Performance and clinical utility of a new supervised machine-learning pipeline in detecting rare ciliopathy patients based on deep phenotyping from electronic health records and semantic similarity

Autor: Carole Faviez, Marc Vincent, Nicolas Garcelon, Olivia Boyer, Bertrand Knebelmann, Laurence Heidet, Sophie Saunier, Xiaoyi Chen, Anita Burgun
Jazyk: angličtina
Rok vydání: 2024
Předmět:
Zdroj: Orphanet Journal of Rare Diseases, Vol 19, Iss 1, Pp 1-12 (2024)
Druh dokumentu: article
ISSN: 1750-1172
DOI: 10.1186/s13023-024-03063-7
Popis: Abstract Background Rare diseases affect approximately 400 million people worldwide. Many of them suffer from delayed diagnosis. Among them, NPHP1-related renal ciliopathies need to be diagnosed as early as possible as potential treatments have been recently investigated with promising results. Our objective was to develop a supervised machine learning pipeline for the detection of NPHP1 ciliopathy patients from a large number of nephrology patients using electronic health records (EHRs). Methods and results We designed a pipeline combining a phenotyping module re-using unstructured EHR data, a semantic similarity module to address the phenotype dependence, a feature selection step to deal with high dimensionality, an undersampling step to address the class imbalance, and a classification step with multiple train-test split for the small number of rare cases. The pipeline was applied to thirty NPHP1 patients and 7231 controls and achieved good performances (sensitivity 86% with specificity 90%). A qualitative review of the EHRs of 40 misclassified controls showed that 25% had phenotypes belonging to the ciliopathy spectrum, which demonstrates the ability of our system to detect patients with similar conditions. Conclusions Our pipeline reached very encouraging performance scores for pre-diagnosing ciliopathy patients. The identified patients could then undergo genetic testing. The same data-driven approach can be adapted to other rare diseases facing underdiagnosis challenges.
Databáze: Directory of Open Access Journals
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