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.

Why Medical Centers Should Prioritize HITRUST in Cloud Providers

As medical centers have moved their operations and data from local infrastructure to the cloud, their ability to directly secure data has decreased. This change in security landscape makes it challenging for medical centers when they need to assess third-party vendors to ensure data is handled in a secure and compliant manner. One of the preferred methods is for providers and vendors to adopt the Health Information Trust Alliance (HITRUST) Certification standard as a way to streamline the vetting process. From a provider’s standpoint, that process saves substantial resources.

In August 2019, DNAnexus announced that its cloud-based genomics platform earned Certified status for information security by HITRUST.  As the first and currently only genome informatics platform to receive HITRUST CSF Certification, this certification further establishes DNAnexus as an industry leader with a demonstrated commitment to protecting the privacy of its healthcare clients patients’ confidential information.

The University of Pittsburgh Medical Center (UPMC), a world-renowned health care provider and insurer, has moved many of their applications and data services to the cloud via the DNAnexus Platform. As a result, UPMC requires vendors to become HITRUST certified so that can more effectively manage information risk and know that all organizational and patient data will remain protected.

UPMC is at the forefront of security and compliance standards. In the future, we predict more medical centers will require vendors to be HITRUST Certified as it streamlines the assessment process. With the DNAnexus Platform, UPMC’s entire network is given the ability to analyze hundreds of thousands of samples efficiently and share data and tools with collaborators – all while maintaining peace of mind that their patients’ data is being handled with the greatest level of care and confidentiality.

“Our customers require that our genome informatics platform protects the privacy and security of their patients’ confidential data,” said E. Loren Buhle, Jr. PhD, Vice President of Security, Quality and Compliance at DNAnexus.  “Becoming HITRUST CSF Certified is another important milestone in becoming the industry leader in data security and protecting ePHI. We now have earned certifications from HITRUST, FedRAMP ‘Moderate’ Authority to Operate, ISO27001 and Privacy Shield.”

Want to learn more about how DNAnexus has met key regulations and is appropriately managing risk? Get in touch! Email us at info@dnanexus.com.

Another Feather in the Cap for PrecisionFDA Platform: A 2019 FedHealthIT Innovation Award

In the four years since its launch, the precisionFDA platform has helped foster collaboration, further innovation, and develop regulatory standards for NGS-based drugs and devices. And now it has been recognized for the second year in a row for its contributions to advancing scientific research through providing a secure and collaborative online environment.

The precisionFDA platform was announced as a 2019 FedHealthIT Innovation Award Winner at a special reception on June 11 at the Washington Press Club, where more than 300 federal health leaders from government and industry gathered to recognize top innovation efforts from the federal health technology and consulting community. Nominated and chosen by our peers from across the federal health IT sector, the awardees were selected based on “driving innovation and results” at Veterans Affairs, Military Health, Health and Human Services, and Centers for Medicare & Medicaid Services.

“We are thrilled that precisionFDA has once again been recognized for creating an ecosystem in which members continue to contribute and innovate,” said DNAnexus’s Chief Cloud Officer, Omar Serang and member of the precisionFDA NGS sequencing team. “Its proven success has inspired other scientific partnerships, and we are proud to power portals that foster such innovative collaboration.”

PrecisionFDA is an online, cloud-based, virtual research space where members of the genomics community can experiment, share data and tools, collaborate, and define standards for evaluating and validating analytical pipelines. This open-source community platform, which has become a global reference standard for variant comparison, includes members from academia, industry, healthcare, and government, all working together to further innovation and develop regulatory standards for NGS-based drugs and devices. Launched in December 2015, the precisionFDA community includes nearly 5,000 users across 1,200 organizations, with more than 38 terabytes of genomic data stored.

Last year, the precisionFDA Next Generation Sequencing (NGS) Team received the FDA Commissioner’s Special Citation Award for Outstanding Achievement and Collaboration, which recognizes superior achievement of the Agency’s mission through teamwork, partnership, shared responsibility, and fostering collaboration to achieve the FDA goals.