DRAGEN Platform Overcomes Resource Constraints for Next-Generation Sequencing, Accelerates Secondary Analysis
Oct. 10, 2017 — San Diego and Cape Town, South Africa— Edico Genome and the Centre for Proteomic and Genomic Research (CPGR) today announced the deployment of the first DRAGENTM Bio-IT platform in Africa. Selected by CPGR to help drive adoption of precision medicine and genomics, DRAGEN will be made available to life science and biotech communities in South Africa. The DRAGEN card is integrated into a scalable and flexible 2U Dell EMC PowerEdge R730 server.
CPGR is a non-profit organization dedicated to providing state-of-the-art ‘omics’ services to South Africa’s life sciences and biotech communities, originating from an initiative by the South Africa Department of Science and Technology(DST). CPGR combines innovative, information-rich genomic and proteomic technologies with bio-computational pipelines to develop customized offerings for users in both academia and industry. CPGR hosts a suite of genomics and proteomics platforms that allow for the design and execution of projects using single or multiple ‘omics’ methodologies, with the goal of generating targeted and systems biological insights. CPGR will utilize DRAGEN to help advance the development of next-generation sequencing (NGS) applications and data analysis pipelines.
“One of our goals is to inspire adoption and entrepreneurship surrounding genomics and personalized medicine in Africa,” said Reinhard Hiller, Ph.D., managing director at CPGR. “We’re dedicated to providing our community with the tools and resources needed to bring South Africa into an internationally competitive bio-economy. With the integration of DRAGEN we significantly enhance our data processing capabilities, enabling us to turn around new pipelines in a fraction of the time.”
DRAGEN is highly reconfigurable, using a field-programmable gate array (FPGA) to provide hardware-accelerated implementations of genome pipeline algorithms, such as BCL conversion, compression, mapping, alignment, sorting, duplicate marking and haplotype variant calling. The platform supports whole genomes, exomes and targeted panels, and includes comprehensive pipelines for Germline, Somatic, RNA, Methylation and Population Calling analysis.
“The continued adoption and integration of next-generation sequencing in Africa will play a vital role in not only the health and wellbeing of its citizens, but also advance the development of the genomics industry around the globe,” said Pieter van Rooyen, Ph.D., chief executive officer at Edico Genome. “The idea for DRAGEN was developed when I was working in Africa and realized firsthand that while sequencing was relatively easy, resource constraints hindered analysis of genomic data. From the start, DRAGEN was designed to deliver rapid analysis with high accuracy all from a single server, and as a native South African I’m proud to be able to enable organizations such as CPGR to expand the use of genomics to academic researchers, physicians and companies.”
By implementing algorithms as logic circuits which can be massively parallelized, DRAGEN is able to deliver best-in-class performance, reducing the time needed to analyze a whole human genome at 30x coverage from 20 to 30 hours using traditional software-based algorithms (BWA-GATK) to approximately 20 minutes. CPGR is the latest addition to DRAGEN’s global customer base, which includes Rady Children’s Institute for Genomic Medicine, Baylor Genetics, the National Human Genome Research Institute (NHGRI) and National Cancer Institute (NCI) and others.
The Centre for Proteomic and Genomic Research (CPGR) is one of Africa’s first fully integrated ‘omics’ service providers, built to leapfrog South Africa’s ability to conduct information-rich biomedical research onto a globally competitive level. Amongst others, the organization offers the following ‘omics’ capacity: Next-Generation Sequencing: NextSeq500 (1x), MiSeq (1x), MiniSeq (1x), IonTorrent PGM (2x), IonProton (1x), for sequencing projects; Microarrays: Affymetrix GS 3000 and Affymetrix GeneTitan for genotyping and gene-expression analysis; Mass spectrometry: ABI 4800 MALDI-ToF/ToF; Waters Xevo TQS triple quadrupole, SCIEX API4000 triple quadrupole and Thermo Q Exactive for MS-Proteomics; High-throughput PCR: QuantStudio 12K Flex Real-Time PCR System, QuantStudio 3D Digital PCR System and ABI 7900 for qRT-PCR and genotyping applications; Automated DNA/RNA QC, library handling and sample processing; dedicated IT infrastructure and bioinformatic applications for data analysis and interpretation.
The CPGR is a non-profit company located in Cape Town, South Africa, based on an initiative by the Department of Science and Technology (DST), and financially supported by the Technology Innovation Agency (TIA). The CPGR combines state-of-the-art information rich genomic and proteomic (‘omics’) technologies with bio-computational pipelines to render services and support projects in the life science and biomedical arena in (South) Africa, all run in an ISO 9001:2015 certified and ISO 17025 compliant quality management system. Among others, the CPGR has recently launched an accelerator program to stimulate the creation of South African start-ups based on ‘omics’ technologies and set up Artisan Biomed to develop and implement Precision Medicine solutions in (South) Africa.
About Edico Genome
The use of next-generation sequencing is growing at an unprecedented pace, creating a need for easy to implement infrastructure that enables rapid, accurate and cost-effective processing and storage of this big data. Edico Genome has created a patented end-to-end platform solution for analysis of next-generation sequencing data, DRAGEN™, which speeds whole genome data analysis from hours to minutes while maintaining high accuracy and reducing costs. Top clinicians and researchers are utilizing the platform to achieve faster diagnoses for critically ill newborns, cancer patients and expecting parents waiting on prenatal tests, and faster results for scientists and drug developers. For more information, visit www.EdicoGenome.com or follow @EdicoGenome.