Building a Global Network for Genomic Data – DNAnexus, an Advanced APN Technology Partner
Today’s announcement of the precisionFDA platform is significant for the genomics research community for a number of reasons. With this pilot platform, a component of President Obama’s Precision Medicine Initiative, the FDA is working towards establishing a community of stakeholders to help drive the standard around secondary analysis, the area of mapping, alignment, and variant calling in genomics research. Secondary analysis allows researchers to see variations from a given individual’s genomic makeup as compared to a reference genome. DNAnexus, an Advanced APN Technology Partner, was selected by the FDA to both power the precisionFDA platform and to build a genomics community to gather and publish reference data analysis pipelines, and reference datasets for the validation of genomic tests. The DNAnexus Platform, which was built on AWS, will deliver precisionFDA and provide the underlying cloud-based compute resources and data management.
Today I’d like to tell you about DNAnexus and its mission, what the company has built on AWS, how the cloud is helping change the face of genomics research, and DNAnexus’ work with the FDA.
Who is DNAnexus?
DNAnexus, based in Mountain View, California, has created the global network for genomics by providing an API-based platform for the sharing and management of data and tools that accelerate genomic research. The company’s mission is to deliver to organizations a secure and trusted genome informatics and data management platform, to enable organizations to tackle some of the most complex bioinformatic challenges, and to power a global network for sharing genomic information and advancing research and healthcare. The DNAnexus Platform enables scientists and clinicians worldwide to accelerate medical advances, improve patient care, and advance R&D in areas such as cancer, heart disease, Alzheimer’s disease, prenatal testing, and agricultural production. The company is an AWS Life Sciences Competency Partner.
There were a number of reasons that DNAnexus chose to build its platform on AWS, including the broad and deep security and compliance profile of AWS. “At the heart of everything we do is security and compliance,” explains Omar Serang, Chief Cloud Officer at DNAnexus. DNAnexus complies with ISO 27001 and 27002 international security standards, which ensures the highest levels of compliance with clinical regulations. “Our platform is fully capable of operating in a clinical environment under CLIA, and we can support the management of PHI data under HIPAA regulations as well,” says Serang. “We find that our security and compliance posture is a huge advantage for us in the market.”
DNAnexus leverages a number of AWS Services, and takes advantage of the global presence of AWS. “We leverage Amazon S3 and Amazon EC2 heavily, and we tend to think of S3 as the center of our universe,” explains Serang. “When you have an object store like S3 that can deliver massive payloads to hundreds and hundreds of EC2 instances without blinking, it’s an amazing capability for us. Essentially, it takes storage performance management completely off the table for us and for our customers.” The company is currently building out in the Beijing region, and has a significant presence in the EMEA, APAC, and North American regions.
The Significance of AWS for Genomics Research
“The cloud is uniquely positioned for genomic research because of the very large scales of data involved with Next Generation Sequencing (NGS) data; the massive dataset sizes from NGS are a very good fit for the cloud,” says Serang. “Additionally, the collaborative nature of genomic science is enabled and enhanced by the accessibility of the cloud.”
According to Serang, the cloud, and particularly AWS, has changed the approach researchers are able to take in genomic research. “The cloud fuels collaboration and enables people to do science that wasn’t possible before,” explains Serang. “Prior to the cloud, researchers sent hard drives around in an attempt to collaborate. We now have a different paradigm where we put data in the cloud and bring the scientists to the data, side-by-side with the EC2 compute resources they need to perform their analysis. AWS is enabling new science, and reducing the turnaround time on many different types of analysis.”
Earlier this year, DNAnexus began discussions around the capabilities of its platform with Dr. Taha Kass-Hout of the FDA. Within six months, the company went from an initial concept of how the DNAnexus Platform could support precisionFDA to a contract. “It’s been a real pleasure working with the FDA scientists, particularly Dr. Kaas-Hout,” says Serang. “I feel Dr. Kaas-Hout is an absolute visionary leader. His vision of community involvement in genomics is incredibly exciting to us.” The DNAnexus Platform has an API, and on top of the API DNAnexus is delivering a web portal that is to be used by the precisionFDA community. “The web portal encapsulates fit-for-function features to be used. All of the genomic analysis, data processing, collaboration and sharing is taking place using the features of the DNAnexus platform,” explains Serang.
The first stage of the precisionFDA project is focused on community engagement. “The overall objective of the pilot is to establish a community of stakeholders around the standardization of secondary analysis, and to get this community to participate in the creation of standards,” says Serang. “The first stage is about stimulating the community to step forward and help drive these standards.” As the project develops, Serang feels that the precisionFDA platform will level the playing field and create opportunities for smaller diagnostic test providers to get tests validated and vetted. “It’s expected that a much broader community of members will be able to benefit from this platform,” explains Serang. “By having access to cloud compute and storage through an extension of the proven DNAnexus Platform, it’s extending the analytic pipelines for smaller diagnostic companies who often do not have the bioinformatic capabilities in-house and can now access best practices tools and references datasets on the precisionFDA platform. It will allow a wider range of companies to participate in the validation process, and ultimately the certification process for NGS-based diagnostics.”
You can read more about DNAnexus’s involvement in precisionFDA on their blog here.