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Benchmark Genome Study Demonstrates Accuracy of Artificial Intelligence in Rapidly Diagnosing Rare Diseases in Critically Ill Patients

Date: October 14, 2021

Pivotal study led by Fabric Genomics and Rady Children’s Institute for Genomic Medicine demonstrates that artificial intelligence can enable the accurate and rapid clinical diagnosis of rare diseases in critically ill newborns based on whole-genome or whole-exome analyses

OAKLAND and SAN DIEGO, Calif.–OCTOBER 14, 2021 –Fabric Genomics and Rady Children’s Institute for Genomic Medicine®, today announced the publication of a retrospective study in Genome Medicine showing that across six leading genomic centers and hospitals, researchers were able to detect more than 90% of disease-causing variants using the Fabric GEM AI algorithm and whole-genome and whole-exome data from previously diagnosed newborns and rare disease patients at Rady Children’s Hospital – San Diego and other clinical sites.

Despite differences in case collection, sequencing methods and bioinformatics pipelines across all sites, Fabric GEM’s performance demonstrated a new standard of accuracy, ranking the causative variant first or second more than 90% of the time. In addition, Fabric GEM ranked specific diseases and conditions associated with these genes to assist clinicians in the ultimate diagnosis of each case. These findings demonstrate how AI can successfully reduce the burden of gene variant review by the clinical geneticist.

“Fast and definitive genetic diagnosis is essential to providing the right treatment in a timely manner for critically ill newborns,” said Stephen Kingsmore, MD, DSc, a co-author of the study and the President and CEO of Rady Children’s Institute for Genomic Medicine.“ Fabric GEM has successfully demonstrated that it can automatically and quickly suggest a very short list of candidate genes for interpretation through whole-genome or whole-exome sequencing.”

Additional centers that participated in the study include the University of Utah, Boston Children’s Hospital, Christian-Albrechts University of Kiel & University Hospital Schleswig-Holstein, Hudson Alpha Institute of Biotechnology, Tartu University Hospital, and the Translational Genomics Research Institute (TGen).

“This study is an exciting milestone demonstrating how AI-powered decision support technologies can empower clinicians. It has the potential to significantly improve patient care with rapid insights distilled from clinical notes, medical databases, and genome sequences. Human review of these critical, but ever-expanding data is becoming infeasible due to their size and complexity. Hence GEM”, said Mark Yandell, PhD., Professor of Human Genetics and Edna Benning Presidential Endowed Chair at the University of Utah, a founding scientific advisor to Fabric and a co-author on the paper.

This study also demonstrated the use of Clinithink’s CLiX focus, a natural language processing (NLP) technology applied to medical notes recorded in electronic medical records. When compared to manual abstraction, this automated approach, which couples CliniThink’s NLP technology with the Human Phenotype Ontology and Fabric GEM, can rival the results achieved through time-intensive, expert-driven curation.

“Finally, clinicians do not have to sacrifice accuracy for speed when faced with a possible rare disease diagnosis in a critical setting like the NICU where time is of the essence,” said Martin Reese, PhD., CEO of Fabric Genomics and a co-author on the paper. “This study provides the rigorous benchmark validation required for its use in the clinic, showcasing how any hospital can bring informed genomics to their patients.”

The complete study, titled “Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases,” can be accessed on the Genome Medicine website or on Fabric’s publication page.


Fabric Genomics is making genomics-driven precision medicine a reality. The company provides clinical-decision support software that enables clinical labs, hospital systems, and country-sequencing programs to gain actionable genomic insights, order-of-magnitude improved diagnostic yields and turnaround time. Fabric’s end-to-end genomic analysis platform incorporates proven AI algorithms and has applications in both hereditary disease and oncology. Headquartered in Oakland, California, Fabric Genomics was founded by industry veterans and innovators with a deep understanding of bioinformatics, large-scale genomics, and clinical diagnostics. 

To learn more, visit fabricgenomics.com and follow us on Twitter and LinkedIn.


Rady Children’s Institute for Genomic Medicine is transforming neonatal and pediatric health care by harnessing the power of Rapid Precision Medicine™ to improve the lives of children and families facing rare genetic disease. Founded by Rady Children’s Hospital and Health Center, the Instituteoffersthe fastest delivery of rapid Whole Genome Sequencing™to enable prompt diagnosis and targeted treatment of critically ill newborns and children in intensive care. The Institute now provides clinical genomic diagnostic services for a growing network of more than 70 children’s hospitals. The vision is for this life-changing technology to become standard of care and enable clinicians nationwide to provide rapid, personalized care. Learn more about the non-profit Institute at RadyGenomics.org. Follow us on Twitter and LinkedIn.