DNAnexus Case Study

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. On DNAnexus, enterprises scale genomic analysis workloads, deploy tools consistently, control data provenance, and facilitate global collaboration in a secure and compliant environment. The DNAnexus Platform enables scientists and clinicians worldwide to accelerate medical advances, improve patient care, and advance research and development in areas such as cancer, heart disease, Alzheimer’s disease, noninvasive prenatal testing, and enhanced agricultural production.

The rapid pace of development in genomics is revolutionizing scientific research, causing a seismic shift in areas like precision medicine and improving the world food supply. The increase in speed and decrease in cost of next-generation sequencing (NGS) technologies has outpaced Moore’s law. The $1,000 genome is now a reality. The bottlenecks are now genome informatics and data portability; researchers don’t have the compute power nor the infrastructure to manage the volume of raw sequence data they are creating. Additionally, the global scope of research and clinical studies requires a secure and compliant environment within which researchers can share and collaborate on datasets and tools in real time.

“The management and analysis of genomic data at the scale needed to power large-scale genome studies requires computational and storage infrastructure that exceeds the capacity of most institutions,” said Richard Daly, CEO of DNAnexus. “We sought a way to provide enterprises performing research and clinical work the resources to focus on the science, and the ability to collaborate with peers in a secure and compliant environment.” To accomplish this, DNAnexus developed a cloud-based genome informatics and data management platform.

DNAnexus carefully examined the available cloud-service options to find a provider that could meet the company’s requirements while also supporting clinical compliance standards. The company chose Amazon Web Services (AWS) as its cloud provider because AWS could deliver tens of thousands of compute cores, store petabytes of data, and offer the reliability, security, and compliance required for highly complex and sensitive research activities.

DNAnexus deploys its customers’ genomic pipelines on Amazon Elastic Compute Cloud (Amazon EC2), using Amazon Simple Storage Service (Amazon S3) for high-performance, high-durability storage and Amazon Glacier for low-cost data archiving. AWS also provided DNAnexus with a Business Associates Agreement (BAA), allowing DNAnexus to offer best-in-class security and compliance with US and international healthcare laws. 

On AWS, the DNAnexus domain-specific data management platform offers tailored compliance and security and provides fine-grained data management for transparency, reproducibility, and data provenance for consistent bioinformatics pipelines and results.

Using AWS, DNAnexus has scaled to more than 56,000 simultaneous compute cores, multiple petabytes of storage, and tens of millions of core-hours of analysis. DNAnexus provides both a GUI and a command-line tool, allowing customers to upload raw DNA data directly from sequencing instruments to the cloud and eliminating the need for costly on-premises computational and storage infrastructure.

Amazon EC2 hosts platform services for DNAnexus customers’ genomic analysis. For DNA analysis, the company developed a custom queuing system that operates on Amazon EC2 instances and robustly handles any interruptions in data processing. DNAnexus leverages the wide variety of instance types and multiple pricing plans for Amazon EC2, including Reserved and Spot Instances. Running on AWS allows DNAnexus to provide visibility into resource consumption, and bill by the minute rather than the hour, offering a compelling pricing model for the DNAnexus customers.

Amazon Web Services' demonstrated compliance to standards such as HIPAA, ISO27001, SOC 1/2/3, ISO9001, FedRamp, and FISMA allows DNAnexus to provide a platform that lets its customers pursue clinically compliant projects of enormous scale and scope, confident in the quality and efficiency of analysis and the security and ease of collaboration.

“AWS allows us to deploy a cloud-based infrastructure that supports our customers’ research and clinical needs,” according to Omar Serang, chief cloud officer at DNAnexus. “The combination of the AWS infrastructure and the DNAnexus platform controls and certified compliance allows us to meet the demanding requirements of HIPAA, CAP/CLIA, GxP, and other privacy laws and regulations.”