Fig. 3: Performance comparison of alternative methods for prediction of two continuous traits in 23andMe.
From: An ensemble penalized regression method for multi-ancestry polygenic risk prediction
We analyzed two continuous traits, a heart metabolic disease burden and b height. PRS are trained using 23andMe data that available for five populations: African American, Latino, EAS, EUR, and SAS, and then tuned in an independent set of individuals from 23andMe of the corresponding ancestry. Performance is reported based on adjusted R2 accounting for sex, age and PC1-5 in a held-out validation sample of individuals from 23andMe of the corresponding ancestry. The ratio of sample sizes for training, tuning and validation is roughly about 7:2:1, and detailed numbers are in Supplementary Data 7 and 8. The PRS-CSx package is restricted to SNPs from HM3, whereas other alternative methods use SNPs from either HM3 or MEGA. LDpred2 and its corresponding EUR and weighted methods are excluded to avoid misinterpretation, as a result of our collaboration restrictions with 23andMe, Inc., preventing us from updating these methods to the latest version of its package. Bars in the figure show the performance of adjusted R2 for each method in each dataset. Colors are described on the right side of the figure. Source data are provided in Supplementary Data 9.
