UK Biobank Democratizes Data Access with its own Cloud-Based Data Analysis Platform

UK Biobank Data Analysis Platform

Among the many lessons learned from the COVID-19 pandemic is that the world remains dangerously exposed to the novel and unknown health risks, despite exponential developments in our ability to improve and prolong life. Access to the right data could help scientists develop faster responses not only for global pandemics, but also for long-term improvements in patient outcomes and quality of life for millions suffering from debilitating diseases. 

Which is why we are happy to collaborate with UK Biobank and Amazon Web Services to unleash the transformative potential of the unparalleled diverse dataset containing phenotypic, genomic, and imaging data from 500,000 volunteers. UK Biobank has enlisted the services of DNAnexus to help develop its own cloud-based Data Analysis Platform. Funding support has come from Wellcome.

As announced earlier this week, the UK Biobank Data Analysis Platform will enable its extensive data resource to be accessed by a far broader range of researchers. The Data Analysis Platform will undergo development and testing through the first half of 2021, with plans to launch to all researchers by summer 2021. 

Over the next five years, UK Biobank data will grow to 15 petabytes — equivalent to the amount of data created annually by the Large Hadron Collider. By developing its own cloud-based Data Analysis Platform, UK Biobank can make the data more easily, securely, and cost-effectively accessible to approved researchers around the world. AWS has offered the UK Biobank computational credits to be awarded as grants by the institution for students and researchers in low to middle income countries to support this work.

“This new platform will democratise access, helping us to unleash the intellects of the world’s best scientific minds – wherever they are – to make discoveries that improve human health.”

Professor Sir Rory Collins, UK Biobank Principal Investigator

DNAnexus has previously worked with UK Biobank and the Regeneron Genetics Center to deliver exome sequencing results back to the UK Biobank Exome Sequencing Consortium (UK-ESC) members, spearheaded by those two organizations. In collaboration with the RGC, DNAnexus also built a web application to enhance the data exploration experience with interactive visualization, filtering, and browsing of integrated phenotypic and genomic information. Designed to democratize data access, the cohort browser allows diverse teams the ability to explore thousands of phenotype fields and millions of genomic variants to rapidly test multiple hypotheses and gain insight into mechanisms of action, biomarkers, and drug targets. The browser was deployed using DNAnexus Apollo, a multi-omics data science platform, which is optimized for large-scale genotype-phenotype datasets such as UK Biobank, TCGA, and other public and proprietary datasets.

This partnership is just one important step towards a world in which data sharing and accessibility is standard. The analysis of UK Biobank data has and will continue to provide a significant contribution to leading-edge developments. We enthusiastically support the foundational UK Biobank project as it breaks new ground in the advancement of disease research through the integration of deep healthcare data with genomics and advanced tools.

How Myriad Genetics is Powering AI & Machine Learning Advancements in Precision Medicine

Myriad AI & Machine Learning

For nearly 30 years, Myriad Genetics has been at the forefront of precision medicine, transforming people’s lives with pioneering molecular diagnostic tests, such as the industry leading myRisk hereditary cancer test for genes including BRCA1/BRCA2 that enable clinicians to understand the role genes play in the onset, progression, and treatment of human diseases. The company employs a number of proprietary technologies to power its products and they do this all at extreme scale for more than one million patients annually.

As part of its ongoing commitment to innovation, Myriad continues to invest in advanced AI and Machine Learning analytical methods to deliver the latest in next-generation technology in clinical validity and utility. Specifically, the company invests in three main categories:

1. Automating data intensive tasks for speed and accuracy

Typical bioinformatics pipeline development involves setting up infrastructure, building a computational process, and analyzing the results. When adjustments are made, this process repeats as many times as necessary until the pipeline has been properly optimized and validated. With complex and data intensive analyses, this process can consume many resources and take a lot of computation time. Myriad and DNAnexus partnered to develop Smart Reuse, a new framework that enables scientists to focus on the specific portions of the pipeline that have been updated. As a result, Myriad achieved a dramatic reduction in time as pipeline development went from weeks to hours, and in some cases they saw up to 100x acceleration. You can learn more about Smart Reuse from our blog where Jeffrey Tratner, Director of Bioinformatics Software Engineering at Myriad, presents at DNAnexus Connect.

2. Scaling human interaction and clinical interpretation

The second category focuses on a classic business problem of how to scale human interaction and clinical interpretation. Approximately 32 million women in the US qualify for hereditary cancer testing due to family history, but less than 5% of the eligible population get tested. The healthcare system can be notoriously complex in understanding whether you qualify for testing or treatment options, getting reliable cost estimates, and navigating payor reimbursement. Typically, this process requires a lot of human interaction. Myriad uses a combination of rule-based decision trees and machine learning to make recommendations for what the likely out of pocket costs will be for the patient. And because the disease is often based on family history, Myriad has developed tools for patient education where they can walk through a workflow that explains what conditions are represented in that person’s family tree and if he or she is a good candidate for genetic testing.

3. Discovering novel indications and biomarkers for new products

Lastly, Myriad harnesses AI for discovery, improving its current tests, and expanding its portfolio. Myriad is able to leverage its wealth of genomic and phenotypic information to better predict cancer risk. For example, how can you use more signals in the gene to modify the risk of traditional cancer genes? With the BRCA1/BRCA2 genes it’s well known that patients have a high risk in developing breast cancer. However, there are other classes of genes that are moderately penetrant (risk of 30-50%) and it’s less obvious what you should do medically. Myriad has discovered additional polygenic risk indicators across the genome that can modify the likelihood of developing breast cancer for moderately penetrant genes, either making the gene more likely or less likely to cause cancer. This allows those of high risk to take proactive steps to care for their health.

When used correctly, AI and machine learning can provide a competitive advantage. However, Myriad understood that they needed a secure environment for R&D scientists to leverage these powerful and computationally intensive analytical methods, which require the latest GPU instances in the cloud for deep learning frameworks like tensorflow. DNAnexus Titan solves this issue, providing a collaborative platform that automatically tracks data provenance to ensure reproducibility.  Scientists around the world are using the platform to spin up the latest GPU instances for a reasonable amount of time, leveraging Amazon Web Services (AWS).

To learn more about how Myriad is powering AI/ML advancements in precision medicine, you can listen to Kevin Haas, SVP of Technology at Myriad, speak at the AWS Healthcare & Life Sciences Web Day. Visit our website to learn more about DNAnexus’ solutions for clinical diagnostics providers.

Bold Innovation for a Promising Future

Fast Company has named DNAnexus to its second annual list of the 100 Best Workplaces for Innovators for our work to revolutionize the use of genomic and other omic information in healthcare.

Advances in genome technologies have led to a deluge of data — and discoveries. At DNAnexus, we strive to develop innovative solutions to manage all of this information in a secure, compliant environment that integrates a wide variety of data types, and enables scientists around the world to collaborate. We are applying the most advanced technologies to enable targeted cancer therapies, facilitate genetic testing, and speed the discovery of lifesaving new drugs.

We constantly find ourselves asking, “What if there was a better way to make sense of molecular data to transform human health?” Our internal research team’s main focus is to advance the AI and machine learning capabilities of the DNAnexus suite of products, and continue innovating within this emerging field. This cross-disciplinary team works to understand and apply new applications and computational methods that are likely to have the biggest impact on the genomics sciences and industry.

Our team is sourced with five sites around the world, representing dozens of nationalities and backgrounds. We embrace diversity and unique perspectives and foster a workplace environment in which everyone is encouraged to contribute and think outside-of-the-box. We believe that great products come from passionate teams who support and embrace collaboration, and we are committed to helping our customers and colleagues achieve their “aha!” moments. By cultivating this culture of respect, passion, trust, and collaboration, we see real benefits, in the form of innovation, employee empowerment, customer satisfaction — and fun!

As much of the world works to surmount health, economic, and social crises, we recognize that innovation is needed now more than ever. We celebrate with the many other organizations that have fostered innovative thinking by investing heavily in exploring new technologies, R&D, and their employees.

Want to join our innovative team? Visit our Careers page to explore open positions.