The following is a guest blog, written by our partners at Edico Genome.
When diagnosing acutely ill babies, it’s a race against time to ensure that physicians have access to accurate diagnoses to set the appropriate course of treatment. During the first few days of life, a few hours can save or seal the fate of patients emitted to the Neonatal Intensive Care Units (NICU) and Pediatric Intensive Care Units (PICU), making it essential to deliver diagnosis in an expedited manner while ensuring accuracy and keeping costs low for widespread adoption.
Seeking a dependable way to drastically cut down on diagnosis times, Dr. Stephen Kingsmore, M.D. D.Sc., President and CEO at Rady Children’s Institute for Genomic Medicine, in partnership with Edico Genome and Illumina, developed a scalable infrastructure to perform diagnosis from beginning to end in 26 hours.
In order to receive such results, Dr. Kingsmore needed to address the largest bottleneck: secondary data analysis. Integrating Edico Genome’s DRAGEN Bio-IT Platform, which is now available on DNAnexus, Dr. Kingsmore was able to reduce analysis time from ~25 hours (using an optimized version of BWA-GATK) down to ~22 minutes.
This drastic acceleration was the result of DRAGEN’s field programmable gate array (FPGA) backed platform, based on a Xilinx FPGA, which provides hardware-accelerated implementation to all of the most widely used types of NGS workflows. In conjunction with Illumina’s optimized sequencing platform, Dr. Kingsmore was able to greatly expedite sample to answer turnaround time and earn the Guinness World Record for Fastest Genetic Diagnosis.
As a result of this initiative, 23 out of the first 48 Rady Children’s Hospital infants tested received diagnosis and 16 received substantial changes in NICU/PICU treatments. For one infant with liver disease, the expedited diagnosis resulted in the cancellation of a surgery that posed a 60 percent risk of mortality. For two other patients, one with heart failure and the other with liver failure, Dr. Kingsmore and his team were able to rule out disease which were a contra-indication to heart and liver transplants, respectively. Without this information, both infants may have been too high risk for transplant or may not have survived the procedure.
DRAGEN is now available in the cloud through the DNAnexus Platform, powered by Amazon Elastic Compute Cloud (Amazon EC2) F1 instance types. DNAnexus connects Edico Genome’s ultra-fast secondary analysis algorithms with Fabric Genomics’ interpretation software, and integrates seamlessly with Rady Children’s custom data interpretation portal. Through the DNAnexus Platform, users can monitor jobs, organize and share data, and compare patients’ data to a diagnostic resource within the network, making it an ideal solution for streamlining and expanding operations to other children’s hospitals across the country.
New and existing DNAnexus customers can now also take advantage of the highly accurate and ultra-rapid DRAGEN pipelines used by Dr. Kingsmore on the DNAnexus Platform. Sign up for our reduced-cost trial here.
To learn more about DRAGEN’s partnership with Dr. Kingsmore and his team, the full white paper can be found here.