A custom phenotypic profile for Fanconi anemia: Addressing gaps in existing disease annotations

Fanconi anemia (FA) is a rare genetic disorder of impaired DNA repair characterized by progressive bone marrow failure, congenital malformations, and cancer predisposition. Early identification of individuals with FA is critical for timely clinical management, yet phenotype-driven approaches to FA identification are hindered by inconsistencies in existing phenotypic profiles. We compared the Human Phenotype Ontology (HPO) annotations for FA in OMIM (215 terms across 22 complementation group entries) and Orphanet (106 terms in a single entry, ORPHA:84), quantifying overlap and anatomical system coverage. To address identified gaps, we developed a comprehensive custom HPO profile by extracting phenotypic terms from the entire Fanconi Cancer Foundation (FCF) Clinical Care Guidelines using OntoGPT, an LLM-based ontology extraction tool, followed by manual curation to ensure accuracy and clinical relevance. OMIM and Orphanet shared only 36 HPO terms (12.6% of their combined 285 unique terms), demonstrating substantial discordance. Our custom profile comprises 264 unique HPO terms, of which 161 (61.0%) are novel and not present in either existing source. The novel terms expand coverage particularly in musculoskeletal (39 terms, 23.8%), genitourinary (26 terms, 15.9%), limb (26 terms, 15.9%), head or neck (20 terms 12.2%), and digestive system (17 terms, 10.4%) phenotypes. Community-curated phenotypic profiles derived from clinical practice guidelines can substantially augment existing disease annotations. Our FA profile, the most comprehensive HPO-based phenotypic characterization of FA to date, is publicly available and provides a foundation for improved clinical decision support and EHR-based computable phenotyping that can accelerate diagnosis for individuals with FA. Furthermore, the LLM-assisted approach offers generalizable methods to improve the diagnostic odyssey for all rare diseases.