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Boston Children’s Hospital has successfully used artificial intelligence (AI) to diagnose 18 children whose rare diseases had eluded explanation for years, marking a major step forward in pediatric healthcare. New research published Thursday (June 18) in the New England Journal of Medicine’s AI-focused publication, NEJM AI, shows that tools developed by the AI company OpenAI, specifically its o3 model, helped geneticists find answers for families who had nearly given up hope.
The research team analyzed the genomes of 376 children with undiagnosed rare diseases, combining clinicians’ notes, patient symptoms, and a filtered list of possible gene candidates. The AI system, working alongside human experts, identified new diagnoses for 18 of these children, including ten with neurodevelopmental conditions, four with neuromuscular disorders, two who had died suddenly, and two with early childhood psychosis.
Dr. Catherine Brownstein, the scientific director of the genetic investigations arm at Boston Children’s Manton Center for Orphan Disease Research, described the achievement as a “total game changer.” She explained that although the diagnostic yield—almost five percent—may seem small, it is significant since many of these cases had already been thoroughly analyzed by human experts. "Each one means an answer for a family," Brownstein said.
One patient, Kyra Benton, spent more than a decade searching for a diagnosis before AI-assisted analysis revealed she had myofibrillar myopathy, a progressive genetic disorder. "Last summer, about a week before my 20th birthday, we got a call from one of the researchers at the lab," she said, describing how relief and hope finally replaced years of uncertainty.
Boston Children’s Hospital has deeply integrated AI into its daily operations, not just for medical discovery but also to streamline administrative tasks. According to OpenAI, the hospital’s use of AI has led to more than 40 previously unsolved rare disease diagnoses, saved 60,000 hours in work time, and redeployed over $7 million in labor costs. The hospital’s Chief Innovation Officer, John Brownstein, noted, “We combine genetic information, phenotypic information, literature search, and the reasoning of AI to deliver diagnoses to families that were once left without any answers.”
Experts caution that AI is not intended to replace medical professionals, but rather to support them in complex cases. Dr. Adam Rodman, a physician at Beth Israel Deaconess Medical Center, told NBC News the results were "truly meaningful" and could help reduce backlogs of undiagnosed cases. Chunhua Weng, a professor at Columbia University, added that results must still be reviewed by doctors to ensure accuracy and trustworthiness.
The research highlights that AI can help identify connections between genes and diseases by rapidly processing vast amounts of medical information, something even highly trained specialists may not have time to do. The hospital continues to refine its AI systems in collaboration with OpenAI, aiming to expand their impact across more specialties and to further improve patient care.
For patients and their families, these advances offer not just answers, but hope for treatment and participation in future clinical trials. As AI becomes more integrated into healthcare, Boston Children’s leaders believe it will play an increasingly central role in diagnosing and treating rare diseases.