Genetic Future

Looking forward to AGBT

i-20703c1cb919bf244a6d0519308e3dde-marco-island-fl.jpgI’ll be at the Advances in Genome Biology and Technology meeting next week – this will be my my first experience of this annual conference on Florida’s picturesque Marco Island, but I already have high expectations based on reports from previous years. The programme is packed with cutting-edge genomics, and to be honest after a few months of Cambridge weather I’m craving even a brief glimpse of blue sky and salt water.

I’ll be giving a talk myself on some fairly preliminary data emerging from work I’ve been doing with the Sequencing R&D team at my new home, the Wellcome Trust Sanger Institute. Briefly, we’ve been looking at ways to use second-generation sequencing technologies to examine a relatively short stretch of DNA in large numbers of individuals simultaneously, by adding tiny, unique DNA barcodes to the fragments from each individual.

My interest in this approach is its ability to generate very rapidly the data required to explore the recent evolutionary history of a particular gene in humans – but it’s a technique that has applications for any group that wants to quickly screen for variation in a targeted region of the genome in a large number of individuals. This has traditionally been a challenging area for second-gen sequencing platforms, for the simple reason that they produce too much data: For a small region of DNA (a few tens of thousands of bases), running a single sample per lane on current systems is simply expensive overkill.

Bar-coding allows us to pool up to 96 samples per lane, making the process cost-effective – although there are still some non-trivial technical obstacles to overcome. The informatic analysis has certainly been a rapid education for me in the challenges of working with high-throughput sequencing data (especially given my very weak background in bioinformatics prior to last year).

The genomics blogosphere will be well-represented at the meeting, with PolITiGenomics’ David Dooling giving a talk on sequencing informatics workflows and MassGenomics’ Dan Koboldt presenting a poster on alignment algorithms for second-gen sequencing platforms, both topics of considerable interest to me as a newbie in the second-gen sequencing arena.

I’m also looking forward to presentations by several of the major competitors in the third-generation sequencing arms race, including Pacific Biosciences and Complete Genomics, who with any luck will provide compelling data to convince me that my prediction about the lack of a $1000 retail human genome sequence this year is completely wrong…

Anyway, assuming I can get a decent internet connection, expect some posts from Florida on the next big things in high-throughput genetics some time next week.

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Comments

  1. #1 Henk
    January 26, 2009

    Looks like a nice place to have your conference!
    As for your talk on barcoding: I thought that the major 2nd gen sequencing companies all already have something like that to offer? At least that was what they were claiming when I talked to them (though maybe not up to 96 samples).

  2. #2 Daniel MacArthur
    January 27, 2009

    Hi Hank,

    Illumina currently offers bar-coding for up to 12 samples per lane, Roche has been offering multiplexing for a long time, and I think SOLiD has a 96-sample indexing system on the way (or maybe already available – I haven’t been following their products closely).

    Our approach offers some advantages over the current Illumina system not only in terms of the number of samples, but also for ease of use and uniformity of coverage. Still, I’m sure all the major platforms will have good commercial multiplexing solutions available at 96-plex or higher pretty soon; we just didn’t want to wait around until that happened before generating data. :-)

  3. #3 Henk
    January 27, 2009

    Ah I see your point! :-)
    I think developing this multiplexing is a very good idea. I see most use of next-gen sequencing in the sequencing of many subjects for 100-1000 genes or maybe exome or something. For this barcoding/multiplexing will prove to be invaluable!

  4. #4 steven
    June 24, 2009

    Hello,

    what did you think of the conference?

  5. #5 Daniel MacArthur
    June 24, 2009

    Great setting, and good science/technology – definitely one I’ll return to next year.

    See my other posts on the conference here, here and here.