Case Studies

Mercator BioLogic Accelerates Genetic Assembly Process with SanDisk ION Accelerator™ Software

Mercator BioLogic developed an innovative approach to the genetic assembly process but needed a high performance storage solution to turn their approach into reality. Mercator BioLogic teamed up with SanDisk to deploy a 4-node Oracle RAC cluster that used 25TB of Fusion ioMemory application accelerators with SanDisk ION Accelerator software.

Solution Focus

  • Bioinformatics
  • Big Data

Summary of Benefits

  • Reduced genetic code assembly from 37 days to 84 minutes
  • Maintained highest level of accuracy

Products

  • Fusion ioMemoryTM SX350 6.4TB application accelerators
  • SanDisk ION AcceleratorTM software
  • Oracle RAC

The Challenge

Mercator BioLogic understands that the process of digitizing (scanning) DNA is imperfect. Currently, an entire chromosome cannot be scanned in a single, unbroken line. This means that after biological samples have been scanned, they must be assembled into a full chromosome map for proper data analysis. The assembly process involves taking multiple chunks of data and accurately matching them together to create a single dataset that represents a set of chromosomes, creating a genome. During this process, the sample DNA is compared with known genetic markers to determine if the specific sample has a genetic tendency towards a known disease. A genetic code baseline is used to help measure a system’s performance when it reassembles the scanned biological sample.

The current industry standard for this assembly process with the genetic code baseline is 37 to 45 days per biological sample. The shortest time to accomplish this assembly, with reduced accuracy, is 27 days. This means that currently a person with a rare cancer who wants a targeted treatment approach would be waiting for more than a month for test results. But the situation is even more daunting; there are thousands of active DNA sequencing requests to resolve, and the current assembly process is performed only on a limited number of specialized machines. A waiting issue like this could easily occur in other industries that do genome processing, such as law enforcement and agriculture.

The challenge that Mercator BioLogic faced was to drastically reduce the 37-day window^1 for assembling the scanned genetic code.

“While researching methods to improve our performance, we read a benchmark study for I/O processing using SanDisk ION Accelerator software. We have been impressed with the performance gains realized with this data acceleration. This system has proven to give more than three times the performance of any other system we’ve seen.”

Roger Arvisais, Founding Partner, Mercator BioLogic

The Solution

With its industry-leading expertise, Mercator BioLogic developed an innovative approach to the genetic assembly process, but they also needed a high- performance storage solution to turn their approach into reality. Mercator BioLogic teamed up with SanDisk to deploy a 4-node Oracle RAC cluster that used 25TB of Fusion ioMemory application accelerators with SanDisk ION AcceleratorTM software. With this system, Mercator BioLogic was able to reduce the time required for genetic code assembly from 37 days to an astonishing 84 minutes for benchmark genomic data. This represents a performance improvement of more than 600x.

Genetic Code Assembly Time

With SanDisk
84 minutes
Without SanDisk
37 days
600x
Faster

“This system has proven to give more than three times the performance of any other system we’ve seen,” remarked Roger Arvisais, a Founding Partner of Mercator Biologic. “There is no other performance enhancement available that produces these results.”

The configuration for the Oracle RAC cluster solution is detailed below. The Oracle RAC utilized ASM to manage the LUNs presented by the SanDisk ION Accelerator software.

Four Oracle RAC nodes, each with:

  • A 2U Grantley platform
  • (2) E5-2697v3 14-Core 2.6GHz processors
  • (8) 32GB 2133 MHz LRDIMMs
  • (1) Mellanox ConnectX-3 56 Gb InfiniBand single-port adapter
  • 1.2TB 2.5” system HDDs in a RAID 1 array
  • RHEL 6.7 OS
  • Oracle 12G RAC

One host system with:

  • A 2U Grantley platform
  • (2) E5-2697v3 14-Core 2.6GHz processors
  • (8) 32 GB 2133 MHz LRDIMMs
  • (2) Mellanox ConnectX-3 56 Gb InfiniBand single-port adapters
  • (2) 1.2TB 2.5” HDDs in a RAID 1 array
  • (4) Fusion ioMemory SX350 6.4TB application accelerators
  • SanDisk ION Accelerator software, version 2.5.2

 

The Result

Using their leading expertise in bio-informatics and a powerful data storage solution from SanDisk, Mercator BioLogic took a giant leap forward in genome mapping. With Fusion ioMemory storage, SanDisk ION Accelerator software, and an Oracle RAC cluster, Mercator BioLogic slashed genetic code assembly from 37 days to less than an hour and a half, with no loss in accuracy. This opens the doors to exciting advances in industries such as: Healthcare: Much faster diagnosis and treatment of genetic-based maladies. Law enforcement: Accurately identifying a perpetrator of a crime with faster, accurate DNA matching. Agriculture and farming: Safer genetic manipulation of vegetation, or the development of healthier animals by better selection of breeding stock through genetic scans.

For more information, see the Alignment, Assembly, and Analysis of Genomic Information white paper on the Mercator BioLogic website (http://www.mercatorbiologic.com).

Footnotes

1 The Planck Institute in Bern, Switzerland accomplished this same task in only 27 days; however, they reduced oversampling from the standard 28 to 18, which can affect accuracy.

The performance results and cost savings discussed herein are based on internal testing and use of SanDisk products. Results and performance may vary according to configurations and systems, including drive capacity, system architecture and applications.

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