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.

At Bio-IT World, Genome Centers Dished on Big Data

BioIT World 2013At the Bio-IT World Conference & Expo last week in Boston, more than 2,500 attendees descended on the World Trade Center to hear about the latest in hardware, analysis, data storage, and much more. The DNAnexus team was out in force, and we were delighted to share updates about our new platform with the many attendees who stopped by our booth.

The conference had a number of excellent keynote talks this year, including Atul Butte from Stanford and Andrew Hopkins from the University of Dundee. We also really enjoyed seeing Steven Salzberg’s acceptance of the Benjamin Franklin Award for Open Access in the Life Sciences — a much deserved honor for one of the veterans of the bioinformatics field.

Perhaps most interesting was a panel discussion about big data featuring members of major genome centers. Panelists included Guy Coates from Sanger, Xing Xu from BGI, Eric Jones from the Broad Institute, and Alexander (Sasha) Zaranek from Harvard Medical School and a company called Clinical Future.

For those of us who remember when it was a big deal to have a terabyte of storage available, it was truly amazing to hear that most of the panelists have 15 petabytes or more of data stored and easily accessible. Still, even with resources like that, some of the panelists encourage their institute members to delete data when possible, such as the unaligned reads from a sequencing run.

Access control is a real problem for managing data at these large centers. Sanger’s Coates said that his institute’s move into the clinical field — complete with consent forms and all the other compliance needs — makes controlling access “a real nightmare” for his team. Jones at the Broad said that this issue basically means people in the field are living on borrowed time as it becomes increasingly important to find the right solution to this challenge. Zaranek noted that Clinical Focus will use the Arvados tool to include security permissions and provenance along with the files to address this issue.

The panelists also specifically discussed cloud computing, with BGI’s Xu saying that the cloud is his center’s main data repository. Still one goal is to facilitate more rapid and efficient exchange of genomic data globally via higher bandwidth, although they have tested this using Aspera. They successfully transferred 24 GB in just 30 seconds across countries, but this feat is not yet economical enough for routine use. Coates said that his group uses cloud options (including Amazon) for research projects, but they are still evaluating how to integrate cloud for the production pipeline in a cost-effective way. At the Broad, Jones said, the need to move to the cloud is understood, but so far internal computing is still enough for institute members; he added that the cloud’s elasticity will ultimately drive adoption, allowing people to run very large jobs that would otherwise interfere with the rest of the institute’s compute resources. Zaranek’s group is using cloud computing from Harvard and from Amazon and said that having both options is incredibly valuable. It will also allow other organizations to access their resources. Coates and Jones said that the real challenge in managing data is when individual researchers start moving data around, because tracking that data and predicting resource needs can become difficult.

These are all issues that we have given a great deal of thought to as we designed and built the new DNAnexus, now available for beta testing. We agree that security and compliance are important components of any compute solution — whether cloud-based or in-house — and that’s why we baked the highest standards right into our new tool. Having flexibility to configure the environment as needed, such as scaling up or down at a moment’s notice, is another key trait of the new platform and one that we believe will be quite useful for scientists in individual labs or at these major genome centers streaming data around the clock.

JP Morgan in Review: Expect Rapid Evolution in Sequence Analysis and Big Data Needs

Last week’s JP Morgan Healthcare Conference was the usual biotech extravaganza, filling downtown San Francisco with so many analysts and investors you could mistake it for Wall Street. The great thing about this event is that it serves as a platform for all of the presenting companies to lay out their plans for the new year — giving the rest of us guidance about what to expect.

jp morgan healthcare conference

Illumina, for example, announced its acquisition of Stanford spinout Moleculo, which has developed a way to generate multi-kilobase reads from sequencing-by-synthesis technologies. With Moleculo’s IP, Illumina will likely have users producing very long sequence reads in the first half of this year, though currently most existing assemblers and other sequence analysis algorithms have been optimized for much shorter reads. If this long-read technology performs as advertised, we anticipate a flurry of activity as developers tweak their aligners and assemblers to make the most of these multi-kilobase reads.

In applied markets, Illumina acquired prenatal testing firm Verinata Health, and Life Technologies announced the formation of Claritas Genomics, a joint venture with Boston Children’s Hospital to develop diagnostics for the Ion Torrent sequencing platform. With these moves, both companies continue their march on the clinical market — giving us even more certainty about the need for sequence analysis and interpretation tools that will fit the requirements of users in clinical labs. These downstream users will be best served with simple but highly customized tools that match their specific environment, tasks, confidentiality mandates, and other attributes.

In general trends, the focus on big data was inescapable at JP Morgan, and served as a particular highlight of a breakfast panel hosted by FierceBiotech. No longer just the concern of chief information officers, big data is seen as equal parts opportunity and pitfall in the biomedical and healthcare field. Lon Cardon from GlaxoSmithKline encouraged people to think of it as good science rather than just “big data.” Meanwhile, John Reynders from AstraZeneca noted that the value of big data lies in the human element — that is, how we query it and what we’re looking for.

Back at DNAnexus headquarters, where we’re putting the finishing touches on our new platform to enable people to make the most of big data, the observations from JP Morgan offer nice validation of the path we’ve been planning. Our new platform has been designed for flexibility, giving users control over which algorithms best fit their data — whether those data sets are small or large in size, based on short-read or long-read sequence, and more. And with the growing use of sequencing in the clinical realm, we have worked hard to make sure the new platform will be a good fit for users who must comply with HIPAA and other regulatory requirements. Check back with us often, and we’ll keep you posted as we get the new platform ready for its debut!