Study: Whole-Genome Sequencing Technology Enables 26-Hour Diagnosis of Critically Ill Newborns, Nearly Halving Previous Record for Speed
KANSAS CITY, Mo. and SAN DIEGO, Sept. 29, 2015 — Rapid diagnosis is essential in acute care situations, particularly in neonatal intensive care units where medical decision-making must happen in minutes and hours, not weeks. Today, Children’s Mercy Kansas City and Edico Genome published results of a study showing the successful diagnosis of critically ill newborns in just 26 hours using a new genomic data analysis technology, DRAGEN™, and optimizing other parameters. Prior to this study, published Sept. 29 in Genome Medicine, the world’s fastest diagnosis of critically ill newborns using whole genome sequencing was 50 hours.
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 about 70 of these, initiation of therapy in newborns can help prevent disabilities and life-threatening illnesses. While the cost of whole-genome sequencing has fallen to the point of feasibility for clinical testing of these and other conditions, the lack of a rapid method for genomic data analysis has long served as a barrier to its use in acute medical care.
“Diagnosing acutely ill babies is a race against the clock, as even one day of waiting can be a matter of life or death,” said the study’s senior author Stephen Kingsmore, M.D., former executive director of Medical Panomics at Children’s Mercy Kansas City, and current president and chief executive officer of the Pediatric Genomics and Systems Medicine Institute at Rady Children’s Hospital-San Diego. “Obtaining a genetic diagnosis in only 26 hours means the right treatment can begin much sooner, eliminating extra anxiety for families and avoiding extra healthcare expenses. Using the DRAGEN processor for rapid genomic analysis reduced the most time-intensive step of the sequencing process from almost a day to less than an hour.”
Both the prior record of a 50-hour diagnosis and now the 26-hour diagnosis were performed as part of Children’s Mercy Kansas City’s whole-genome sequencing research program for neonates who are acutely ill with a likely genetic disease. The hospital’s breakthrough process, known as STAT-Seq and developed by Dr. Kingsmore, relies on technology such as DRAGEN along with in-house software to translate data into actionable clinical information.
In the retrospective study, blinded DNA samples from infants with known genetic diseases were reanalyzed using various parameters and technologies. The greatest time-savings were achieved with Edico Genome’s DRAGEN, the first processor designed for genomics applications. DRAGEN sped up data analysis from 22.5 hours to 41 minutes, while also achieving high sensitivity and specificity of 99.5 percent. The accelerated speed theoretically would enable 350 whole genome sequences a year using a single Illumina HiSeq 2500.
“These results demonstrate that DRAGEN rapidly and accurately analyzes genomic data, offering significant benefits to patients, physicians and the healthcare system overall,” said Pieter van Rooyen, Ph.D., chief executive officer of Edico Genome. “Genomics is rapidly becoming a critical component for medical care, yet most hospitals don’t have supercomputers or the personnel to manage the large servers required for subsequent data analysis. DRAGEN, the world’s-first processor for next-generation sequencing, fits easily into the footprint of a hospital’s existing molecular genetics lab, enabling the fastest diagnoses possible.”
In addition to the study’s use of DRAGEN, which enabled a 15-hour improvement in whole-genome sequencing diagnosis, clinicians optimized several other parameters to achieve the 26-hour result:
- Developed ultra-rapid run mode on an Illumina HiSeq 2500 sequencing instrument, saving five hours
- Replaced manual interpretation and reporting process with in-house VIKING software program, saving three hours
- Optimized in-house software, RUNES (Rapid Understanding of Nucleotide variant Effect Software), to more quickly detect mutations in gene sequences, saving two hours
About Children’s Mercy Kansas City
Children’s Mercy, located in Kansas City, Mo., is one of the nation’s top pediatric medical centers. The 354-bed, not-for-profit hospital provides care for children from birth through the age of 21, and is ranked by U.S. News & World Report as one of “America’s Best Children’s Hospitals.” For the third time in a row, Children’s Mercy has achieved Magnet nursing designation, awarded to fewer than seven percent of all hospitals nationally, for excellence in quality care. Its faculty of more than 700 pediatric subspecialists and researchers across more than 40 subspecialties are actively involved in clinical care, pediatric research, and educating the next generation of pediatric subspecialists. For more than a century, Children’s Mercy has provided the highest level of medical care to every child who passes through its doors, made possible through generous community support.
About Edico Genome
Edico Genome, developer of the world’s first next-generation sequencing Bio-IT processor, DRAGEN™, is helping usher in the new era of precision medicine by enabling customized treatments and data-driven insights tailored to the individual. At the heart of personalized medicine is next-generation sequencing (NGS), which is growing at an unprecedented pace. By increasing the speed and accuracy of NGS data analysis, such as whole genome sequencing, Edico Genome’s computing platform makes it easier to discover links between DNA sequence variations and human disease, allowing clinicians and researchers to reveal answers more quickly. For more information, visit www.EdicoGenome.com or follow @EdicoGenome.