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New Cloud-Native Database Offers Rapid Diagnosis of Rare Childhood Genetic Disease

By: Brittany Wade 

May 18, 2022 | We live at a unique time in history, said Stephen Kingsmore, Rady Children’s Institute for Genomic Medicine, as he began his Bio-IT World Conference & Expo presentation earlier this month. Scientists can now decode whole genomes and issue a baby's diagnosis in just seven hours as the cost of genomic sequencing plummets and speed increases. As a result, knowledge of genetic diseases is growing exponentially. 

He went on to tell the story of a previously healthy young girl who lost consciousness after having dinner with her family. Unable to maintain adequate blood pressure, she was given several tests and put on extracorporeal membrane oxygenation (ECMO). Her tests returned positive for rhinovirus/enterovirus, a self-limiting pathogen with an excellent prognosis. However, she was also given genetic testing due to its high availability and accessibility. The genetic tests confirmed genetic cardiomyopathy, exacerbated by viral cardiomyopathy. She received a heart transplant and made a speedy recovery but would have died if treated solely for a viral illness. 

Stories like these motivate Kingsmore and have fueled his work on pediatric and newborn genetic testing and screening for over a decade. The math is simple: as genetic testing becomes the standard of care, 1 in 5 patients demonstrates improved outcomes. Otherwise, they often show a rapid decline that precludes them from the transplant list, usually before medical staff knows they need a transplant in the first place. 

Even with decreasing costs, one would assume genetic testing for every pediatric patient is too expensive, but, surprisingly, it saves healthcare dollars, says Kingsmore. For example, implementation monitoring demonstrated a savings of 2.5 million dollars for 178 patients due to shorter hospital stays and less expensive care management protocols (DOI: S0002-9297(21)00192-0). Still, Kingsmore suspects the current savings are grossly underestimated after factoring in the cost of multiple hospital stays that occur when patients are unaware of their genetic condition or how to treat it. 

Genome to Treatment 

Though genetic testing saves money and drastically improves diagnostic abilities, a rapid diagnosis proves little benefit if a physician cannot treat the disease. Enter Genome-to-Treatment, a system that integrates over 1,500 interventions for over 400 rare genetic disorders. Now, critically ill and newly diagnosed patients receive accurate treatment plans regardless of the rarity or severity of their disease. 

Where Genome-to-Treatment shines is in newborn screening. Under a universal delivery system, every newborn would receive diagnostic rapid whole-genome sequencing in just three days. The screening would be as simple as pricking the heel and taking a Guthrie card sample within 24 hours after birth. It currently tests for approximately 30 genetic disorders, but the goal is to test for every congenital disease for which there is an effective therapy. Of the 8,000 genomes analyzed, 1 in 3 newborns received a diagnosis with 99.9% specificity. 

A Universal Database 

With approval from the World Health Organization (WHO), Kingsmore knew his next step of screening 140 million babies across high- and medium-income countries would require a robust data management system.

Stavros Papadopoulos, Founder and CEO of TileDB, created an efficient and cost-effective cloud-native universal database to meet those high data management demands. TileDB stores varied forms of data allowing for exploration, analytics, data science, machine learning, and holistic governance on one platform. Efficient performance translates to low cost, said Papadopoulos; consolidating data to one platform offers adaptability and superior performance at a minimum expense. 

TileDB uses multi-dimensional (i.e., dense or sparse) arrays to store tables, ranges (LiDAR), synthetic aperture radar (SAR), population and single-cell genomics, imaging, graphs, video, etc. Its storing capabilities make it possible to share, log, and monetize data. With groundbreaking technology from Papadopoulos and the seasoned experience of Kingsmore, the future of genetic testing and screening proves to be on the rise and in excellent hands. 

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