A New Twist on Diagnostics Development: Partnership with SynBio Pioneers to Accelerate NGS-based Diagnostic Testing

Methylation and low-frequency variation detection made easier? By combining our integrated, comprehensive computational platform with synthetic DNA innovator Twist Bioscience’s NGS Methylation Detection System and Unique Molecular Identifier (UMI) Adapter System, researchers now have even more powerful tools in their NGS analysis Kit.

DNA methylation (the process of adding methyl groups to DNA segments) is an epigenetic modification that regulates gene expression and interplays with genetic and environmental alterations. Aberrant DNA methylation has been confirmed as one of the hallmarks of cancer, an area in which researchers are studying its patterns for use as a potential biomarker for prognosis, diagnosis, treatment response, and therapeutic targets. In the case of colorectal cancer, for example, methylation profiles obtained from blood liquid biopsy have shown potential in early-stage detection of disease.

Twist’s NGS Methylation Detection System provides robust sample preparation and target enrichment solutions for identifying methylated regions in the human genome, and its UMI Adapter System detects low-frequency variants in low-input sample sources such as cell-free DNA (cfDNA). Together, they can be used to better characterize and understand the genetic mechanisms linked to not only cancer, but also neurodegeneration and rare diseases.

The addition of the DNAnexus platform to this end-to-end NGS-based workflow means users will be able to easily explore and analyze the complex datasets generated by the systems in a single, scalable, cloud-based environment, thereby reducing their data analysis timeline after performing a sequencing run.

This, in turn, could reduce the time to design, validate, and commercialize new, high- quality, next-generation sequencing (NGS)-based diagnostic tests. “With the integrated DNAnexus platform, Twist customers can now reduce the complex data analysis bottleneck, which we believe will offer significant time savings and cost advantages,” said DNAnexus president John Ellithorpe, PhD.

The core of Twist’s DNA synthesis and engineering platform is a proprietary technology that “writes” DNA on a silicon chip. The company is leveraging this technology to manufacture a broad range of synthetic DNA-based products, including synthetic genes, tools for NGS preparation, and antibody libraries for drug discovery and development.

“Our customers can now access industry-leading computational infrastructure platforms to support their bioinformatics needs and reduce their data analysis timeline after performing a sequencing run with our NGS Methylation Detection and UMI Adapter

Systems,” said Twist CEO Emily M. Leproust, PhD. “This collaboration with DNAnexus is another example of our ongoing commitment to providing our customers with the tools they need for complete, customized, end-to-end workflows.”

Learn more. Engage with DNAnexus today.

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.

DNAnexus Presents at JP Morgan Healthcare Conference

JP Morgan Healthcare 2016Today kicks off the 34rd annual JP Morgan Healthcare Conference, which continues to be healthcare’s greatest deal-making and high-powered networking event of the year. Each year industry leaders unveil new products, as attendees scope out emerging trends in healthcare’s rapidly-evolving sectors such as digital health and diagnostics. Last year the introduction of the the HiSeq X Ten from Illumina made great waves as it would continue to drive down sequencing costs and democratize genomics. We look forward to this year’s announcements in genomics which will undoubtedly be focused on what can be achieved with large scale sequencing.

However, biotech wasn’t always big business; leading up to 1980 it was Big Pharma that attributed to the majority of drug discovery. If you’re curious on how biotech evolved from risky investment to booming business, Luke Timmerman and Meg Tirrell do an outstanding job chronicling biotech’s coming of age in The Signal podcast.

DNAnexus is honored to be presenting this year. Richard Daly, CEO, will deliver a presentation on Tuesday, January 12th at 2pm PST in the Elizabethan D room at the Westin St. Francis. In his talk, titled The Network is the Solution in Genomics, Richard will discuss the convergence of genomics and cloud computing and how DNAnexus has acquired market leadership in this sector by building out a global network via its integrated genome informatics and data management platform.

2015 was a breakout year for DNAnexus, expanding our global network of key customers and partners by 6-fold, many of which we have announced publicly. We help biopharmaceutical companies (Regeneron), leading genome centers (Baylor College of Medicine, Stanford University), pioneering diagnostic test providers (Natera, CareDx, Intermountain), sequencing service providers (The Garvan Institute, WuXi NextCODE), research consortia (ENCODE, CHARGE, 3000 Rice Genomes Project) and the US Government (precisionFDA) accelerate their genomics programs globally. Our focus on secondary analysis and building out a partner/collaboration network drives substantial growth. Laboratory information management systems (LIMS) and sequencing instruments easily integrate with DNAnexus, as well as downstream tertiary analysis and reporting solutions.

DNAnexus workflow

Genomics has been called the original big data, and it’s only going to get bigger. Organizations participating in global large-scale sequencing projects studying thousands or even millions of genomes are becoming the norm. In an article, Big Data: Astronomical or Genomical?, in PLOS Biology projects that by 2025 the genomics industry will outpace three other major big data generators: astronomy, YouTube, and Twitter, in projected annual storage and computing needs by a factor of 2-20x. Our own projections suggest more than 400,000 TB of genomic data in 2016, and only 0.01% of the world’s population has been sequenced.

As big data aggregates online, new standards will need to emerge for discovering and querying datasets, for authenticating requests, encrypting sensitive information, and controlling access. DNAnexus, along with the Global Alliance for Genomics and Health and others are already working together to develop approaches that facilitate interoperability.

At DNAnexus, we believe the cloud is the only technology that is capable of keeping pace with big data. It eliminates time and the capital expenditure of creating and upgrading local infrastructure for data analysis. The elasticity of the cloud allows for near limitless scalability and immediate availability to resources. And with the cloud’s online nature, researchers are able to share data and tools and collaborate instantaneously with others around the world. Our industry is long overdue to replace hard drives and FedEx as the means for collaboration, and patients and researchers worldwide will benefit from a simpler means to collaborate. DNAnexus, and its global genomics network, is addressing the challenges of genomics big data.