Edico Genome’s DRAGEN Bio-IT Platform Now Available on BaseSpace® Sequence Hub

Removing the NGS Analytics Data Bottleneck with Field-Programmable Gate Arrays (FPGAs)

The following is a guest blog, written by our partners at Edico Genome.

The next-generation sequencing (NGS) analysis demand is growing at an exponential rate, creating a shortage of computing power to analyze the rapidly growing body of data. Current projections1 calculate genomic data to continue doubling every seven months, a stark acceleration in comparison to Moore’s Law, which states CPU capabilities will double every two years (Figure 1, below). The void left in-between creates a bottleneck for genomics labs.

Picture1

Figure 1

Providing an alternative to traditional CPU-based systems, Edico Genome’s DRAGEN™ (Dynamic Read Analysis for Genomics) Platform leverages FPGA (Field-Programmable Gate Array) technology to provide customers with hardware-accelerated implementation of genome pipeline algorithms. Leveraging FPGAs, DRAGEN allows customers to analyze NGS data at unprecedented speeds with extremely high accuracy2 onsite, in the cloud, or through a blended hybrid cloud.

BaseSpace Sequence Hub, hosted on Amazon Web Services, enables the cloud-based deployment of the Edico Genome DRAGEN pipeline. Edico Genome’s DRAGEN Genome Pipeline is now readily available, enabling rapid analysis of whole genome sequencing and targeted resequencing panels.

How does DRAGEN work?

Unlike conventional CPU-based systems that inefficiently execute lines of software code to perform an algorithmic function, FPGAs implement these algorithms as logic circuits, providing an output almost instantaneously. In addition, these logic circuits are replicated thousands of times, allowing for massive parallelism, unlike CPUs which are limited to running only one task per core. FPGAs are also fully reconfigurable, enabling customers to switch between functions and pipelines within seconds. See Figure 2.

Picture2

Figure 2

As a result, FPGA-based solutions, such as DRAGEN, can deliver high accuracy while functioning with exceptional speed, efficiency, and parallelism.

DRAGEN can process an entire human genome at 30x coverage in about 20 minutes, as compared to over 20 hours using a traditional CPU-based system3. Edico Genome’s partnership with Rady Children’s Institute of Genomic Medicine is a testament to how DRAGEN’s FPGA platform is revolutionizing genomic testing. Utilizing DRAGEN, Dr. Stephen Kingsmore set a Guinness World Record in 2016 for the Fastest Genetic Diagnosis for successfully diagnosing a critically ill newborn in 26 hours.4

Such results are consistent among DRAGEN customers, and are now readily available directly through  BaseSpace Sequence Hub with the DRAGEN Genome Pipeline. Other widely adopted pipelines for Transcriptomes, Methylation, Cancer and more, will all be made available on BaseSpace Sequence Hub.

To learn more about DRAGEN, visit www.edicogenome.com/basespace. And to learn more about BaseSpace Sequence Hub, contact us.

For Research Use Only. Not for Use in Diagnostic Procedures.

References

  1. Stephens ZD, Lee SY, Faghri F, et al. Big Data: Astronomical or Genomical? PLoS Biology. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494865/. Published July 2015. Accessed July 31, 2017.
  2. Miller NA, Farrow EG, Gibson M, et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0221-8. Published September 30, 2015. Accessed July 31, 2017.
  3. Miller NA, Farrow EG, Gibson M, et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Medicine. https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0221-8. Published September 30, 2015. Accessed July 31, 2017.
  4. Genome, E. (2017). Dr. Stephen Kingsmore Sets Guinness World Records Title for Fastest Genetic Diagnosis. [online] Prnewswire.com. Available at: http://www.prnewswire.com/news-releases/dr-stephen-kingsmore-sets-guinness-world-records-title-for-fastest-genetic-diagnosis-300256566.html [Accessed 21 Jun. 2017].

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