The engine making rapid NGS diagnoses possible
Pieter Van Rooyen is the founder and CEO of Edico Genome, a San Diego-based company that has developed the world’s first bio-IT processor designed to analyse NGS data at ultra-rapid speeds.
FLG: San Diego is gaining a reputation for being the Genomics Capital of the world, particularly in bringing NGS into the clinic. This is something you’ve had experience in through your work with Dr. Stephen Kingsmore. You had a key role in setting the world record for the fasted genetic diagnosis, but it isn’t just speed for speed’s sake is it? What are the benefits of reducing time?
PVR: In a critical situation in a Neonatal Intensive Care Unit (NICU), every second counts and so speed becomes pivotal. Obtaining a genetic diagnosis faster means the right treatment can begin much sooner. In many cases this can mean the difference between life and death.
Accelerated data analysis also means research can be done more efficiently, leading to cures for genomic diseases like cancer or Alzheimer’s. In addition, speed translates to massive cost savings in terms of compute resources and storage. For instance, we replace a cluster of 50 or more computers with a single 1U server with DRAGEN. This technology also enables us to reduce storage by a significant margin.
FLG: How did Edico get started working with Stephen Kingsmore and the Children’s Mercy Hospital in Kansas City?
PVR: Stephen was planning a new study to validate the utility of ultra-rapid whole genome sequencing in the NICU at the Children’s Mercy Hospital in Kansas City. Stephen had previously achieved getting to a genetic diagnosis of critically-ill newborns in just 50-hours and wanted to further improve upon it. The largest bottleneck in that process was the analysis of the genomic data, which required almost 24 hours. Our DRAGEN technology addresses this problem and eliminates time as a major obstacle. Together we were able to achieve what is now known as the “26-Hour Genome.”
FLG: How does Edico hope to influence the future of genomics?
PVR: By 2025, genomic data is predicted to be the biggest of big data applications, bigger than YouTube, Twitter, and astronomical data. Because the data’s growing faster than intel processors are able to keep up with, a fundamentally different approach is needed. DRAGEN really is the only viable solution and will enable anyone working with next generation sequencing to accelerate their work while also minimizing the amount of storage needed to handle the massive amounts of data. As an example of the explosion of data, Edico’s customers, using DRAGEN, have processed more than 2 Peta bytes of data the previous 3 months. This number is growing and our customers are on track to process almost 10 peta bytes of data in 2016.
Based on our work on the “26 Hour Genome,” we’ve also continued to collaborate with Stephen and the Rady Children’s Hospital (where he is now) on defining, developing, and commercialising a technology solution that can be scaled and replicated at many locations and applications, beginning with NICU’s. We hope this is just the start of DRAGEN’s influence on clinical settings.
FLG: You moved to San Diego from South Africa 16 years ago to start a wireless chip company. What has made San Diego the ideal location for you to start all your businesses?
PVR: San Diego, being the home to the leading wireless chip companies like Qualcomm, was the ideal place to come at the time to start my first company making a 3G cell phone chip. Coincidentally, it’s also at the forefront of genomics, home to the two largest genomics company in the world, Illumina and Life Technologies (now part of Thermo Fisher), which really led to where I am today. There’s unique infrastructure in San Diego, both talent wise and start-up wise, to facilitate new ideas and make them come to fruition, especially in genomics.