How DNAnexus and Edico Genome are Powering Precision Medicine on Amazon Web Services (AWS)
By Aaron Friedman and Ujjwal Ratan, Partner Solutions Architects at AWS focused on Healthcare and Life Sciences
Diagnosing the medical mysteries behind acutely ill babies can be a race against time, filled with a barrage of tests and misdiagnoses. During the first few days of life, a few hours can save or seal the fate of patients admitted to the neonatal intensive care units (NICUs) and pediatric intensive care units (PICUs). Accelerating the analysis of the medical assays conducted in these hospitals can improve patient outcomes, and, in some cases, save lives.
Precision medicine relies on the aggregate of these types of tests (and others) to advance healthcare. Due to decreasing costs and faster turnaround times, genome sequencing is one such test that is gaining adoption throughout healthcare. Understanding a patient’s genetic predisposition to different diseases is fundamental to establishing a medical risk baseline. In certain cases, such as in NICUs, a patient’s genetic profile can unlock the specific cause of a disease and inform the subsequent medical interventions that might work.
Today, we’d like to tell you about two of our AWS Partner Network (APN) Partners, DNAnexus and Edico Genome, who are working together to advance the principles of precision medicine, and are already changing lives through genomics.
DNAnexus, an AWS Life Sciences Competency Partner, offers data management, next-generation sequencing data analysis, and secure collaboration for large-scale life sciences enterprises. The DNAnexus platform-as-a-service (PaaS) solution provides a secure and unified system that scales to meet its clients’ unique needs, such as merging de-identified clinical data with genetic data. The API-based DNAnexus platform enables customers (e.g., pharma, researchers, hospitals) to create custom workflows to analyze genomics data as they see fit, such as to develop new drugs or diagnose rare diseases.
Naturally, the data generated by these processes is sensitive and its protection is paramount. DNAnexus has architected their platform to align with key security and compliance frameworks, such as HIPAA, 21 CFR Part 11, CLIA, and FedRAMP.
Introducing Edico Genome
Edico Genome, an APN Standard Tier Partner and Amazon EC2 F1 Instance Partner, is focused on facilitating the growth of precision medicine. By accelerating one of precision medicine’s central components, genome sequencing analysis, without sacrificing accuracy, Edico Genome enables researchers and clinicians to understand the relationships between genetic variation and disease.
Edico Genome accelerates sequencing analysis by using field-programmable gate arrays, or FPGAs, in its Dynamic Read Analysis for GENomics (DRAGEN) solution. In contrast to conventional CPU-based systems, which must execute lines of software code to perform an algorithmic function, FPGAs use logic circuits to accelerate algorithms and provide outputs 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, allowing users to quickly switch between different functions and pipelines
Today, Edico Genome is deployed on our FPGA-based Amazon EC2 F1 instances and can process a whole genome sequence in about 70 minutes on an f1.2xlarge instance type and about 30 minutes on an f1.16xlarge instance type. These speeds can be over 10 times faster than current state-of-the-art algorithms.
How They’re Working Together
Recently, DNAnexus and Edico Genome announced a joint partnership to integrate Edico Genome’s DRAGEN solution, deployed on Amazon EC2 F1 instance family, into the DNAnexus platform. This integration gives customers the ability to leverage the speed of DRAGEN to analyze genomes coming from high-throughput sequencers, while also inheriting the security and compliance controls that DNAnexus has implemented. At a high level, here’s what this collaboration looks like:
DNAnexus ingests raw data (called base calls or reads) from genome sequencers such as Illumina’s NovaSeq. These reads are fed into DRAGEN, which is running on an EC2 F1 instance, to speed up the identification of genome variations that can influence disease progression. Results are stored in Amazon Simple Storage Service (Amazon S3) using industry-standard compression algorithms. Depending on the use case, customers can then collaborate across research sites while adhering to the regulatory requirements around sensitive data by using the capabilities built into the DNAnexus platform.
Collaborating to Improve Clinical Care
Rady Children’s Institute for Genomic Medicine is one of the global leaders in advancing precision medicine. To date, the institute has sequenced the genomes of more than 3,000 children and their family members to diagnose genetic diseases. 40% of these patients are diagnosed with a genetic disease, and 80% of these receive a change in medical management. This is a remarkable rate of change in care, considering that these are rare diseases and often involve genomic variants that have not been previously observed in other individuals.
The institute adopted the DNAnexus platform to gain a secure, flexible, and scalable environment for local and distributed sequencing and analysis. Using DNAnexus with DRAGEN provides Rady with a highly optimized, end-to-end, whole genome sequencing analysis solution. Edico Genome’s DRAGEN data analysis pipeline is central to Rady’s ultra-rapid genomic data analysis, because it significantly reduces costs and turnaround time while maintaining accuracy. (Edico and Rady also previously worked together to set a Guinness World Record for fastest genetic diagnosis.)
“Our goal is to ensure that genome-powered precision medicine is available to every child who needs it. To do this, we needed a rapid research-to-bedside pipeline and be able to scale it and make it accessible to hospitals around the world,” said Stephen Kingsmore, M.D., D.Sc., president and chief executive officer at Rady Children’s Institute for Genomic Medicine. “DNAnexus has the technology and expertise to facilitate this ambitious project, Edico Genome’s rapid testing capability allows for rapid diagnosis of critically ill newborns.”
Based on the success of this partnership, Rady Children’s Institute is expanding this integrated solution to their partners nationally, fostering a growing genomic database that healthcare providers can access to quickly diagnose rare diseases in children.
Collaborating to Advance Precision Medicine
One of the most rewarding things about working in Healthcare and Life Sciences at AWS is seeing how our APN Partners can work together to change the lives of people. The DNAnexus and Edico Genome partnership is one such example that is making a lasting impact on the healthcare industry. We look forward to seeing the results of this partnership advance precision medicine, and deliver results like the ones experienced at Rady Children’s Institute across the clinical landscape.
To learn more about how DRAGEN on DNAnexus can securely accelerate sequencing analysis, and take advantage of a reduced rate for analysis (valid through October 31, 2017), see the DRAGEN on DNAnexus promotional offer.
To learn more about how customers and APN Partners are using genomics on AWS, check out Genomics in the Cloud on the AWS website.