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Article

Improving automated deep phenotyping through large language models using retrieval-augmented generation.

Genome medicine - 18 Aug 2025

Garcia Brandon T, Westerfield Lauren, Yelemali Priya, Gogate Nikhita, Rivera-Munoz E Andres, Du Haowei, Dawood Moez, Jolly Angad, Lupski James R, Posey Jennifer E

Abstract excerpt

BACKGROUND: Diagnosing rare genetic disorders relies on precise phenotypic and genotypic analysis, with the Human Phenotype Ontology (HPO) providing a standardized language for capturing clinical phenotypes. Rule-based HPO extraction tools use concept recognition to automatically identify phenotypes, but they often struggle with incomplete phenotype assignment, requiring significant manual review. While large...

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PMID: 40826123
DOI: 10.1186/s13073-025-01521-w
PMCID: PMC12359922

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