AGBT in Review: Highlights and High Hopes for Data

Last week’s Advances in Genome Biology and Technology (AGBT) meeting was every bit the fast-paced roller coaster ride we were anticipating. As expected, there were no major leaps announced by the established vendors, although Illumina, Life Tech’s Ion Torrent, and Pacific Biosciences all had a big presence at the conference.

View from my hotel room: I got lucky with an ocean front room

The biggest splash by far came from Oxford Nanopore Technologies, which emerged from stealth mode with a talk from Chief Technology Officer Clive Brown. The company’s technology sequences DNA by detecting electrical current as the strand moves through a nanopore. Brown said the technology had been used successfully to sequence the phi X genome (a single 10 KB read got the sense and antisense strands) and the lambda genome (a 48 KB genome also covered in a single pass). Brown reported raw read error rate of 4 percent, mostly caused by the DNA strand oscillating in the nanopore instead of moving smoothly through it. Other significant features: the nanopore can read RNA directly, detect methylation status, and be used directly from a sample (such as blood) – no prep required.

What I thought was most interesting, though, was that at a meeting known for being wall-to-wall sequencing technology, this year’s event really focused more on two arenas: clinical genomics and data analysis. The conference kicked off with a session on clinical translation of genomics, with speakers including Lynn Jorde from the University of Utah and Heidi Rehm from Harvard. Both talked about the key challenges in data analysis and interpretation, with Rehm in particular stressing the need for a broadly accessible data platform with clinical-grade information that could be ranked with confidence level and would pull data together from a variety of disparate sources. Notably, the clinical talks generally were limited by small sample sizes, and sometimes wound up with results that were inconclusive in recommending a particular course of treatment. That’s to be expected in the early stages of moving sequence data into a clinical environment, of course, but it also underscores the opportunities here once low-cost sequencing becomes widely available.

The trend was clear: data, data, data. And the only way to make the most of all that data will be to pave the way to an environment where information can be accessed and shared easily, with as many tools as possible to interrogate, analyze, and validate it.

Load Up on Caffeine … AGBT Is Almost Here

View from the Marcos Island Marriott, the AGBT venue

We’re gearing up for the Super Bowl of the next-gen sequencing field – the Advances in Genome Biology and Technology (AGBT) meeting held annually in Marco Island, Fla. In a typical year, there would be major announcements from the established sequencing vendors at this event, but given that Life Technologies and Illumina already went public with their big news at JP Morgan, and the Roche bid for Illumina will likely still be playing out, the big stories from this year’s meeting will probably revolve around major research findings, technology applications, and what’s going on with the sequencing upstarts. (Oxford Nanopore, for example, will be announcing plans to commercialize its instrument later this year and providing attendees a sneak peek. GnuBio will also be presenting on its desktop sequencer, the iGnuIT 1000.)

As usual, this year’s agenda is chock full of thought-provoking presentations, including a talk by DNAnexus co-founder Arend Sidow, who will be presenting on the use of deep whole-genome sequencing to monitor breast cancer progression (Thursday, Feb. 16, at 4:35pm).

We’ll be there to meet with colleagues, customers, and potential collaborators. We’ll also be presenting two posters on current DNAnexus projects. If you’ll be there, we encourage you to stop by — find out more about us, get a demo, have some wine and cheese, you name it. Here’s a quick preview of what we’ll be showcasing:

  • Candidate Gene Variants in “Micronesian” Autosomal Recessive Aplastic Anemia – Brigitte Ganter, Majed Dasouki, S. Abhyankar, M. Furness, R. Calado
    This work was done with collaborators at the University of Kansas Medical Center and National Heart, Lung, and Blood Institute (NHLBI). In the project, researchers performed exome sequence and nucleotide-level variation analyses for two siblings with aplastic anemia, a condition where bone marrow does not produce sufficient new cells to replenish blood cells. The results led to the identification of 12 candidate homozygous variants in 9 different genes. In this poster, we’ll discuss how DNAnexus was used to identify these variants and characterize their potential role in aplastic anemia.
  • Expanding and Enhancing Access to the Sequence Read Archive (SRA) Through a Complementary New Web-Based Mirror – Brigitte Ganter, Evan Worley, Bing Xia, Andreas Sundquist
    As we announced last October, we teamed up with Google to develop a complementary hosted mirror of NCBI’s Sequence Read Archive (SRA). Through a typical user scenario, we will discuss the underlying data processing pipeline, key features of the new web-based interface and how researchers can use it to quickly identify and browse datasets of interest, link-out to PubMed references, and integrate data into follow-on analysis workflows.

Sequence Data: The View from JP Morgan

Last week, Andrew Lee, Vice President of Strategic Operations, and I attended the JP Morgan Healthcare Conference, an annual investor conference here in San Francisco that brings some 25,000 people to the city. The big news this year came from Life Technologies and Illumina, which both announced platforms that will be capable of sequencing an entire human genome in a day. Life Tech in particular noted that its same-day genome sequence will cost $1,000 in reagents — effectively putting an end to a race that began 10 years ago, when scientists first started seriously competing to achieve the $1,000 genome.

With this price point achieved, we expect people to sequence genomes at a much faster clip than ever before. Indeed, a survey from GenomeWeb and Mizuho Securities found that scientists anticipate that sequencing data will increase 32 percent this year over 2011, and increase another 38 percent next year compared to this year. That’s exciting on the data analysis front: As the volume of DNA data grows exponentially, it’s even more important to have a scalable platform to manage, store, and analyze that data securely and efficiently. The GenomeWeb/Mizuho survey also found that people expect to spend more on informatics in 2012 than they did in 2011.

After all, mainstream genome sequencing won’t be possible until the analysis costs come down by orders of magnitude. Even with so much attention on cutting the price tag for sequencing technologies, that didn’t translate to matching improvements for data costs. The race to the $1,000 genome may be over, but as it turns out, that was just the first leg of a relay. Now the baton has been passed to the data management and analysis folks, and it’s our turn to run as fast as we can.