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.

More Rapid Responses to Rare Disease

Families facing rare diseases know a thing or two about patience. They often face diagnostic odysseys that take years. Even when answers are forthcoming, therapies might not be. 

At DNAnexus, we’re proud to partner with several organizations to provide more rapid rare disease discovery, drug development, and delivery.   

One of these is Ultragenyx, a biopharmaceutical company based in Novato, CA, which is committed to bringing novel products to patients for the treatment of serious and debilitating rare and ultra-rare genetic diseases. The company has rapidly built a diverse portfolio of approved therapies and product candidates aimed at addressing diseases with high unmet medical need, yet clear underlying biology.

Delivering Safe and Effective Therapies

Ultragenyx is in the business of time. Its strategy is predicated upon time and cost-efficient drug development, with the goal of delivering safe and effective therapies to patients with the utmost urgency.

Thanks to DNAnexus Titan, we were able to provide Ultragenyx with a more streamlined way to unlock the power of multi-omics data and accelerate its discovery process. The unified NGS analysis platform brought its data and pipelines together in one secure environment for enhanced data analysis, collaboration, visualization, and sharing of results.

With the right infrastructure in place, Ultragenyx simplified the complexities of secondary analysis infrastructure, allowing researchers to focus on what’s important – rapid rare disease discovery

“You save the bioinformatician’s time, compute time, and therefore decrease turnaround time. This enables R&D researchers to answer questions and get rare disease treatments to market faster. You can’t put a price tag on that.”

SEAN DAUGHERTY
Associate Director of Bioinformatics, Ultragenyx

Data Sharing & Accelerated Rare Disease Discovery

Data sharing is key when researching a rare disease with many subtypes driven by diverse and distinct genetic alterations. Our partnership with St. Jude Children’s Research Hospital and Microsoft has resulted in a cloud-based, data-sharing ecosystem that has proved to be a model for harmonized genetic data and collaboration across the pediatric cancer community.

The more samples researchers are able to analyze, the more power they have for genomic discovery and clinical correlative analysis. The St. Jude Cloud has the power of more than 1.25 petabytes of data, and has already enabled many discoveries, such as new insight into a rare C11orf95 fusion in ependymoma and the classification of 135 pediatric cancer subtypes by gene expression profiling and map mutational signatures.

By allowing data to be authenticated, tracked, and monitored in a single, secure, and compliant system, our platforms reduce many of the logistical difficulties that researchers might otherwise face. 

We’re happy to support large-scale, global collaborations that are accelerating genetic discovery and providing actionable insights that will help the not-so-rare 300 million people impacted by genetic diseases get help sooner, rather than later. 

How Regeneron Bypasses Bottlenecks to Iterate at the Scale and Speed of Science

How Regeneron Bypasses Bottlenecks to Iterate at the Scale and Speed of Science

At the Regeneron Genetics Center (RGC), scientists are uncovering important genomic variants involved in human health and disease and enabling important research into novel drugs and therapies.  RGC receives 500,000 samples per year and generates about 500 billion reads per hour. To date, the center has sequenced over 1.5 million samples and created one of the largest catalogs of human genetic variation.

To gain insights from all that data, RGC needed infrastructure capable of capturing and handling large quantities of genome and phenotype information. In a recent webinar, William Salerno, RGC’s Senior Director of Genome and Sequencing Informatics discussed the RGC’s infrastructure and how the center built a system capable of meeting its current and future data analysis needs.

The RGC accomplishes its data analysis using a combination of local infrastructure, cloud computing, and the DNAnexus Platform. RGC uses the platform to run various production and analytical workflows and for its data management and sharing needs. One component of the RGC platform is GLnexus, software that RGC researchers developed with DNAnexus and other partners that enables large-scale data merging. RGC researchers have tested it on over a million exome samples so they are confident that it scales to meet their needs.

RGC needed a solution that includes metadata capture and pipeline version control that enables extensive logging and troubleshooting. The platform provides a comprehensive security framework for keeping genomics data safe and secure to support the analysis and processing of genomics data. Salerno highlighted one example where RGC created an autonomous cloud environment for a partner that needed to analyze genomic and phenotypic data related to COVID-19. RGC was able to get the environment up and running in two days, and the partner was able to easily import data into the cloud and control who could access it.

For scientists looking to build the infrastructure that can support large-scale genomics, Salerno highlighted some key factors to consider during the webinar. There are the costs associated with the platform. This includes those for the physical infrastructure but also costs for audits, quality control, system redundancy, troubleshooting policies, managed services, and disaster recovery. Another important factor to consider is how metadata will be generated and captured on the platform.

The RGC is committed to ensuring that its work is equitable, open access and transparent. To that end they make open-source versions of the genome analysis pipelines that they use on the Titan Platform available to the scientific community. 

To learn more about how RGC’s platform is enabling scalable genome research, download the whitepaper or listen to the webinar