Genetic Future

I’ll be spending the next few days at the Biology of Genomes meeting at Cold Spring Harbor, NY – one of the most awaited events on the genomics calendar. I plan to blog here about the major themes emerging from the meeting; you can also follow me on Twitter if you want shorter, punchier updates, and I’ve set up a FriendFeed group for more complex topics.

The meeting kicked off last night with a session on cancer genomics that gave a sense of the serious amounts of data currently being generated on the genetic origins of tumour development. Most of the work in this area has a fairly homogeneous flavour: researchers take tumour and normal tissue from the same individual, then sequence either the whole genome or a substantial fraction of it and look for differences in the cancer genome not present in normal tissue. Such differences (termed somatic mutations) reflect genetic changes that have occurred during the evolution of cancer in that patient.
However only some of those changes will actually be causative mutations (i.e. actually responsible for the progression of orderly human tissue into the sprawling cellular anarchy of cancer), while others will simply be side-effects of the increasingly unstable genetic architecture of cancer cells. Distinguishing these two categories of mutations – called drivers and passengers  - will require sequencing very large numbers of cancer samples to identify those changes that occur multiple times in independent patients.
The ideal experimental strategy, then, is to sequence the entire tumour and normal genome for thousands of individual patients. That’s a daunting task, but advances in DNA sequencing technology are making it feasible to consider projects of this scale.
Last night we got a sense of the findings emerging from large-scale analyses of cancer genomes.


Mike Stratton from the Sanger Institute presented an overview of structural variants (large insertions, deletions, and other rearrangements of DNA) present in 24 cancer samples – the sheer number and diversity of the observed changes was overwhelming. Other speakers (e.g. Elaine Mardis from Washington University) presented high-resolution snapshots of individual cancer genomes generated from whole genome sequencing, giving a sense of the challenges involved in identifying and validating the variants involved. Some of the patterns emerging from these studies were hinted at by previous small-scale studies, but our new-found ability to explore diversity over entire genomes is allowing researchers to identify completely unexpected findings.
The overall picture was pretty clear: large-scale DNA sequencing is already transforming our understanding of the genetic architecture of cancer, but we are still at the very beginning of this process. 

Comments

  1. #1 Misha
    May 8, 2009

    Daniel:

    I’d love to know what you thought of the CSHL ELSI panel on privacy.

    best,
    m

  2. #2 Daniel MacArthur
    May 8, 2009

    Hey Misha,

    I’m ashamed to say I didn’t go – I unfortunately had another meeting scheduled at the same time, and science won over ethics!

  3. #3 Misha
    May 11, 2009

    Ach, isn’t that always the case…:-)

  4. #4 Dana Waring
    May 12, 2009

    Hey! I am listening to this! :) I am looking forward to what comes together ElSI-wise for the CSHL Personal Genomes mtg this fall. Daniel, are you going to that meeting as well?

    And thanks for this recap – really fascinating stuff.

  5. #5 Daniel MacArthurck
    May 19, 2009

    Hey Dana,

    Sorry, I missed your comment somehow – no, unfortunately I won’t be able to make the Personal Genomes meeting. You can imagine how much I wish I could. :-(

  6. #6 Paul Gardner
    June 3, 2009

    I tried posting this over at sciencemag blog, but they kept telling me my text was wrong.

    Why are CSHL kowtowing to a subscription-based media outlet?

    I’m sure GenomeWeb would love scientists to stop blogging. They’re a subscription based news service that is quite happy to pull their stories from open access pubs and blogs which they are then selling to their subscribers. It’s a great business model for them.

    Restricting information seems to be a wrong-headed approach to me. However, it would certainly be polite and politic for bloggers to ask before posting information on a researcher’s unpublished results.

  7. #7 Daniel MacArthur
    June 3, 2009

    Hi Paul,

    CSHL isn’t really kowtowing to GenomeWeb as far as I can tell – GW has alerted them to a potential violation of their policy protecting presenters from having their work discussed publicly, and CSHL is acting to close the loophole.

    I don’t think there’s any evidence that GW wants scientists to stop blogging. Quite the contrary, in fact – GW’s Daily Scan sends a lot of traffic my way; and in general I think GW doesn’t see their longer, sourced articles as being in competition with the generally brief, unsourced posts from bloggers (and I would tend to agree with them on this).

    Finally, CSHL’s new policy doesn’t seem to restrict blogging beyond asking bloggers to seek permission before writing about presented work. This is fair in the context of CSHL’s overall policy towards reporting of presentations, and I will certainly be doing this for future meetings.

  8. #8 Daniel MacArthur
    June 3, 2009

    Oh, and commenting on the Science blog seems to be completely broken – I got the same error message. Very odd…

  9. #9 Cold Spring Harbor
    December 14, 2009

    There were many helpful discoveries, in medical field or biology coming from Cold Spring Harbor lab. It’s time to start appreciating and rewarding their work.

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