Customer Stories / Healthcare and Life Sciences / United States

2024
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Scaling Clinical Diagnostic Operations and Unlocking Genomic Innovation Using AWS with Natera

Learn how Natera, a global leader in cell-free DNA testing, built a data and analytics solution to democratize its data for delivering personalized healthcare solutions using AWS.

Near real-time data

insights

46 data elements

extracted per test, increased from 25

150% cost reduction

in data processing

Hours to days

for the innovation cycle instead of weeks to months

Reduced quarterly batch processing

of variant data to automated background processes with no human effort

Overview

Natera’s innovative cancer testing and analysis solutions have impacted the lives of countless patients and their families. As the company grew in size, it sought to enhance its internal data sharing processes and optimize the use of data for analytics and decision-making. Natera rearchitected its data estate using Amazon Web Services (AWS), implementing a data mesh strategy to reduce the cost and effort of data processing, enhance observability, and unlock near real-time insights from the data. This complete data strategy on AWS is helping the organization accelerate innovation with generative artificial intelligence on AWS, thus increasing the speed of providing treatment to patients.

Opportunity | Using AWS MAP to Accelerate the Rearchitecting Journey for Natera

Natera specializes in cell-free DNA testing for oncology, women’s health, and organ health, providing insights to guide personalized care decisions. The company’s proprietary genomic datasets, in combination with real-world data, including clinical and demographic patient data, provide a comprehensive picture of patient journeys across various disease areas. This is useful to enhance precision medicine.

An area of priority for Natera was streamlining the extraction of insights from this data, a time-consuming process to get a cohesive view of what the team was looking for. To streamline this workflow and deliver more timely, actionable intelligence to guide decision-making, Natera aimed to create a centralized data and analytics solution within the company’s established compliance policies for defined user roles across the organization. “We wanted to shift from having to replicate data into other data solutions by giving users the opportunity to work on the data products in the data mesh,” says Mirko Buholzer, vice president of software engineering at Natera. “We were looking at AWS to form the backbone of the tooling and capabilities we needed.”

kr_quotemark

The innovation cycle went down from weeks and even months—depending on if the data wasn’t available and we had to collect or make it available—to days or hours."

Mirko Buholzer
Software Engineering Lead, Natera

Solution | Creating a Data Solution Using Amazon DataZone, AWS HealthOmics, and Amazon Bedrock

Natera used AWS Migration Acceleration Program (AWS MAP) to accelerate its cloud migration and modernization journey. As a part of this initiative, Natera transitioned a number of its variant calling pipelines to AWS HealthOmics, which helps transform genomic, transcriptomic, and other omics data into insights. The resulting genomic testing data is then stored in AWS HealthOmics variant store, and Amazon Athena, a simplified, flexible way to analyze petabytes of data where it lives, is used for querying it . Subsequently, this data is transformed in Amazon Redshift, which helps to modernize data analytics workloads and deliver insights for businesses. The processed genomic data gets integrated with real-world data that has been abstracted by Natera’s nursing teams.

To automate the extraction of data elements from clinical documents, Natera uses Amazon Bedrock—a fully managed service that offers a choice of high-performing foundation models—and Amazon Textract, which helps to automatically extract printed text, handwriting, layout elements, and data from any document. “Using Amazon Bedrock, we extract 46 data elements per disease type compared to 25 elements earlier,” says Alyssa Antonopoulos, senior director of data and informatics at Natera. “We chose Amazon Bedrock for its performance and for its security measures that can help us maintain HIPAA compliance.” Natera has also observed improved accuracy in data extracted through Amazon Bedrock, especially in tricky data elements such as medications and dates.

Once the data is extracted and integrated, the team uses Amazon QuickSight, which provides unified business intelligence, to surface insights to business users. In parallel, these products are published to a data mesh that Natera built using Amazon DataZone—which helps to unlock data across organizational boundaries with built-in governance capabilities—where they are accessible by multiple users. “Using Amazon DataZone, researchers have a single pane of glass to access data,” says Buholzer. “It brings everyone to one place to do their work.”

Outcome | Unlocking Value through Further Integration and Innovation

With this solution, Natera has demonstrated how real-world data can be seamlessly integrated into a complete data solution, using Amazon DataZone, AWS HealthOmics, and Amazon Bedrock. This provides for the use of diverse, high-quality datasets to drive more informed decision-making and unlock valuable insights that can lead to improved patient outcomes and accelerated test development.

The biggest impact comes from the integration of systems and centralization of data. Previously, it was difficult to have a coherent view of all available data, but users can now perform direct operations on all data that is on the centralized platform, removing the need to move data between different locations and improving overall efficiency. This centralization also makes for enhanced data governance and compliance, because Natera can monitor who subscribes to which data types.

Users have access to near real-time data insights and no longer depend on other teams for data access. “The pipeline is near real time,” says Antonopoulos. “We aren’t querying stagnant data anymore, and we can draw insights from the data much more rapidly.” Fluid access to data is unlocking new insights into Natera tests and their impact on patient journeys.

Faster innovation is another key win. “The innovation cycle went down from weeks and even months—depending on if the data wasn’t available and we had to collect or make it available—to days or hours,” says Buholzer. “We can do those queries in near real time now.”

Natera’s relationship with AWS is one of true, two-way collaboration. “It’s been great to work alongside AWS, and we appreciate their willingness to help us and meet our use cases,” says Buholzer. “The familiarity of our engineering teams with AWS also helped to scale this solution up quickly.”

About Natera

Natera specializes in genetic testing using noninvasive, cell-free DNA technology with a focus on oncology, women’s health, and organ health. Doctors and clinics use Natera’s tests to design treatment plans and provide precision medicine to patients.

AWS Services Used

Amazon DataZone

Amazon DataZone is a data management service that makes it faster and easier for customers to catalog, discover, share, and govern data stored across AWS, on premises, and third-party sources.

Learn more »

Amazon QuickSight

Amazon QuickSight powers data-driven organizations with unified business intelligence (BI). With QuickSight, all users can meet varying analytic needs from the same source of truth through modern interactive dashboards, pixel-perfect reports, natural language queries and embedded analytics.

Learn more »

Amazon Bedrock

Amazon Bedrock is a fully managed service that offers a choice of high-performing foundation models (FMs) from leading AI companies like AI21 Labs, Anthropic, Cohere, Luma (coming soon), Meta, Mistral AI, poolside (coming soon), Stability AI, and Amazon through a single API,
along with a broad set of capabilities you need to build generative AI applications with security, privacy, and responsible AI.

Learn more »

Amazon HealthOmics

AWS HealthOmics is a purpose-built service that helps healthcare and life science organizations and their software partners store, query, and analyze genomic, transcriptomic, and other omics data and then generate insights from that data to improve health.  

Learn more »

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