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Mount Sinai AI Uses Routine Lab Data to Gauge Disease Risk From Rare Genetic Variants

Published in Science, the study derives continuous penetrance scores from EHR labs to clarify uncertain results pending validation.

Overview

  • Researchers trained separate machine-learning models for 10 autosomal dominant conditions using more than 1.3 million electronic health records and routine lab values.
  • The approach generated 0–1 “ML penetrance” scores for 1,648 rare variants across 31 genes, estimating how likely each variant is to cause disease.
  • Real-world data indicated some variants labeled uncertain showed clear disease signals, while others long considered pathogenic showed limited measurable impact.
  • Higher scores aligned with differences in clinical measures such as cholesterol levels, heart rhythm and kidney function, offering phenotype-linked risk insight.
  • The team says clinical use will require expansion to additional diseases and variant types, inclusion of more diverse populations, and longitudinal outcome tracking.