for incident disease ranging from 2.03 to 4.28 (p-values 1.96×10−59 to <1.00×10−100) and the bottom 2.5% into HRs ranging from 0.20 to 0.61. The estimated difference in age at disease onset between top and bottom 2.5% of PRSs was 6 to 13 years. Among early-onset cases, 21.3-32.9% had a PRS in the highest decile and in CHD and AF. Conclusions The properties of PRS were similar in all five diseases. PRS identified a considerable proportion early-onset cases, and for all ages the performance of PRS was comparable to established clinical risk scores. These findings warrant further clinical studies on application of polygenic risk information for stratified screening or for guiding lifestyle and preventive medical interventions.

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