Balancing the efforts of chart review and gains in PRS prediction accuracy: An empirical study

Phenotypic misclassification in genetic association analyses can impact the accuracy of PRS-based prediction models. The bias reduction method proposed by Tong et al. (2019) has demonstrated its efficacy in reducing the effects of bias on the estimation of association parameters between genotype and phenotype while minimizing variance by employing chart reviews on a subset of the data for validating phenotypes, however its improvement of subsequent PRS prediction accuracy remains unclear. Our study aims to fill this gap by assessing the performance of simulated PRS models and estimating the optimal number of chart reviews needed for validation.

To comprehensively assess the efficacy of the bias reduction method proposed by Tong et al. in enhancing the accuracy of PRS-based prediction models, we simulated each phenotype under different correlation structures (an independent model, a weakly correlated model, a strongly correlated model) and introduced error-prone phenotypes using two distinct error mechanisms (differential and non-differential phenotyping errors). To facilitate this, we used genotype and phenotype data from 12 case-control datasets in the Alzheimer's Disease Genetics Consortium (ADGC) to produce simulated phenotypes. The evaluation included analyses across various misclassification rates of original phenotypes as well as quantities of validation set. Additionally, we determined the median threshold, identifying the minimal validation size required for a meaningful improvement in the accuracy of PRS-based predictions across a broad spectrum.

This simulation study demonstrated that incorporating chart review does not universally guarantee enhanced performance of PRS-based prediction models. Specifically, in scenarios with minimal misclassification rates and limited validation sizes, PRS models utilizing debiased regression coefficients demonstrated inferior predictive capabilities compared to models using error-prone phenotypes. Put differently, the effectiveness of the bias reduction method is contingent upon the misclassification rates of phenotypes and the size of the validation set employed during chart reviews. Notably, when dealing with datasets featuring higher misclassification rates, the advantages of utilizing this bias reduction method become more evident, requiring a smaller validation set to achieve better performance.

This study highlights the importance of choosing an appropriate validation set size to balance between the efforts of chart review and the gain in PRS prediction accuracy. Consequently, our study establishes a valuable guidance for validation planning, across a diverse array of sensitivity and specificity combinations.