News: DNAnexus Offers Service for Clinical Testing Labs

This week we’re pleased to announce the launch of our specialized platform-as-a-service (PaaS) for the next-generation sequencing-based diagnostics market.

What does that mean? With this service, we are focusing specifically on clinical enterprises that want to eliminate the common costs and challenges associated with building clinically compliant pipelines for next-generation sequencing data analysis.

As demand for genomic data in the clinic ramps up, diagnostics companies that have traditionally used on-premise solutions are facing increasing challenges to scale their resources while meeting HIPAA and other regulatory requirements.

Clinical testing labs that are reconsidering those on-premise data centers need more than just a cloud provider; they also need a partner with expertise in genomics and bioinformatics to help build reliable, robust pipelines. That’s where we come in: with this PaaS, DNAnexus offers all of our usual rock-solid cloud computing along with access to our team of expert scientists and engineers who know this field inside and out.

Through our PaaS, clinical testing labs will be able to scale up their enterprise infrastructures for analyzing and managing DNA data. We provide a configurable API-based platform that allows users to move their analysis pipelines into the cloud, where they can utilize their own algorithms as well as industry-recognized tools and resources to create customized workflows in a secure and compliant environment.

One of our early clinical adopters, cancer researcher Boris Bastian from the University of California, San Francisco School of Medicine, said in a statement: “Working with the DNAnexus team has been invaluable for us as we deploy our data analysis pipeline to the cloud and work toward a production-grade clinical test. The DNAnexus platform is well-suited for rapid pipeline development and enterprise-readiness. We have relied heavily on their expertise in cloud-based solutions and benefited from their experience in managing data in a clinically appropriate manner.”

As part of this offering, we have ensured that our platform meets HIPAA, CLIA, and many other regulatory requirements for users working with sensitive medical information.

 

ISMB Recap: Looking for Knowledge and Imagination

ISMB Berlin 2013Earlier this week we were lucky enough to attend the annual Intelligent Systems for Molecular Biology meeting in Berlin, an excellent venue for deep dives into computational biology.

Many of the great talks at this event were held within the SIG (Special Interest Group) meetings on topics as diverse as network biology, SNPs, structural bioinformatics, and integrative RNA biology. But as expected, the keynotes were terrific as well.

The opening keynote came from Gil Ast of Tel Aviv University and provided a fascinating look at alternative splicing, epigenetics, and chromatin organization. Ast noted that 95% of genes have been found to undergo alternative splicing, with as many as 10 isoforms per gene corresponding to tremendous transcriptional diversity. Almost half of alternative splicing occurs in the form of exon skipping, Ast said. Interestingly, vertebrates are the group that appears to have the highest form of alternative splicing, with humans having the most within the group.

On a broader level, what we really took from Ast’s talk was the importance of having wet labs and computational groups working together to form a solid testing/validation loop. That’s something we value the importance of at DNAnexus, too, which is why we have designed our platform to enable bioinformatics experts to work closely with collaborators who may be less comfortable with the computational side.

Another comment that really captured our own view came from Goncalo Abecasis at the University of Michigan, who told attendees in his keynote presentation that data is not the same as understanding. That sounds simple enough. However, there’s nothing simple about transforming data into knowledge. One of the key drivers of the DNAnexus platform is the concept that it should be easier for scientists to pull knowledge out of their data; we strive to simplify data analysis and management by offering an easy-to-use interface on top of infrastructure that we maintain so our users can efficiently find the answers to their research questions. Our goal in establishing a repertoire of available apps that anyone can select and arrange in a custom workflow also allows researchers to stay focused on creating knowledge from data by reducing the time required to create the optimal analysis pipeline.

We were glad to get the opportunity to speak with so many IT developers at ISMB about our new app program, which aims to deliver new genomics tools to our user community. Anyone is welcome to apply to participate in this program; we are providing members with an initial $1,000 credit for use in accessing cloud-based storage and computational resources and free technical support from the DNAnexus engineering team. Contact us at developers@dnanexus.com to learn more.

ABRF: A Quick Meeting Recap

Here at DNAnexus, we’re lucky to have a terrific team supporting our goals. In this blog post, we wanted to share highlights from the recent ABRF meeting from the perspective of our marketing manager, Cristin Smith. Here’s her recap.

Just when we thought the Marco Island resort couldn’t be beaten for location, here comes the annual Association for Biomolecular Resource Facilities (ABRF) conference, held at the lakeside Disney Contemporary Resort right in the heart of Disney World, complete with a view of Space Mountain. I’m pretty sure the team back home in Mountain View was a little concerned that we weren’t going to come back.

The meeting’s opening keynote came from Trisha Davis, who runs the Yeast Resource Center at the University of Washington. Her work has focused on using yeast as a proving ground for various technologies, noting that as her center has evolved, so too has her team’s ability to really drill down into targeted interrogations of the organism. During her talk, entitled “Technology Development in a Multidisciplinary Center,” she noted how important it is to integrate multiple complex analyses in an attempt to relate genotype to phenotype.

On the final day of the meeting, “Omics Technologies to Transform Research, Health & Daily Life” also resonated with me. This was Harvard professor George Church’s vision of a future where genome sequence information is widely used and readily available. He spoke about some current logistical limitations, such as the fact that a $100 blood draw is cost-prohibitive, and that the field will have to move toward buccal swabs and other technologies that may cost only $1 to process in order for ’omic testing to become affordable. Citing some 37 next-gen sequencing technologies as the driver for the rapid drop in sequence costs, he said that his own estimate of the current genome price — from sample to interpretation — is $4,000. In order for genome sequencing to become medically useful, Church noted a few factors that will have to be addressed: a focus on completeness and standards to give FDA confidence in these technologies; the need for significantly more genetic counselors than we have right now; and better interpretation software that makes genome analysis truly straightforward.

Overall, we were excited to see how eager the core lab community is to receive technology improvements that generate a higher quantity and quality of sequence data for their customers in support of their research. This enthusiasm was a great setting to unveil our newly redesigned booth at the exhibit hall. It’s hard to find a more tech-loving crowd than the people who run core facilities, and we were glad to meet so many of them last week.