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!

Need a Lucky Break? DNAnexus Is Giving Away a 4-Day AGBT Badge

agbt 2013 meetingIt’s hard to believe January has already arrived — and that means scientists throughout the genomics community have their eyes on next month’s Advances in Genome Biology & Technology (AGBT) meeting in Marco Island, Fla.

For some people, that entails booking flights and checking the sunblock supply. For others, though, the next few weeks will be spent in a last-ditch effort to get into the wildly oversubscribed conference. If you’re one of those people, we have an opportunity for you: join our contest to win a prepaid AGBT badge.

AGBT is far and away one of the most important scientific meetings of the year, and DNAnexus is proud to be among the sponsors this year. We are honored to be supporting an event that has consistently maintained high standards for scientific talks, posters, and social events for more than a decade.

agbt marco island marriott
(Source: Marco Island Marriott)

As a sponsor of the conference, we are able to purchase a full, four-night registration — but instead of giving it to one of our employees, we are instead choosing to give it away to a deserving scientist who has no other chance to attend this meeting. This giveaway is not tied to what we do and has no strings attached from DNAnexus; it’s just an opportunity for us to recognize someone for truly innovative and compelling research.

Any scientist working at a university or other research institution may enter. Simply send a short note from your workplace email to agbt13@dnanexus.com with the following information:

  1. Name and mailing address
  2. Brief description of your research (no more than 400 words)
  3. A sentence or two on why you should be selected to attend the conference

Deadline for submissions: January 23. The entries will be judged by our founders: Andreas Sundquist, Arend Sidow, and Serafim Batzoglou. The winner will be informed by January 25 and publicly announced in February. Stay tuned and connect with us socially (Twitter, Google+, etc.) to find out who wins and what we’ll have in store at AGBT.

And if you’ve already gotten your AGBT badge, please let your colleagues who weren’t so lucky know about this contest. We’re looking forward to spending four days in Florida listening to the best genomics research going on — and we can’t wait to help a lucky scientist come too!

The fine print: Award includes a full conference badge and four nights of lodging. The winner is responsible for transportation to and from the meeting and all other expenses. No purchase necessary. Void where prohibited. Contest is not open to DNAnexus employees or consultants. Applicants must be over the age of 18. This contest is not affiliated with or sponsored by the AGBT conference. 

Dispelling the Myths of the Cloud

cloud computing in genomicsWhat comes to mind when you hear the word “cloud”? Does the Amazon cloud immediately pop into your head?

Despite the cloud’s widespread recognition in the media, many are still uncertain about the benefits of cloud computing.  In a recent national survey, 95% of respondents who claimed they have never used the cloud actually have. In fact, they do so unwittingly nearly everyday via online banking and shopping, social networking, emailing etc.

Some scientists still seem skeptical of the cloud’s place in next-generation sequencing. If you tend to gravitate to skepticism, please read my article, Dispelling the Myths of the Cloud for the Skeptical Scientist, on BitesizeBio.com.

It provides an overview of how the cloud can be useful to scientists in a multitude of ways, such as infinite scalability, enabling instant and limitless access to storage and compute resources, eliminating up-front commitment to expensive hardware. Another advantage, Data security, is the cloud’s core competency, which cannot be measured up to any other internal infrastructure.

The “cloud” may be generating a lot of buzz in the NGS community, but is it worthy of all the hype? It appears that all signs point to yes.