Leading Genome Research Center Migrates to DNAnexus on Azure

DNAnexus on Microsoft AzureToday we announced that the trusted DNAnexus genome informatics and data management platform is now also available on Microsoft Azure, Microsoft’s open, flexible, enterprise-grade cloud computing platform. Leveraging Azure, DNAnexus provides organizations a single, secure, scalable, and collaborative platform to accelerate the application of genomics within healthcare and research. The Stanford Center for Genomics and Personalized Medicine (SCGPM) is the first organization to access DNAnexus on Azure.

scgpmA key advantage to conducting genomic research in the cloud is the enhanced collaboration facilitated by data accessibility, consistency, and scalability. SCGPM researchers already have existing collaborations on the DNAnexus Platform hosted by Amazon Web Services, by extending adoption of DNAnexus on Azure means that researchers can collaborate even more widely. By leveraging DNAnexus on Azure’s powerful data-handling capabilities, a distributed network of scientists and researchers have secure access to terabytes of data through a common user interface.

DNAnexus and Microsoft are both valued partners to Stanford’s core sequencing facility. SCGPM and David Heckerman, distinguished scientist and director of Microsoft Genomics, have been in close collaboration for years. By extending the DNAnexus Platform to Azure, it is now easier for SCGPM researchers to work closely with David’s team. We believe we are just seeing the tip of the iceberg in terms of the potential for medical discovery.

DNAnexus is proud to support SCGPM on its mission to translate genomics into patient-centered medicine, and we look forward to enabling the discoveries that unfold.


DNAnexus on Microsoft AzureInnovation Through Collaboration

Through additional partnerships, Microsoft recently developed computational methods to accelerate the best practices pipeline for genome resequencing sevenfold. By improving the efficiency of the Burrows-Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK), researchers and medical professionals are able to get actionable results in just four hours, compared to the previous twenty-eight. This is critical for medical professionals to accelerate diagnosis and treatment for patients.

Genomic sequencing and analysis has become a key component of the diagnosis and treatment of cancer and other genetic conditions. This effort has both relied on and stimulated innovative technologies. At DNAnexus, we firmly believe that in order to continue innovating and further break down the technical barriers to disease, community collaboration is essential. The sharing of data and ideas between organizations – and even industries – spurs the innovation critical to medical breakthroughs. Microsoft is a global leader in technological innovation, and by partnering with leading research centers, universities, and the private sector, it is poised to make great contributions to the genomics revolution.

The DNAnexus Platform sits at the forefront of cloud-based data security, compliance, and controlled access. By co-developing with DNAnexus, Microsoft will be able to deploy their tools into an investigative environment while leveraging extensive research experience. We are excited to be collaborating with Microsoft and to offer these cutting-edge bioinformatics tools available to the genomics community via the DNAnexus Platform in the future.

Facilitating Collaboration on DNAnexus

The need for enhanced collaboration is a trend in the genomics industry we have been following for a while. DNAnexus equips end-users with out-of-the-box clinical compliance and streamlines communication between healthcare providers, reducing information silos for more efficient collaboration.

However, this notion of partnership goes deeper than groups of scientists working together to parse through datasets. Innovation and exploration are best served through collaboration, thus successful innovation in the genomics industry also relies on disparate industries working together towards a common goal. By tapping into the genomics network, the community is able to learn from each other to advance research, leading to accelerated medicine and tailored patient care.

DNAnexus is excited about the opportunity to partner with Microsoft, given their commitment to advancing the field of genomics, and their depth and breadth of experience offering solutions to the healthcare industry.

The U.S. Cancer Moonshot and a Culture of Collaboration

Yesterday, United States Vice President Joe Biden hosted the National Cancer Moonshot Summit. Scientists, oncologists, donors, and patients convened for a daylong conference intended to pick up the pace of research towards curing cancer. Rather than focusing on one specific type of cancer, the conference broadly discussed more than 100 types of cancer; emphasizing strategies for prevention, early detection, wide access to treatment, and encouraging collaboration among researchers. You can read a first-hand account from our CMO, David Shaywitz, here.

As part of the Moonshot effort, DNAnexus, in partnership with PatientCrossroads, has committed to develop the Integrated Data Engagement Analytics (IDEA) platform to facilitate the collection, analysis, and sharing of genetic, proteomic, and EMR/phenotypic data to accelerate disease research. PatientCrossroads and DNAnexus are currently engaging in a pioneering effort to help patients obtain the raw genetic files and medical records and then integrate these data along with patient reported outcomes data obtained by PatientCrossroads on a secure and compliant platform that allows authorized researcher access to this information and use it to develop novel insights — the IDEA platform. You can review the complete list of public and private sector Cancer Moonshot commitments announced in the White House press release.

Here at DNAnexus, we are particularly devoted to reducing the technical barriers to accessing and working with research datasets.  We believe that a culture of openness in genomic research will lead to greater medical breakthroughs. Most data sharing in cancer genomics research has been centralized through rich, yet controlled-access databases like The Cancer Genome Atlas (TCGA) or International Cancer Genome Consortium (ICGC) — both of which properly approved researchers can easily access on the DNAnexus Platform. Read more about some of the genomic community collaborative initiatives DNAnexus is a part of: precisionFDA, open access cancer genomics pilot, and ICGC.

 

Once in a Blue Moon Competition: precisionFDA Truth Challenge

The FDA, the Global Alliance for Genomics and Health (GA4GH)  and National Institute for Standards and Technology (NIST) recently teamed up to create a once-in-a-blue-moon challenge for genomic scientists! Dubbed the precisionFDA Truth Challenge, genomic innovators were invited to test their informatics pipelines on two datasets, the well-characterized Genome in a Bottle’s (GiaB) NA12878 (HG001) reference sample and a new reference sample HG002, of which the results were unknown.

PrecisionFDA_TruthChallenge_Image

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 analytical pipelines. Community members span academia, industry, healthcare organizations and government.  All of these organizations are working together to further innovation and develop regulatory science around NGS tests. So far, the community currently includes more than 1,500 users across 600 organizations, with more than 10 terabytes of genetic data stored.

This is the second challenge issued through precisionFDA, following the precisionFDA Consistency Challenge.   The Truth Challenge is about discovering the consistency and accuracy of informatics pipelines when analyzing a human sample whose truth data is unknown. NIST and GiaB released the truth data May 26, 2016, after the close of the challenge.

What makes this challenge so exciting?

NIST released NA12878 in 2014, the first gold standard whole human reference genome, in collaboration with GiaB and the FDA. Since then,  it has arguably become one of the most studied biospecimens. Researchers from around the world use NA12878 as training data for assessing pipeline performance.

Since many pipelines use some sort of machine learning algorithm when trying to determine whether a reported mutation is real or not,  the difficulty that arises is ensuring a pipeline doesn’t overfit the training data. Pipelines can ultimately be tuned, in order to maximize performance on the training dataset, and if the test data happens to be similar to the training data the pipeline’s performance would be abnormally consistent and accurate. A great resource in understanding why scientists split data into train and test roles in order to assess the accuracy, reliability, and credibility of their predictive models (the algorithm that goes into a pipeline) can be found here.

In order to test performance of pipelines in real-life, scientists needed a second reference sample and associated truth callset of which NGS pipelines have not been trained on. This is exactly what NIST and GiaB have provided in reference sample HG002.

Scientists can now evaluate algorithms using test data that is separate from the training data, an attribute  that is broadly accepted as fundamental to the evaluation methodology. Moreover, unlike NA12878, the new reference sample HG002 is male, which poses new challenges to algorithms since there is only one copy of the X chromosome, and brings new opportunity for evaluating NGS methods along this dimension.

The winners

As the clock struck midnight EST on May 25, 2016, the precisionFDA Truth Challenge closed with 36 entries across 21 teams, spanning 5 countries;  truly an international competition of epic proportions!

The winners of the Truth Challenge will be announced at the upcoming Festival of Genomics in Boston on June 29th at 8:45am EST by Elizabeth Mansfield, PhD, Deputy Director for Personalized Medicine in FDA’s Center for Devices and Radiological Health’s Office of In Vitro Diagnostics and Radiological Health. Registration is free. Want to learn more about precisionFDA?  Stop by the DNAnexus booth (# 240)  during the Festival to receive a demo of the precisionFDA platform from a member of the precisionFDA team.

Want to recreate the Truth Challenge for yourself? Join the precisionFDA community today and evaluate a pipeline of your choice against HG002. Happy testing!