Removing the NGS Analytics Data Bottleneck with Field-Programmable Gate Arrays (FPGA’s)

Edico Genome’s FPGA-backed DRAGEN Bio-IT Platform Now Available on DNAnexus

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

With rapid adoption across a variety of practices, next-generation sequencing (NGS) is on track to become one of the largest producers of big data by 2025. While the integration of NGS poses exceptional breakthroughs in its applied practices, one major problem threatens its expansion: a lack of computing power to analyze the rapidly growing body of data.

Current projections 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. The void left in-between creates a bottleneck for genomics labs.

Designed to uncork this big data bottleneck, 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 accuracy and unwavering dependability.

Uncorking the big data bottleneck with DRAGEN

In contrast to conventional CPU-based systems, which must execute lines of software code to perform an algorithmic function, FPGAs implement algorithms as logic circuits, providing an output almost instantaneously. By replicating these logic circuits thousands of times over, DRAGEN is able to achieve industry-leading speeds by 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.

As a result, DRAGEN delivers high accuracy while functioning with industry-leading speed, efficiency, and parallelism. DRAGEN can process an entire human genome at 30x coverage in about 90 minutes, as compared to over 30 hours using a traditional CPU-based system, saving customers time and money. DRAGEN’s Genome Pipeline is now available on DNAnexus at a reduced trial rate until October 31, 2017. To sign up for exclusive promotional pricing, visit: https://www.dnanexus.com/edico-trial .

At Bio-IT World: Promoting Technological Innovation to Advance Precision Medicine

We are excited to join the 3,000+ researchers, clinicians, and pharmaceutical and IT professionals attending the Bio-IT World Conference in Boston next week. The DNAnexus team will be onsite and headquartered in booth #316, please stop by to learn how DNAnexus helps improve secondary analysis, facilitates collaboration, and provides a scalable and secure platform for genomic research. Register here to attend the conference.

A highlight of the event every year is the Bio-IT World Best Practices Awards. This prestigious award highlights outstanding examples of how technological innovation can be powerful forces of change in the life sciences. This year, our partner M2Gen is a Best Practices Award finalist!

M2Gen has partnered with 15 of the nation’s leading cancer centers via the Oncology Research Information Exchange Network (ORIEN) to deliver informatics-based solutions to accelerate therapy discovery and development. The DNAnexus cloud platform supports molecular data access, management, collaboration, and analysis for ORIEN. This cloud-based approach creates value for all stakeholders, impacting the point-of-care and driving basic cancer research in both academic centers and industry. The multiple categories of the Best Practices Awards will be announced live during the plenary session on Thursday May 25th.

Dr. Hongyue Dai, PhD, CSO of M2Gen, will be in the DNAnexus booth to answer questions and showcase M2Gen’s innovative cancer data network. Come by booth 316 at 10:00am ET on Thursday to learn more.

We will also be showcasing projects with our clinical and software partners. See our full list of activities below. Can’t make it to one of our events? Stop by booth 316 anytime during the conference, or email us to schedule a meeting with a member of our team.

Scaling the World’s Fastest Clinical Genomic Pipeline for Critical Care in Pediatrics
Narayanan Veeraraghavan, PhD, Director of IT, Rady Children’s Institute for Genomic Medicine
Wednesday, May 24, 10:00am-10:30am
DNAnexus Booth #316

Genomic Solutions in Microsoft Azure
Singer Ma, Scientific Operations Director, DNAnexus

Wednesday, May 24th, 2:30pm-3:00pm

Microsoft Booth #529

Rapid Variant Discovery with Sentieon
Brendan Gallagher, Business Development, Sentieon
Wednesday May 24, 3:30pm – 4:00pm
DNAnexus Booth #316

Meet & Greet with M2Gen
Hongyue Dai, PhD, Chief Scientific Officer, M2Gen

Thursday May 25, 10:00am-10:30am

DNAnexus Booth #316

Rady Children’s Quest to Finding That Needle in a Haystack

Rady Children’s Institute for Genomic Medicine (RCIGM), located in San Diego, has announced a pioneering effort to deliver life-changing genetic diagnoses for children suffering from rare diseases. Led by president and CEO, Dr. Stephen Kingsmore, Rady is building an end-to-end clinical whole genome data analysis solution, built on the DNAnexus Platform, for children’s hospitals nationally.

The impact of diagnosis by WGS is often life changing. The team routinely tests critically ill children for over 5,000 diseases, of which more than 500 have highly effective treatments. For example, if the test reveals a mutation in a gene involved in digestion, causing the inability to process a particular nutrient thereby leading to buildup of a poisonous byproduct, a simple change in diet can limit the effects of the disease. The sooner this condition can be diagnosed the less damage the child will suffer. In these cases, minutes literally matter.

Dr. Kingsmore’s vision is to ensure genome-powered diagnosis is accessible to every child who needs it. Building a world-class pipeline at a single hospital isn’t enough. RCIGM needed a solution that could scale and be deployed at institutions around the world. DNAnexus provides the technology and expertise that allows RCIGM to grow an innovative pediatric-focused genomics network, distribute its clinical tools and collaborate with colleagues in a secure and compliant environment.

This work was done as part of RCIGM’s collaboration with the The Newborn Sequencing In Genomic medicine and public HealTh (NSIGHT) program. NSIGHT addresses how genomic sequencing can replicate or augment known screening results for newborn disorders, what knowledge sequencing can provide for conditions not currently screened, and what additional clinical information could be learned from sequencing relevant to the clinical care of newborns. The NSIGHT program is funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) and the National Human Genome Research Institute (NHGRI), components of the National Institutes of Health.

DNAnexus provides a flexible platform that connects Edico Genome’s ultra-fast variant calling algorithms with Fabric Genomics’ interpretation software, and integrates seamlessly with Rady Children’s custom data interpretation portal. Users monitor jobs, organize and share data, and compare patients’ data to a diagnostic resource within the network. At DNAnexus, we are proud to support Dr. Kingsmore and RCGIM’s endeavor to prevent, diagnose, and treat childhood diseases through genomics research.