Bridging the knowledge gap: 4 questions with Microsoft's Geralyn Miller on designing genetics-based apps

The growing deluge of personal genetic information has enormous value as a tool for research — even more so if gene mapping tools and information can be made accessible to non-biologists and applied in everyday life.

This content is sponsored by Microsoft. 

That is the central goal of the partnership between Microsoft and Sequencing.com, a platform that allows users to store, analyze and share their genetic information. Simply put, the platform enables individuals to upload their genetic information — generated via Helix, 23andMe, Veritas, Ancestry.com, National Geographic, HLI or any other source — to Sequencing.com and use their personal information in health and wellness powered by Microsoft's cloud.

Hosting genetic information in a central, accessible repository is integral to advancing genetic research. However, it is only half the battle when it comes to democratizing precision medicine, as the complexity of this data renders it useful only to biologists or bioinformaticists. To bridge this knowledge gap, Microsoft is helping arm developers with software to design genetics-based apps without having to understand genomics.

Becker's Hospital Review caught up with Geralyn Miller, director of genomics in Microsoft's artificial intelligence and research division, to discuss Microsoft's inroads in genomics and programming.

Editor's note: Responses have been lightly edited for style and clarity.

Question: Recently Microsoft partnered with Sequencing.com to further research regarding technology, genomics and precision medicine. Can you talk about real time personalization technology and the opportunity for real-time personalization application programming interface, or +RTP API, in user apps and population health?

Geralyn Miller: Providing an exceptional healthcare experience starts with enhancing the personal experience. Apps powered by Real-Time Personalization® (+RTP) API can utilize genetic information to provide personalized, real-time insights and guidance to app users. The +RTP API makes genetic-based information incredibly easy to work with and understand. It lowers the barrier to entry for app developers to be able to use genetic data.

The +RTP technology enables mainstream mobile app developers with no experience in genetics to be successful creating lifestyle, wellness and fitness apps that incorporate genetic data. Examples of the types of apps being built using +RTP technology include weight optimization, sleep optimization, diabetes prevention, heart health, childhood fitness, childhood education, healthy baby, cognition and brain health, and longevity, among others.

Q: Genetic data is extremely sensitive. How do Sequencing.com and Microsoft make precision and gene mapping tools both available and secure?

GM: Sequencing.com relies on the security and compliance of the Microsoft cloud to store data and process information. Short-term storage, including genetic data files and the results from processing and data analytics, is hosted on Azure, Microsoft's cloud computing service. The Altruist Database storage and the +RTP API are also on Azure. In addition, Sequencing.com has integrated the Microsoft Genomics service for alignment and variant calling into their primary bioinformatics app, called EvE. Users who upload FASTQ, BAM or SAM files and use the EvE Premium app will be able to select Microsoft Genomics service for generating lists of variants. Sequencing.com is also working with Microsoft to integrate the Microsoft Genomics service into their default pipeline. The system default is used if a non-bioinformatician uploads a FASTQ, BAM or SAM file, such as if a lab or healthcare professional uploads the clients' WGS raw data files. For example, if a person selects a FASTQ file when starting a wellness app, Sequencing.com's default pipeline will perform alignment and variant calling in the background without any need for user interaction.

Q: Microsoft and Sequencing.com held the event "Hack the Genome" in April 2017. Can you talk about the goals of the event, as well as what you saw as some of the most interesting takeaways/findings?

GM: The two-day event held on the Microsoft campus in Redmond, Wa., focused on developing health and wellness apps that provide a unique, personalized user experience. We had 35 participants from different fields in this hackathon. Attendees were computer engineers, graduate students, start-up founders and hobbyists. Most participants in the hackathon had no prior genomics experience.

Participants used the +RTP API to add personalization to their apps in the Sequencing.com platform. Each team that participated in the hackathon was successful in creating a meaningful application — a testimony to the power of the +RTP platform to abstract away the complexity of genomics from the app developer.

The hackathon demonstrated +RTP technology removes the roadblock of "mandatory genomics knowledge" for a developer. A working knowledge of coding — .NET/C#, Swift, Objective-C, Java, PHP, HTML, Python, etc. — is enough to be successful with +RTP technology.

Sequencing.com and Microsoft are organizing a second "Hack The Genome Hackathon" in the first half of the 2018 in New York City.

Q: +RTP technology clearly has a place in the app market for users who are interested in personal wellness technology. Do you see +RTP technology playing a role in hospitals or health systems? What value will this provide them?

GM: Current forecasts indicate the world will soon be inundated with hundreds of exabytes of genetic data. This data needs to be analyzed by medical professionals in conjunction with clinical data from EMR systems. +RTP technology will play a key role in extracting relevant and important information from this vast and complex data. Researchers can use genotypic and phenotypic information extracted for new treatment models or drug discoveries.

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