• Question: We're told that genome sequencing takes just days/hours now, yet only a few genomes get published. How come they take so long?

    Asked by rebeccanesbit to Vicky, Samantha, Rachael, Matt, Leila, Karolina, Jean-Paul, Haihan, Andrew, Alison on 29 Dec 2013.
    • Photo: Karolina Chocian

      Karolina Chocian answered on 29 Dec 2013:

      Sequencing short bits of DNA is easy now and takes only hours but sequencing a whole genome is a more difficult task. especially if its something completely new and you don’t have anything to compare it to. we actually now have way more than just “a few” genomes. actually somewhere in 4000-ish (googled it). lots of them are bacteria – because they are small and much simpler. we have about 200 eukaryotic genomes sequenced- they are more difficult as they have a lot of “non-coding” DNA (some people used to call it “junk” but that turned out to be very untrue). Anyway, they are repetitive sequences and they are much harder to sequence due to the nature of the techniques used 🙂
      Hope that explains it a bit 🙂

    • Photo: Vicky Forster

      Vicky Forster answered on 29 Dec 2013:

      Hello! Good question, Karolina has most of the points covered, but just to add a little which is relevant particularly to the work I do in cancer research. We do sequence large numbers of cancer patient genomes in order to find particular genes which may for example determine how certain patients respond to chemotherapy drugs, or whether patients are likely to survive the disease. This is very useful information and in the future may allow us to tailor treatments specifically to each patient. However, the reality of whole genome sequencing is that it has only just become affordable enough for us to do large numbers of samples to do these studies. Whole genome sequencing costs between £5000-10000 per sample, so as you can probably appreciate, looking at large numbers of cancer patient genomes is incredibly expensive. A few years ago, it was prohibitively so. So, it’s not so much limited now by time, as you state, but by money and funding. Additionally, scientists will also often have to publish their research before they make their genome sequencing data available globally – so in summary, i would expect a lot more of these genomes to be available over the next few years. If you are interested in finding about more, look up the ‘1000 genomes project’.

    • Photo: Leila Abbas

      Leila Abbas answered on 30 Dec 2013:

      Another reason it takes so long is that although the sequencing itself has become a lot quicker, putting all that sequence data in the right order is still a massive task. Imagine if someone gave you a huge jigsaw puzzle – it might only take a few minutes to get the pieces out of the box, but it could take you days to put it together.

    • Photo: Haihan Tan

      Haihan Tan answered on 30 Dec 2013:

      Like what Leila has mentioned, accurately piecing sequence fragments together, especially for an unknown genome, is one of the biggest bottlenecks right now. Karolina touched on repetitive sequences and the difficulty of getting good sequence data from these – another problem that comes from these is that their repetitive nature makes it doubly difficult to join these together by computer programs.