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Deep phenotyping on EHR narratives facilitates genetic diagnosis by clinical exomes


Chunhua Weng, Ph.D.,
Columbia University


Integration of detailed phenotypic information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotypic information, electronic health records (EHRs) have the potential to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. In this talk, I will describe a high-throughput EHR phenotype extraction and analysis framework that performs Human Phenotype Ontology (HPO) concept extraction and normalization from EHR narratives and prioritizes disease genes based on the HPO-coded phenotypic manifestations. Our results on four retrospective cohorts from multiple institutions show the promise of leveraging EHR data to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the implementation of genomic medicine on scale.