Innovations in whole genome sequencing speed answers and hope for newborns and children with rare, genetic diseases
San Diego—Feb. 12, 2018–Scientists at the Rady Children’s Institute for Genomic Medicine (RCIGM) have compressed the time needed to decode rare genetic disorders in newborns through DNA sequencing to less than a day.
Through close collaboration with leading technology and data-science developers — Illumina, Alexion, Clinithink, Edico Genome, Fabric Genomics and Diploid—the RCIGM team has engineered a seamless process—enhanced by in-house expertise—to deliver analysis and interpretation of life-threatening genetic variations in just 19.5 hours.
The GUINNESS WORLD RECORDS™ title was achieved on Feb. 3, 2018. The previous speed record of 26 hours was set in 2015 by Stephen Kingsmore, M.D., D.Sc., president and CEO of Rady Children’s Institute for Genomic Medicine. Dr. Kingsmore has pioneered the rapid turnaround and delivery of genetic test results to neonatal and pediatric intensive care (NICU/PICU) physicians.
“Our evolving ability to find the answers to medical mysteries through rapid Whole Genome Sequencing is providing hope for babies and children with rare, genetic diseases,” said Dr. Kingsmore. “By speeding delivery of genomic insights, we are equipping physicians with the information they need to provide precision care for the youngest and most fragile patients.”
The Institute is staffed by a select team including board-certified medical geneticists, bioinformaticians, software engineers, clinical laboratory scientists, genetic counselors and physicians who channel their expertise into research to advance genomic pediatric medicine.
Genetic diseases are the leading cause of death in infants in North America affecting an estimated four percent of newborns. Rare genetic diseases also account for approximately 15 percent of admissions to children’s hospitals.
“We believe Dr. Kingsmore and his team are prototyping the future of pediatric care through their research and use of whole genome sequencing to accelerate diagnosis and reduce suffering,” said Francis deSouza, president and CEO of Illumina.
RCIGM has optimized an ultra-rapid, accurate and scalable process to decode human genomes by integrating several time-saving technologies. Key components come from Illumina, the global leader in DNA sequencing, including Nextera DNA Flex library preparation and whole genome sequencing via the NovaSeq 6000 and new S1 flow cell format.
Other pipeline elements include Clinithink’s natural language processing (NLP) platform that quickly combs through a patient’s electronic medical record to extract crucial phenotype information; Edico Genome’s highly accurate DRAGEN Bio-IT Platform performs ultra-rapid sequence alignment and variant calling.
Interpretation capabilities are provided by Fabric Genomics’ clinical decision support software, OPAL, enabling rapid diagnosis by helping to pinpoint the source of genetic disease out of hundreds of possibilities.
In addition, Alexion’s rare disease and data science expertise enabled the translation of clinical information into a computable format for guided variant interpretation. The team also used Diploid’s autonomous gene variant interpretation software, MOON, to provide provisional diagnosis.
The entire RCIGM workflow is engineered to speed and scale up genomic data interpretation to reduce the time and cost of whole genome sequencing. The team’s goal is to make rWGS accessible and available to any child who needs it.
By sequencing a blood sample, just one test can screen for thousands of diseases and quickly identify the root causes of a child’s condition to facilitate medical decision making.
Most important, early intervention may avoid unnecessary treatment, invasive surgeries, and reduce hospitalization time, ultimately reducing suffering, bringing down the cost of care and improving quality of life for affected babies and children.
Currently, rapid Whole Genome Sequencing (rWGS) is being offered only through research studies offered to patients at Rady Children’s Hospital-San Diego and children’s hospitals participating in RCIGM’s clinical trials. Among the hospitals collaborating with RCIGM are Children’s Hospital of Orange County, Children’s Minnesota, Colorado Children’s and Nicklaus Children’s Hospital (Miami).
Rady Children’s Institute began performing genomic sequencing in July 2016. By the end of January 2018, the team had completed testing and interpretation of the genomes of more than 335 children enrolled in its research studies. One-third of the patients have received a genomic diagnosis with 69 percent of those benefitting from an immediate change in clinical care.
The Institute is now focused on building a research-to-bedside pipeline extending from RCIGM to children’s hospitals nationwide.“Our hope is that pediatric genomic medicine will one day become routine so that ultimately all children who need it can have access to this life-saving technology,” said Kingsmore.
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About Rady Children’s Institute for Genomic Medicine:
The Institute is leading the way in advancing precision healthcare for infants and children through genomic and systems medicine research. 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 partnering hospitals. The vision is to expand delivery of this integrated translational research process to enable the practice of precision pediatric medicine at children’s hospitals across California, the nation and the world. RCIGM is a subsidiary of Rady Children’s Hospital and Health Center. Learn more at www.RadyGenomics.org. Follow us on Twitter and LinkedIn.
About Rady Children’s Hospital-San Diego:
Rady Children’s Hospital-San Diego is a 551-bed pediatric care facility providing the largest source of comprehensive pediatric medical services in San Diego, southern Riverside and Imperial counties. Rady Children’s is the only hospital in the San Diego area dedicated exclusively to pediatric healthcare and is the region’s only designated pediatric trauma center. In June 2017, U.S. News & World Report ranked Rady Children’s among the best children’s hospitals in the nation in all ten pediatric specialties the magazine surveyed. Rady Children’s is a nonprofit organization that relies on donations to support its mission. For more information, visit www.rchsd.org and find us on Facebook, Twitter and Vimeo.
Clinithink is the healthcare and life science industry’s preferred text analytics provider, enabling innovative discoveries by unlocking the value in unstructured free text data. Clinithink’s patented CLiX natural language processing (NLP) solution can “read” and encode millions of free text documents in hours, making the contents available for analysis. The solution enables rapid extraction of detailed, rich phenotype information for both individual patients and populations. This accelerates diagnosis of rare disease, rare disease prevalence estimation, clinical research protocol design and clinical trials recruitment. For more information, visit http://www.clinithink.com or contact us at clinithink.com/contact/
Alexion is a global biopharmaceutical company focused on serving patients and families affected by rare diseases through the innovation, development and commercialization of life-changing therapies. Alexion is the global leader in complement inhibition and has developed and commercializes the first and only approved complement inhibitor to treat patients with paroxysmal nocturnal hemoglobinuria (PNH), atypical hemolytic uremic syndrome (aHUS), and anti-acetylcholine receptor (AchR) antibody-positive generalized myasthenia gravis (gMG). In addition, Alexion has two highly innovative enzyme replacement therapies for patients with life-threatening and ultra-rare metabolic disorders, hypophosphatasia (HPP) and lysosomal acid lipase deficiency (LAL-D). As the leader in complement biology for over 20 years, Alexion focuses its research efforts on novel molecules and targets in the complement cascade, and its development efforts on the core therapeutic areas of hematology, nephrology, neurology, and metabolic disorders. Further information about Alexion can be found at: www.alexion.com.
About Edico Genome
Edico Genome is the leading secondary analysis solution provider for next-generation sequencing, delivering its powerful DRAGEN Bio-IT platform to clinical, research and genome centers around the globe. Leveraging field programmable gate array (FPGA) technology, DRAGEN delivers best-in-class accuracy, speeds, scalability and costs, enabling customers of all sizes to focus on what matters most – delivering breakthrough results. The comprehensive set of DRAGEN pipelines can be run onsite, in the Cloud or through a seamless hybrid cloud blend, allowing organizations to scale as their throughput fluctuates. Edico Genome has contributed to two GUINNESS WORLD RECORDS™ titles for speed, and received top marks for its accuracy in the recent PrecisionFDA Challenge. For more information about DRAGEN, visit www.edicogenome.com.
About Fabric Genomics
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, resulting in faster and more accurate diagnoses and reduced 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 www.fabricgenomics.com, and follow us on Twitter, LinkedIn, and Facebook.
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