Rady Children’s Institute, Edico Genome Collaborate
News Oct 19, 2016
Researchers from Rady Children’s Institute for Genomic Medicine and Edico Genome have worked together in successfully demonstrating ultra-rapid, 26-hour whole-genome based diagnoses of critically ill newborns in the neonatal intensive care unit (NICU) and pediatric intensive care unit (PICU). The ultra-rapid NICU whole-genome test is powered by Edico Genome’s DRAGEN™, the world’s first bio-IT processor designed to rapidly accelerate the analysis of genomic data while maintaining high accuracy.
Rady Children’s Institute for Genomic Medicine and Edico Genome will work together to evolve the DRAGEN platform to impact additional areas of clinical genome analysis. This vision includes scaling the ultra-rapid NICU testing to additional NICUs and PICUs utilizing an all-in-one appliance deployed onsite or in the cloud and including analysis of additional clinically relevant variant types.
Rady Children’s Institute for Genomic Medicine began providing whole genome sequencing in July 2016 with clinical interpretation in a meaningful, timely and highly accurate manner to critically ill children. This rapid method allows the simultaneous evaluation of nearly all of the 4,500 known genetic diseases in a single test. Rapid diagnosis is essential in acute care situations, particularly in NICUs where medical decision-making must happen in minutes and hours, not weeks.
“Rapid diagnosis of critically ill newborns is no longer an academic exercise, it’s a reality for critically ill newborns admitted to the NICU and PICU at Rady Children’s Hospital . The information we receive from this rapid and comprehensive testing is already helping our medical teams make treatment decisions and impacting the lives of these babies and their families,” said Stephen Kingsmore, M.D., D.Sc., president and chief executive officer of the Rady Children’s Institute for Genomic Medicine.
“Development of this ultra-rapid test could not have been possible without the dedicated efforts of our key partners, including Edico Genome. We look forward to working with Edico on evolving the platform and making this rapid testing capability available to additional NICUs around the globe.”
Up to one-third of babies admitted to a neonatal intensive care unit in the United States have a genetic disease, and more than 20 percent of infant deaths are caused by genetic illnesses. Treatments are currently available for more than 500 genetic diseases; for many of these, initiation of therapy in newborns can help prevent disabilities and life-threatening illnesses. The cost of whole-genome sequencing has fallen to the point of feasibility for clinical testing of these and other conditions, and the DRAGEN bioinformatics chip is reducing time needed for analysis, facilitating the use of genomic medicine in acute medical care.
“Rapid diagnostics is essential to fundamentally changing our ability to inform clinical care,” said Narayanan “Ray” Veeraraghavan, Ph.D., director of information technology, Rady Children’s Institute for Genomic Medicine. “Deploying whole-genome based testing at the bedside becomes practical and actionable when results are consistently and expeditiously returned to the attending physician(s).”
In 2015, while at Children’s Mercy Kansas City, Dr. Kingsmore and his team successfully diagnosed critically ill newborns in 26 hours, as published in the journal Genome Medicine, using time-shrinking technologies including in-house software, Edico Genome’s DRAGEN Bio-IT Processor for data analysis and one of Illumina’s high-throughput sequencing instruments.
“We could not be prouder that newborn babies are receiving rapid and potentially life-saving care based on the speed and accuracy of DRAGEN,” said Pieter van Rooyen, Ph.D., chief executive officer of Edico Genome. “This ultra-rapid NICU testing is the first clinical application of the DRAGEN platform. It’s not enough for one institute to implement this technology though – this testing needs to be scaled for easy use by NICUs around the world. We look forward to working with Dr. Kingsmore and his team to realize the vision of an all-in-one appliance where the ultra-rapid test can be performed onsite or in the cloud and can be expanded to include analysis of additional clinically relevant variants, such as structural and copy number variants.”
DRAGEN accelerates secondary analysis of next-generation sequencing data, reducing the time required for analyzing a genome at 30x coverage from approximately 30 hours to nearly 22 minutes. DRAGEN uses a field-programmable gate array (FPGA) to implement genome pipeline algorithms, including BCL conversion, compression, mapping, alignment, sorting, duplicate marking and haplotype variant calling.
The platform includes whole genome and exome, transcriptome, joint genotyping, methylation, and GATK pipelines, and allows users to develop custom algorithms as well as refine and improve existing pipelines. Updated versions are made available for customers through simple remote downloads.
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