Open-Source Artificial Intelligence System Supports Diagnosis of Mendelian Diseases in Acutely Ill Infants

Abstract

Mendelian disorders are prevalent in neonatal and pediatric intensive care units and are a leading cause of morbidity and mortality in these settings. Current diagnostic pipelines that integrate phenotypic and genotypic data are expert-dependent and time-intensive. Artificial intelligence (AI) tools may help address these challenges. Dx29 is an open-source AI tool designed for use by clinicians. It analyzes the patient’s phenotype and genotype to generate a ranked differential diagnosis. We used Dx29 to retrospectively analyze 25 acutely ill infants who had been diagnosed with a Mendelian disorder, using a targeted panel of ~5000 genes. For each case, a trio (proband and both parents) file containing gene variant information was analyzed, alongside patient phenotype, which was provided to Dx29 by three approaches: (1) AI extraction from medical records, (2) AI extraction with manual review/editing, and (3) manual entry. We then identified the rank of the correct diagnosis in Dx29’s differential diagnosis. With these three approaches, Dx29 ranked the correct diagnosis in the top 10 in 92–96% of cases. These results suggest that non-expert use of Dx29’s automated phenotyping and subsequent data analysis may compare favorably to standard workflows utilized by bioinformatics experts to analyze genomic data and diagnose Mendelian diseases.

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“…The application of AI to Mendelian disease is more difficult due to the frequent absence of family data. Nevertheless, some interesting applications of AI have been developed in acutely ill infants, in which trios were available [ 34 ]. Although the medical contribution remains an indispensable requisite for the correct interpretation of the results derived from the AI protocols [ 35 ], it is expected that in the future, the improvement of AI protocols will allow for the correct genetic diagnosis in many sporadic cases.…”