Tech Overlook

Microsoft unveils genomics innovation and new partners at ASHG 2018


The world’s leading geneticists will converge in San Diego October 16-20 for the American Society of Human Genetics (ASHG) Annual Meeting. This year’s event will showcase some amazing new advances in genomics, and Microsoft Genomics will have exciting news and updates to share.

The latest in genome analysis

The strength of any analytical insight will always depend on the strength of the data used to generate it. If you want to perform repeatable genomic analysis that generates durable datasets, you should rely on industry standards that are constantly validated, versioned and properly curated.

With that in mind, Microsoft is deepening its commitment to genomics with the fourth iteration of the open source Genome Analysis Toolkit (GATK4). The toolkit update is designed to optimize performance for researchers as they strengthen data pipelines and power successful genomic analyses, so they can reduce the risk of noise or artifacts within the data set and extract more insight from the genome.

A growing partner network

To ensure that genomics researchers have access to a broad array of tertiary analysis and orchestrated cloud technology options, Microsoft is working with several new partners:  BizData, Eagle Genomics, Genoox, Gentera Biotechnology, L7 Informatics, Parabricks, Qiagen and Veritas Genetics. They will be with us at ASHG 2018, sharing their insights and demonstrating how their data tools and services will help broaden and deepen what researchers can achieve in genomics. We continue to expand our genomics partner ecosystem, with now more than 20 partners, from wet lab sequencing prep out to interpretation.

“We are very excited to partner with Microsoft Genomics and utilize Whole Genome Sequencing and the Arvados platform to answer the most interesting and difficult questions in genomics.” notes Ward Vandewege, Veritas’ VP of Engineering,  “Running on Microsoft Azure, we can demonstrate the possibilities of genomic analyses at scale by taking advantage of Veritas’ sequencing capabilities and Arvados’ open-source federated platform bringing the analyses to data.”

Anthony Finbow, CEO of Eagle Genomics commented: “We are delighted to partner with Microsoft Healthcare on its Genomics service and look forward to working together to unlock the potential of the microbiome and solve some of the grand challenges of our age. We are seeing strong demand for our knowledge discovery platform amongst enterprise customers in the biotech and pharma, food and personal care industries as they embrace the digital reinvention of Life Sciences R&D. Microsoft Genomics will help tackle the computing and scaling challenges, accelerating the adoption of the technologies and the launch of new products and therapies, heralding a new era in scientific discovery.”

A promising research study at The Icahn School of Medicine at Mount Sinai

Dr. Robert Klein from the Klein Lab at the Icahn School of Medicine at Mount Sinai is leading a team of bioinformaticians and geneticists seeking evidence for how our genes are involved in cancer risks, assisted by new technologies and the cloud to analyze the largest “big data” sets.

The Mount Sinai research team had been successful in gene sequencing, but they were starting to run into a bottleneck. “We weren’t getting enough space on the computer to store the data as we’re downloading it, running it, and working with it,” Dr. Klein said. “The data was just getting too big.”

With the Microsoft Genomics service, Dr. Klein added, “I give it the input data that would come from the sequencers, it can uniformly realign everything and let me do the joint calling for the analysis I want.” Microsoft Genomics enables “a way to try the large re-analysis of whole genome sequencing data.”

A powerful new way to analyze long-read bio data

In what’s likely to be our most exciting development at the event, we plan to demonstrate a completely new method for analyzing long-read genomic data and capturing major structural rearrangements.

Through collaborative research with Stanford University, we’ve developed a powerful new genomics algorithm that runs on an Intel Altera field-programmable gate array (FPGA) infrastructure within Microsoft Azure. It is an entirely new way of utilizing and understanding long-read genetic data, and will also be one of the first public-facing services based on FPGAs—the same board-level architecture that underpins the incredible machine learning capabilities of Microsoft Project Brainwave.

This revolutionary genomics service will make it easier for researchers to build and complete a whole new set of explorations using long-read data in the cloud. We can’t wait to see what the genetics community makes of it and hear how you plan to apply these powerful new capabilities when the service formally launches.

An exciting genomics success

At last year’s ASHG annual meeting, we presented a summary of how Microsoft Genomics was supporting collaborative pediatric cancer research at St. Jude Children’s Research Hospital.

This year, Microsoft and St. Jude are pleased to share early global adoption of the hospital’s global data sharing and research initiative. The St. Jude Cloud is using Microsoft cloud technology to successfully deliver pediatric cancer data to more than 2,000 clinicians and researchers among 300 organizations in 28 countries. St. Jude is using collaborative research in the cloud to make the genome more actionable, and it’s taking powerful steps forward in the understanding and treatment of pediatric cancer.

What the future holds

At ASHG, you can hear a poster presentation from Microsoft data scientist Erdal Cosgun, Ph.D. on research he conducted with his intern Min Oh. They explored the consistency of the quality scores with machine learning for next-generation sequencing experiments. He will present a machine learning approach for estimating quality scores of variant calls derived from BWA+GATK best practice powered by the Microsoft Genomics service.

You can also try out our Public Preview of Microsoft Genomics service GATK4. Between now and December 31, 2018, bring your Azure account and 20 whole genome samples to run with Microsoft Genomic Service at no cost. Let us know if you need to open a free trial Azure account and we can help you get started.

Stop by Microsoft Genomics at ASHG 2018 and find out more how we’re making deep genomic analysis easier and more accessible.



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