Photo of newborn baby holding adult thumb to represent sequencing of newborns to speed up genetic disease diagnosis
Credit: millaf/Fotolia

The results of a research project led by Rady Children’s Institute for Genomic Medicine (RCIGM) show that an automated, virtual disease management system that includes fast whole genome sequencing and analysis could help to manage genetic diseases better.

The proposed Genome-to-Treatment (GTRx) system would enable many patients suspected of having a genetic disease to have a diagnosis within as little as 13.5 hours.

“GTRx is intended to provide immediate guidance to frontline neonatologists and intensivists to select optimal therapies for critically ill infants and children in intensive care units as time is of the essence,” said Stephen Kingsmore, President & CEO of RCIGM and principal investigator of the study, in a press statement.

“This study continues to validate the clinical utility of rapid whole genome sequencing and how Rapid Precision Medicine can improve outcomes for those diagnosed with a rare disease.”

The idea behind GTRx, which is still at the prototype stage, is to circumvent the long ‘diagnostic odyssey’ that many patients with genetic diseases endure. This current process takes an average of 5 years and can be extremely stressful for families and potentially damaging for those affected if treatment is delayed.

The researchers also want to help clinicians and healthcare providers process complex genetic information from rapid genomic sequencing to help give patients better and more targeted treatment.

RCIGM is known for its focus on genomic medicine and has been working to speed up whole genome sequencing for the purposes of genetic disease diagnosis in newborns for a number of years.

The new GTRx prototype brings together different research streams and was completed with the help of industry partners Alexion, AstraZeneca, Fabric Genomics, Genomenon, Illumina, and SL Data Strategies, as well as Keck Graduate Institute, Rady Children’s Hospital–San Diego, and UC San Diego departments of Pediatrics and Neuroscience.

As described in the Nature Communications paper presenting GTRx and the work behind it, the team first aimed to shorten the time of the rapid sequencing process managing an average of 13.5 hours. They also incorporated automated data analysis and interpretation, as well as different treatments and therapy options.

To try and ensure accuracy, an expert panel assessed the efficacy of almost 10,000 drugs, devices, dietary, and surgical interventions for 563 severe, childhood-onset genetic diseases. In total, 1527 treatments or interventions were deemed effective for 421 genetic diseases, and this information was included in the system.

“We developed GTRx to both increase the number of children who receive optimal, immediate treatment and to facilitate broader use of rapid whole genome sequencing by physicians working in local hospitals who may not be as familiar with genetic diseases as sub- and super-specialists in regional, academic, tertiary or quaternary centers,” said Kingsmore. “Our goal is to upskill these physicians by providing patient diagnosis- and disease-specific information in real time.”

The researchers are hoping this system could go into much wider use in the future, following further testing and validation. Currently it is available for research purposes.

“Upon validation of clinical utility, we will expand the system to additional genetic diseases and clinical use, as well as incorporating ongoing, expert, open community-based review,” explained Kingsmore.

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