PMCID
PMC13131751

CalPred yields calibrated intervals for polygenic risk prediction.

medRxiv : the preprint server for health sciences
Authors
Abstract

Polygenic scores (PGS) have emerged as a useful biomarker for stratification of high-risk individuals in genomic medicine, with prediction intervals arising as a principled approach to incorporate statistical uncertainty in their individual-level predictions. In contrast to recent reports by Xu et al, we show that CalPred provides well-calibrated prediction intervals that contain the trait phenotypes at targeted confidence levels. CalPred maintains calibration when PGS performance varies across contextual factors (e.g., ancestry, age, sex, or socio-economic factors) whereas PredInterval - a recently introduced method that focuses on marginal calibration across all individuals - exhibits miscalibration.

Year of Publication
2026
Journal
medRxiv : the preprint server for health sciences
Date Published
04/2026
DOI
10.64898/2026.04.21.26351410
PubMed ID
42078335
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