From 13 Years to 13 Hours: Rady Children’s Institute for Genomic Medicine Demonstrates Fastest Time to Life-Changing Diagnosis for Infants with Rare Disease

Baby in a NICU incubator

It took an international research effort 13 years to complete the first sequence of the human genome – the code of life. Now, Rady Children’s Institute for Genomic Medicine (RCIGM), in collaboration with Illumina, Inc. and Alexion Pharmaceuticals, Inc., is refining an ultra-rapid sequencing process to diagnose rare disease in 13.5 hours.

In a letter published today in the New England Journal of Medicine, RCIGM outlines the technique by which they have reduced the time to delivery of a molecular diagnosis via whole genome sequencing from their previous world speed record of 19.5 hours.

“Speed matters for critically ill infants with rare disease,” said Stephen Kingsmore, MD, DSc, President and CEO, of the Institute. “For this particular baby, the diagnosis allowed doctors in the intensive care unit to initiate precise treatment which reversed the child’s life-threatening condition.”

For the case in point, the total time from when the laboratory sample preparation began to when the provisional diagnosis was called was 13.5 hours. Approximately 4 hours later, the infant was started on precise treatment. The baby responded very well and was discharged from the hospital three days later.

Since the fall of 2020, when that first child was sequenced under the accelerated research protocol, a total of seven cases have been sequenced in under 14 hours via the same process by RCIGM. Three involved critically ill patients admitted to intensive care at Rady Children’s Hospital-San Diego. Another four were retrospective cases.

The Institute worked closely with leading technology and data-science developers –Illumina and Alexion– to engineer and optimize a seamless process to decode human genomes.

“Ending the diagnostic odyssey can improve patient outcomes and save lives,” said Phil Febbo, MD, Chief Medical Officer at Illumina. “We are proud to partner with Rady Children’s to help implement rapid whole genome sequencing in a way that’s multidisciplinary, integrated, and precise within a medical delivery system that is unparalleled.”

Illumina is the global leader in DNA sequencing and has been working with RCIGM since 2015. The process to conduct whole genome sequencing (WGS) starts with Illumina’s DNA PCR-Free Prep for rapid library preparation followed by sequencing of WGS samples using the latest NovaSeq™ v1.5 reagents. Analysis is conducted through the powerful DRAGEN™ v3.7 software. For variant annotation and interpretation, TruSight™ Software Suite can be included.

In addition, Alexion has contributed their rare disease and data science expertise to enable the translation of clinical information into a computable format for guided variant interpretation.

“Children represent half of the patients affected by rare diseases, many of which are exceptionally difficult to diagnose,” says Sebastien Lefebvre, Senior Director, Data Sciences, Genomics and Bioinformatics at Alexion Pharmaceuticals. “We are proud to collaborate with Rady Children’s and excited to see these promising tools advance our collective efforts to help more critically ill children.”

While the 13.5-hour sequencing process was achieved in a research setting, RCIGM has developed a clinical Rapid Precision Medicine™ delivery system optimized for speed and accuracy. In medically urgent cases, RCIGM routinely returns preliminary clinical results in less than three days.

“We’re delighted to be able to repeatedly replicate this expedited method under a research protocol in a real-world setting,” said Dr. Kingsmore. “This shows that in the future, it will be possible for clinicians to order whole genome sequencing on morning rounds and receive a molecular diagnosis by the same evening.”

Located on the campus of Rady Children’s Hospital in San Diego, Rady Children’s Institute houses a state-of-the-art genome sequencing lab. RCIGM’s multi-disciplinary team of experts specialize in providing timely, disease-specific guidance to physicians caring for newborns and children with rare genetic disease. RCIGM works with a growing network of children’s hospitals nationwide.

Since 2016, the team has completed sequencing the genomes of more than 2,000 children. Approximately one-third of the patients have received a diagnosis with two-thirds of those benefitting from an immediate change in clinical care—resulting in improved outcomes for one-quarter of those diagnosed.

“Ultimately, we’d like to make this innovation widely available to so all children who need it can have access to this life-saving technology,” said Dr. Kingsmore.


About Rady Children’s Institute for Genomic Medicine:

We are transforming pediatric critical care by advancing disease-specific healthcare for infants and children with rare disease. Discoveries at the Institute are enabling rapid diagnosis and targeted treatment of critically ill newborns and pediatric patients at Rady Children’s Hospital-San Diego and a growing network of more than 60 children’s hospitals nationwide. The vision is to expand delivery of this life-changing technology to enable the practice of Rapid Precision Medicine™ at children’s hospitals across the nation and the world. RCIGM is a non-profit, research institute embedded within Rady Children’s Hospital and Health Center. Learn more at Follow us on Twitter and LinkedIn.

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