Meghaan M. Ferreira Ph.D. Contributor GEN and Clinical OMICs
Edico Genome and Congenica to Provide All-in-One Clinical Decision Support Package
Technological advances have led to dramatic decreases in the cost of genetic sequencing, ushering in a genomics revolution that aspires to transform medicine. However, developing solutions that can effectively, efficiently, and affordably translate these advances to a clinical setting remains challenging, which is why two genomics companies, Congenica and Edico Genome, have partnered to offer their complementary technologies as an all-in-one solution for data analysis, interpretation, and reporting.
“Both companies are very much driven to deliver these joint solutions in a clinical diagnostic setting,” commented Congenica’s Chief Business Officer, Shikha O’Brien, Ph.D., on the companies’ mutual commitment to bringing genomics-based medicine to fruition through their individual technologies.
Congenica’s cloud-based software platform, Sapientia, enables clinical geneticists to analyze and interpret the gamut of next-generation sequencing data and generate a comprehensive diagnostic report to support clinical decision-making.
The knowledge base underlying Sapientia aggregates data from its users and places it into a knowledge base that can inform future analyses. However, according to O’Brien, “[Sapientia’s] beauty is that it brings all of the information required for variant interpretation together in a single, dynamic interface. All of this information being held together creates an accurate and in depth audit trail to really support the work of our clinical colleagues.”
Referred to as “secondary analysis,” Edico Genome’s hardware-accelerated platform, DRAGEN (Dynamic Read Analysis for Genomics), analyzes raw-read data from sequencing instruments, identifies variants, and outputs a VCF (Variant Call Format) file that Sapientia and other downstream software reads. Unlike other, software-based, secondary analysis platforms, DRAGEN uses a field-programmable gate array (FPGA) processor that facilitates ultra-rapid analysis—without compromising accuracy. This distinctive approach “gives [DRAGEN] an efficiency that is just unachievable in pure software,” commented Gavin Stone, vice president of marketing and development at Edico Genome.
“You can make a [software-based approach] run relatively fast, but then you’re going to have to throw a super computer at it to get it down to an hour,” he added. Software-based approaches require more CPUs to process next-generation sequencing data quickly, and that kind of computing power doesn’t come cheap. “Cloud providers charge a dollar amount per instance, per hour,” Stone explained. “The only way to decrease the cost is to use an FPGA where you can use one instance to analyze a genome in ten minutes.”
Edico Genome and Congenica already have mutual clients who use DRAGEN and Sapientia, including researchers in the U.K.’s 100,000 Genomes Project and the University College of London’s (UCL) Rapid Pediatric Sequencing Project. The latter is a pilot study designed to evaluate the effectiveness of using whole genome sequencing to diagnose rare pediatric diseases that emerge in an intensive care clinical setting—a place where minutes matter.
When Clinical OMICs spoke with Stone, he had just attended Rady Children’s Frontiers in Pediatric Genomic Medicine Conference: “It’s really like an episode of House every time. You have no idea what’s wrong, the baby’s presenting a set of symptoms, and the situation is just continuously deteriorating by the minute.” The case study, Precision Medicine for Newborns by 26-Hour Whole Genome Sequencing, provided examples of how genetic sequencing technology, like DRAGEN, is being used to save children’s lives at Rady Children’s Hospital.
Rare metabolic diseases, such as molybdenum cofactor deficiency, which causes seizures and neurological damage and can cause irreparable harm and even death if not promptly diagnosed and treated. “If you have a child who has been seizing for six weeks, which is what conventional genetic testing takes, that child is going to be severely intellectually impacted,” explained David Dimmock, M.D., medical director of Rady Children’s Hospital’s Genomics Institute.
Dr. Dimmock and his colleagues estimate that early diagnosis of a genetic disorder would change the care of 15,000 to 20,000 children a year in the U.S. that end up in high-level newborn intensive care units (NICU). Unfortunately, many children’s hospitals have limited genetics services, which preclude access to diagnostic testing using whole exome or genome sequencing for children suffering from these disorders.
The “simplistic, straightforwardness at the user-end of these kinds of packaged tools actually increases the market penetration of actual sequencing,” commented Dr. Dimmock on the usability of DRAGEN. The formal partnership between Edico Genome and Congenica will allow them to integrate their technologies into a single, robust, low-cost, easy-to-use system that can provide rapid diagnosis from DNA sequencing—making it more affordable and accessible for hospitals and patients.
This article was originally published in the May/June 2017 issue of Clinical OMICs. For more content like this and details on how to get a free subscription to this digital publication, go to www.clinicalomics.com.