At Rhode Island NGx Conference, Informatics Is Clearly on the Rise

We are back from Cambridge Healthtech Institute’s NGx Next-Generation Sequencing Data Analysis conference last week and more inspired than ever. The central theme from the 2012 meeting in Rhode Island? From listening to attendees and attending talks, the focus was on next-generation sequencing applications and their related challenges. Or more simply put, how the heck are we going to manage all this data? It appears this is the dawning of the cloud.

 

The plenary sessions on the first day really set the stage for the meeting and, it seemed to me, put a spotlight on the informatics and analysis issues that scientists are facing right now. Dick McCombie from Cold Spring Harbor Laboratory noted that his sequencing center is now producing about a terabase of genome sequence every month. George Weinstock, associate director of the Genome Institute at Washington University in St. Louis, said that if data output trends continue, in three years the Genome Institute will be churning out 100,000 human genomes per year. He also referred to two large data centers that were built across the street from the institute in the last several years to keep pace with the sequence being generated. Going forward, he said, continuing to add such centers at remarkably high cost will no longer be a solution.

 

Here at DNAnexus, we agree wholeheartedly with that sentiment. Comments like this support our core value of moving the data storage and informatics headaches into the cloud so that biologists can focus on what they actually want to do. We think that whether users are from large genome centers or small institutions, there is significant benefit to putting data in the cloud so people do not have to worry about internal data management resources and challenges.

 

It was also interesting to hear how significantly the balance is shifting between biology and the computational side. According to Weinstock, some 40 percent or 50 percent of the institute staff are informatics or analysis people — a major increase from the norm just a few years ago. In another talk, Vanessa Hayes from the J. Craig Venter Institute said that for every one person they have generating data, they have 10 others engaged in managing and interpreting that data. It’s quite an eye opener when you think back to the days when computational biology was a small add-on to the average wet lab.

 

Hearing about the increasing number of people dealing with data analysis resonates with us; after all, this is why we built the DNAnexus tool to enable collaborations. We think that a community-based approach is important for this field, so we came away from the NGx conference more convinced than ever that our cloud-based solution has a lot to offer people working with DNA sequence data. Feel free to check out our current offering now with a complimentary trial, or sign up at www.dnanexusX.com to receive updates as we prepare to launch our new community-centered platform soon.

At ESHG, Clinical Utility Steals the Spotlight

The annual European Human Genetics Conference, better known as ESHG for its sponsor, the European Society of Human Genetics, just wrapped up and we are still digesting all the great information presented there. Some 2,000 people descended on Nürnberg, Germany, for the meeting, and we were pleased to be among them — both as attendees and as an exhibitor.

As expected, ESHG 2012 drew top-notch speakers presenting really interesting science. A talk from Peter Lichter of the German Cancer Research Center in the opening plenary session on single-cell sequencing for pediatric brain tumors generated discussion throughout the event. A session on prenatal diagnosis was also very crowded, and Stanford’s Hank Greely spoke about the implications of fetal gene screening.

As routine clinical use appears imminent, there was a lot of conversation around whether clinicians and patients are truly ready for this kind of information — as well as the different regulations governing this kind of information from one country to another. Les Biesecker from NHGRI presented the results of a study indicating that patients are in fact prepared for this kind of data, and Alexandra Soulier from Inserm spoke about a study in France showing tremendous hope for the use of next-generation sequencing in the clinic. Soulier noted that the French study targeted young, highly educated respondents, so the positive results might not be representative of the general population.

The conference was the first one I’ve attended that had its very own smartphone app. Attendees seemed to really enjoy using it, but that didn’t mean everyone at the conference was a card-carrying tech expert. In fact, much of the feedback I heard from biologists and clinical researchers was that they are eager to make the most of sequence data, but worry they do not have the bioinformatics expertise or resources to do so. This serves as a good reminder that tools developed for this field will need to be simple to use for non-specialists — that means clear interfaces, less jargon, and an intuitive feel for the process. It was nice validation that ease-of-use, which has long been one of the primary goals here at DNAnexus, will indeed be critical for expanding access to sequence analysis in this field.

 

At Bio-IT World, All Eyes Were on the Cloud and Big Data!

As expected, the 10th annual Bio-IT World Conference & Expo was both exhausting and invigorating. With three jam-packed days of great talks, demos, and networking opportunities, we came away from the meeting eager for a long nap. A huge thank you to all the people who stopped by our booth and engaged us in really interesting conversations! Talking with current and potential users has sent us back to Mountain View with the reinforced knowledge that our product really is making a difference in people’s lives — and making next-gen sequence data easier to manage and analyze for labs that don’t have production-scale compute resources, as well as for IT groups that find themselves juggling a lot of different computing needs. This gives us an even greater sense of urgency in launching our new platform this summer.

One of the most interesting facts about this year’s Bio-IT World conference was a shift in focus in the exhibit hall. In years past, there have always been a lot of vendors showing off servers, cluster improvement tools, chip accelerators, and other hardware offerings. This year, hardware was unusually hard to come by. It seems that the field has tacitly acknowledged that cloud-based data storage is indeed the way to go for the vast majority of genomic labs.

Scientists who spoke at the conference or visited our booth offered further validation of that trend. After years spent trying to figure out how to write scripts that work best on a cluster or with an FPGA, the biologists were relieved to be back where they wanted: focused on the data, not on the compute infrastructure. When talking to attendees in our booth, it was clear that the most pressing thing for this community is getting the right scientific answer, a sentiment that resonates with us.

In a keynote talk, Jill Mesirov from the Broad Institute spoke about the critical need to integrate tools and workflows for analysis and management of large data sets. She introduced GenomeSpace, the Broad’s new platform that combines various tools, including the UCSC genome browser, Cytoscape, GenePattern, Galaxy, and more.

On the commercial side, the emphasis on putting compute infrastructure behind the scenes so that scientists can focus on answers was reinforced by a number of news announcements tied to new cloud-based services from organizations including Illumina, BGI, and others. While the commercial services haven’t officially launched yet, we look forward to trying them out later in the year as they’re released.

Finally, we’re delighted to see that people are already flocking to our new Landing page at dnanexusX.com, which has information on the new DNAnexus platform to be launched this summer. If you haven’t signed up already, we encourage you to do so. This way you will be the first to learn about the capabilities the new platform will support and exact timing of the roll out. It’s simple: just enter your e-mail address and we will keep you posted with ongoing information about our best-in-class security, unified environment for instant collaborations, custom workflows, and more. You’ll also be automatically entered in a monthly drawing for a free iPad in May and June. Sign up early for the best chance of winning! Stay tuned — the winner for the April drawing has been pulled and will be announced shortly on our blog.