Ancestry-aligned polygenic scores combined with conventional risk factors improve prediction of cardiometabolic outcomes in African populations.

Abstract

Background: Cardiovascular diseases (CVD) are a major health concern in Africa. Improved identification and treatment of high-risk individuals can reduce adverse health outcomes. Current CVD risk calculators are largely unvalidated in African populations and overlook genetic factors. Polygenic scores (PGS) can enhance risk prediction by measuring genetic susceptibility to CVD, but their effectiveness in genetically diverse populations is limited by a European-ancestry bias. To address this, we developed models integrating genetic data and conventional risk factors to assess the risk of developing cardiometabolic outcomes in African populations.

Methods: We used summary statistics from a genome-wide association meta-analysis (n = 14,126) in African populations to derive novel genome-wide PGS for 14 cardiometabolic traits in an independent African target sample (Africa Wits-INDEPTH Partnership for Genomic Research (AWI-Gen), n = 10,603). Regression analyses assessed relationships between each PGS and corresponding cardiometabolic trait, and seven CVD outcomes (CVD, heart attack, stroke, diabetes mellitus, dyslipidaemia, hypertension, and obesity). The predictive utility of the genetic data was evaluated using elastic net models containing multiple PGS (MultiPGS) and reference-projected principal components of ancestry (PPCs). An integrated risk prediction model incorporating genetic and conventional risk factors was developed. Nested cross-validation was used when deriving elastic net models to enhance generalisability.

Results: Our African-specific PGS displayed significant but variable within- and cross- trait prediction (max.R² = 6.8%, p = 1.86 × 10^-173). Significantly associated PGS with dyslipidaemia included the PGS for total cholesterol (logOR = 0.210, SE = 0.022, p = 2.18 × 10^-21) and low-density lipoprotein (logOR =  - 0.141, SE = 0.022, p = 1.30 × 10^-20); with hypertension, the systolic blood pressure PGS (logOR = 0.150, SE = 0.045, p = 8.34 × 10^-4); and multiple PGS associated with obesity: body mass index (max. logOR = 0.131, SE = 0.031, p = 2.22 × 10^-5), hip circumference (logOR = 0.122, SE = 0.029, p = 2.28 × 10^-5), waist circumference (logOR = 0.013, SE = 0.098, p = 8.13 × 10^-4) and weight (logOR = 0.103, SE = 0.029, p = 4.89 × 10^-5). Elastic net models incorporating MultiPGS and PPCs significantly improved prediction over MultiPGS alone. Models including genetic data and conventional risk factors were more predictive than conventional risk models alone (dyslipidaemia: R² increase = 2.6%, p = 4.45 × 10^-12; hypertension: R² increase = 2.6%, p = 2.37 × 10^-13; obesity: R² increase = 5.5%, 1.33 × 10^-34).

Conclusions: In African populations, CVD and associated cardiometabolic trait prediction models can be improved by incorporating ancestry-aligned PGS and accounting for ancestry. Combining PGS with conventional risk factors further enhances prediction over traditional models based on conventional factors. Incorporating data from target populations can improve the generalisability of international predictive models for CVD and associated traits in African populations.