Multiethnic polygenic risk scores improve risk prediction in diverse populations.
- Authors
- MΓ‘rquez-Luna, Carla; Loh, Po-Ru; South Asian Type 2 Diabetes (SAT2D) Consortium; SIGMA Type 2 Diabetes Consortium; Price, Alkes L
- Year
- 2017
- Journal
- Genetic epidemiology
- PMID
- 29110330
- DOI
- 10.1002/gepi.22083
- PMCID
- PMC5726434
Methods for genetic risk prediction have been widely investigated in recent years. However, most available training data involves European samples, and it is currently unclear how to accurately predict disease risk in other populations. Previous studies have used either training data from European samples in large sample size or training data from the target population in small sample size, but not both. Here, we introduce a multiethnic polygenic risk score that combines training data from European samples and training data from the target population. We applied this approach to predict type 2 diabetes (T2D) in a Latino cohort using both publicly available European summary statistics in large sample size (N =Β 40k) and Latino training data in small sample size (N =Β 8k). Here, we attained aΒ >70% relative improvement in prediction accuracy (from R =Β 0.027 to 0.047) compared to methods that use only one source of training data, consistent with large relative improvements in simulations. We observed a systematically lower load of T2D risk alleles in Latino individuals with more European ancestry, which could be explained by polygenic selection in ancestral European and/or Native American populations. We predict T2D in a South Asian UK Biobank cohort using European (N =Β 40k) and South Asian (N =Β 16k) training data and attained aΒ >70% relative improvement in prediction accuracy, and application to predict height in an African UK Biobank cohort using European (NΒ =Β 113k) and African (NΒ =Β 2k) training data attained a 30% relative improvement. Our work reduces the gap in polygenic risk prediction accuracy between European and non-European target populations.
Accuracy of main prediction methods in simulations using subsets of chromosomesWe report results for A) 2:1 training sample size ratio (row 1 of Table 1) and B) 1:1 training sample size ratio (row 2 of Table 1). We report prediction accuracies for each of the 5 main prediction methods as a function of M/Msim, where M=232,629 is the total number of SNPs and Msim is the actual number of SNPS used in each simulation: 232,629 (all chromosomes), 68,188 (chromosomes 1-4), 38,412 (chromosomes 1-2), and 19,087 (chromosome 1). Numerical results are provided in S5 Table.
Accuracy of main prediction methods in analyses of type 2 diabetes in a Latino cohort as a function of P-value thresholdsWe report prediction accuracies for each of the 5 main prediction methods as a function of (A) EUR P-value threshold, where applicable (with optimized LAT P-value threshold, where applicable) and (B) LAT P-value threshold, where applicable (with optimized EUR P-value threshold, where applicable). Numerical results are provided in S12a Table and S12b Table.
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