Natera leverages a scalable, cost-effective Clinical Genomics Data Platform to democratize real-world variant and clinical data for R&D, and to inform earlier, more personalized treatment decisions.
Client profile
Natera, Inc. is a global leader in cell-free DNA testing that specializes in oncology, women's health, and organ health. Natera's proprietary technology combines novel molecular biology techniques with a comprehensive suite of bioinformatics software, enabling detection down to a single molecule in a tube of blood. This synergy underscores Natera’s commitment to leveraging advanced technology to make personalized genetic testing and diagnostics an integral part of the standard care, to help inform earlier for more targeted interventions that lead to longer and healthier lives.
Industry
Insurance
01 The ChallengeNatera, Inc., a global leader in cell-free DNA testing, is on a mission to make personalized genetic testing and diagnostics an integral part of standard care, helping to inform earlier, more targeted interventions that lead to longer and healthier lives for millions of people.
Natera’s long-term business strategy is centered on improving its existing genetic tests and developing novel ones, and leveraging its vast genomic and clinical data to enable more accurate, personalized diagnoses and care decisions. By simplifying access to paired DNA variants and clinical data, Natera seeks to collaborate with partners in biopharma, biotech, and life sciences, to streamline clinical trials, accelerate drug discovery, and improve time-to-market for new tests and therapies. This approach positions Natera as a leader in personalized genetic testing and diagnostics, while also helping to democratize and commercialize anonymized data, to support ongoing R&D efforts in the industry.
Natera’s flagship product, a personalized molecular residual disease (MRD) test, Signatera, has already enabled Natera to start transforming how various cancers are treated and managed, through its tumor-informed approach:
With over 200,000 patients tested and extensive clinical validation, this test established Natera as a trusted leader in MRD testing.
Despite the success of its MRD test, however, Natera was looking for more efficient ways to prepare, manage, and leverage its vast, continuously growing genomic and clinical datasets on its existing comprehensive genomics database (CGDB) solution.
To address these challenges and capitalize on emerging opportunities, Natera’s leaders recognized the need for a modern, cloud-based CGDB solution. They expected their new Clinical Genomics Data Platform to:
Recognizing the complexity of developing such a platform, Natera joined forces with Provectus, an AWS Premier Tier Services Partner with AWS competencies in Data & Analytics and Migration.
Through collaboration with Provectus, Natera sought to overcome its current challenges and unlock new business opportunities. Their new Clinical Genomics Data Platform would address immediate data management and analysis needs, while positioning Natera as a partner of choice for clinico-genomic data analysis in early-stage cancer within the Healthcare & Life Sciences industry.
To bring this vision to life, Natera set the stage for a collaborative effort that would transform Natera’s data-driven drug discovery and research operations, and revolutionize the landscape of personalized genetic testing and diagnostics, and precision oncology.
02 The ApproachProvectus started by developing a comprehensive data and analytics strategy for Natera, to deliver a highly scalable and cost-effective CGDB solution — Clinical Genomics Data Platform — powered by AWS services.
The solution was implemented in three major phases:
The partnership began with a Migration Readiness Assessment (MRA), during which Provectus developed a Prototype of the platform using AWS HealthOmics and Amazon QuickSight.
The Prototype, delivered in a matter of weeks, showcased that it is possible to:
This initial phase was crucial in demonstrating the potential of the envisioned platform, and set the stage for full-scale development.
The Clinical Genomics Data Platform was designed and built as Natera’s foundational solution for storing, processing, analyzing, visualizing, and collaborating on large-scale genomic and clinical data. The platform was developed and implemented in a matter of months.
A strategic partnership with AWS significantly enhanced the development of the Clinical Genomics Data Platform, ensuring alignment with Natera’s long-term goals. This collaboration empowered the project team to fully harness AWS’s cutting-edge services, including privileged access to beta features.
In addition to these core functionalities, the Clinical Genomics Data Platform incorporated several specialized components, which were realized as follows:
Together, these components enhance Natera’s genomic data management and analysis capabilities, enabling seamless, end-to-end data flow from raw genomic processing to cohort analysis and reporting.
Natera’s molecular residual disease testing solution was the first product to benefit from the Clinical Genomics Data Platform.
This implementation demonstrated the platform’s ability to:
The Clinical Genomics Data Platform has proven its potential to revolutionize cancer treatment and management long-term by enabling Natera to handle personalized genetic testing and diagnostics, achieving results faster and on a larger scale.
In genomic data processing, performance and cost efficiency are key. Provectus implemented strategic optimizations for Natera’s Clinical Genomics Data Platform to improve processing speeds, enhance scalability and reduce operational expenses.
To optimize performance and achieve a 300x faster annotation speed, parallel processing of genomic data was implemented, allowing for simultaneous data tasks that cut down processing time. Database queries and indexing were optimized to ensure rapid data retrieval.
For cost optimization, a 2x reduction in data processing and management costs was achieved by implementing auto-scaling, which dynamically adjusted compute resources based on demand. A range of AWS and open-source services was used for continuous cost analysis and optimization, while data lifecycle management policies were established to move infrequently accessed data into cold storage, reducing ongoing storage expenses.
Following the successful deployment of the Clinical Genomics Data Platform, Natera was ready to expand its capabilities by migrating additional data pipelines. These efforts include integrating pipelines for variant calling and annotation on Whole Exome Sequenced Germline and ctDNA samples, clinical metadata approved for research, and genetically derived ethnicity information.
These optimizations enabled Natera to process larger volumes of genomic data with increased speed and cost-efficiency. By replacing legacy tools and eliminating third-party software licensing fees, the platform saved Natera tens of millions of dollars, while increasing performance efficiency by 300x, empowering teams with self-service analytics, and improving their capacity to provide timely and affordable genetic testing and diagnostic services. Additionally, it empowered Natera’s biopharma partners to harness rich genomic insights, accelerating their innovation efforts in drug discovery and development.
03 The ResultsThe Clinical Genomics Data Platform has significantly improved Natera’s capabilities for genomic data processing and analysis.
Note: The initial successful migration of the VCF annotation workflow from Natera’s CGDB to AWS HealthOmics was a significant achievement that increased batch processing capacity from 45 to 30,000 samples (processed in six hours), all while maintaining 100% integrity of the migrated data.
The Clinical Genomics Data Platform enables Natera to improve its in-house operations, accelerate research, enhance clinical decision-making, optimize resource use, and improve data accessibility for faster, more informed analysis.
The Clinical Genomics Data Platform enables Natera to:
The Clinical Genomics Data Platform is a powerful resource for Natera’s clients and partners, from hospitals and clinics using MRD tests to pharmaceutical companies leveraging genomic insights to fuel their innovation efforts.
Biopharmaceutical companies can leverage Natera’s modernized platform to identify patient segments with high unmet medical needs, optimize clinical trial designs, and accelerate drug discovery and development. It is a source of high-quality, easily accessible paired genomic and clinical data that can lower R&D costs and speed up the delivery of new treatments to the market.
The paired clinical and genomic data, available on the Clinical Genomics Data Platform, is also useful to healthcare providers such as oncologists. This data helps physicians better understand how patients respond in the real world and can be used for research, investigator-initiated clinical trial design, and to inform treatment decisions for their patients.
Natera can also rely on this unique, clean and structured data as real-world evidence to support regulatory approvals and demonstrate the clinical utility of its own tests. This strengthens their case for insurance reimbursement, boosting Natera’s revenue from test sales.
“With the Clinical Genomics Data Platform, Natera has the tools it needs to democratize and commercialize its data, packaging and selling anonymized datasets to stakeholders in the biomedical field, including biotechnology firms, pharmaceutical companies, life sciences organizations, and research institutions. Thus, the platform serves as a tool that directly supports Natera’s strategic vision: to unlock the potential of its data and AI assets – an opportunity that is worth tens of billions of dollars across the life sciences sector.”
The data commoditization trend reflects a shift in the biomedical field, where high-quality, large-scale genomic and clinical datasets are becoming essential to power R&D initiatives driving innovation industry-wide. The platform’s ability to efficiently process, annotate, and organize complex real-world data makes it particularly attractive to drug development companies and scientific institutions looking to uncover new insights into disease mechanisms, identify novel therapeutic targets, and design more effective clinical trials.
One example, a unique dataset prepared on the Clinical Genomics Data Platform, combines extensive molecular data, including full exome sequencing, with detailed clinical information and longitudinal follow-up for early-stage cancer patients.
What sets this dataset apart is its focus on early-stage cancers and the inclusion of Natera’s proprietary MRD test results, providing a holistic view of cancer progression and treatment response. The dataset includes different tumor types (lung cancer, renal cancer, bladder cancer, etc.), genetic variants, and treatment outcomes, offering researchers insights into the early stages of cancer development and the effectiveness of interventions.
By leveraging the platform’s querying capabilities and the Cohort Builder tool, researchers can perform complex analyses and generate hypotheses in seconds instead of hours or even days. This rapid, self-service access to such a dataset accelerates the pace of cancer research, enabling faster identification of novel biomarkers, more precise patient stratification for clinical trials, and the development of highly targeted therapies.
The Clinical Genomics Data Platform has become Natera’s foundational solution for large-scale processing, management, analysis, and commercialization of petabytes of real-world genomic and clinical data. By delivering 300x faster performance, enabling self-service analytics and insights, and eliminating costly third-party dependencies, the platform has already generated tens of millions of dollars in operational savings. Just as importantly, it helped Natera to start realizing its long-term vision to drive innovation in cancer detection, improve patient outcomes, and unlock new revenue streams through data and AI monetization in a market worth tens of billions.
This transformation positions Natera as a leader driving innovation in personalized genetic testing and diagnostics. It enables Natera to accelerate scientific discoveries in genomics and, ultimately, contribute to enhanced cancer detection efficiency, affordability, and precision, ensuring longer, healthier lives for millions.
