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  • New Tech at AGBT

    I thought it might be useful to collate the bits and pieces about new platforms discussed during AGBT (Those that don't already have a thread), for those of us unlucky enough not to attended. Grabbing the info from various tweets listed at: http://pathogenomics.bham.ac.uk/blog...-day-2-tweets/

    If any one at AGBT could supply additional information from the talks, that'd be appreciated or any links to blogs covering the tech.

    GnuBIO

    Read Length: 1000bp
    Accuray: Phred 70+
    Holopolymers: Phred 70+ to 9bp
    Sample Prep: < 1min

    System is rackable, ~30lbs, Dry Instrument fludics in cartridge. Beta Mid-2012, commercial end of 2012? Real time Variant calling, each base queried 6 times.

    Source:



    Technique/Chemistry: ?
    Website: http://gnubio.com/

    LaserGen

    Raw base accuracy 99.8%
    100bp reads
    ~$99K for instrument?
    $1K per run?

    Technique/Chemistry:?
    Website: http://lasergen.com/

    So what do people think, do they sound interesting or is it all irrelevant and they'll be buried under ONTs upcoming announcement?

  • #2
    Originally posted by aeonsim View Post

    So what do people think, do they sound interesting or is it all irrelevant and they'll be buried under ONTs upcoming announcement?
    Buried.


    Comment


    • #3
      I agree with "buried".
      All equipment purchases are going to be re-thought in light of ONT...

      Comment


      • #4
        Even with 4% error rates? Will they deliver in improving that? That's not acceptable for clinical use. It may be very useful for a lot of other stuff.

        Comment


        • #5
          Originally posted by GW_OK View Post
          I agree with "buried".
          All equipment purchases are going to be re-thought in light of ONT...
          ILMN and LIFE are selling off today...I wonder why?

          Comment


          • #6
            Originally posted by Geneus View Post
            ILMN and LIFE are selling off today...I wonder why?
            So, doesn't Illumina have stakes in ONT?

            Comment


            • #7
              Originally posted by larissa View Post
              So, doesn't Illumina have stakes in ONT?
              Yes...an investment. But apparently they (ILMN) will not get access to these two new platforms from Oxford. Too bad for them.

              Comment


              • #8
                No way Illumina will take this lying down. I'll bet we'll hear major announcements from them. They have a track record of coming from behind and taking over, let's see if they still have the hunger to do it. I only see this as the field opening up to truly next generation technologies.

                Comment


                • #9
                  They better do something with Roche coming after them.

                  Comment


                  • #10
                    Originally posted by larissa View Post
                    They better do something with Roche coming after them.
                    Maybe Roche will drop their pursuit of ILMN and go after ONT...now that would be BIG news.

                    Comment


                    • #11
                      Yes it does look like they maybe buried now. Unless they can find something that carves them out a niche in the market that nanopores can't currently target. I see the odd comment suggesting that the laser Gen chemistry might be compatible with illuminas tech if it's an improvement to there chemical it could end up being purchased.

                      I wonder if illumina will announce a 1.2tb a run upgrade for the Hiseq and compete on data volume and higher accuracy.

                      Comment


                      • #12
                        Originally posted by larissa View Post
                        Even with 4% error rates? Will they deliver in improving that? That's not acceptable for clinical use. It may be very useful for a lot of other stuff.
                        If this is a raw per-molecule error (as I assume with a "single molecule" technology), then I consider it acceptable. Illumina and SOLiD technologies use hundreds of identical sequencing reactions per cluster to generate a consensus read, and it's unlikely they would have the same accuracy with single molecules per cluster.

                        It has been mentioned that the errors are almost entirely deletion errors. It would be possible to sequence more molecules and do a fairly simple alignment process on the sequences to identify deletions and get a consensus.

                        Assuming the error is random enough (bearing in mind the press releases suggest there is some bias), multiple sequencing experiments should increase the chance of a reliable read fairly quickly. With two strands sequenced (e.g. forward and reverse) and completely random error, you double the Q value (i.e. from ~Q14 / p = 0.04 to ~Q28 / p = 0.0016). The bias would increase the chance of two strands having an error at the same location, which would probably mean there'll be some tricky regions that still can't be sequenced accurately, regardless of how many times it is done in parallel.

                        Bear in mind that tricky regions are already accepted as a fact of life with previous sequencing technology. In particular, very long highly repetitive regions, or regions that are hypervariable within individuals are a problem with current technology.

                        Comment


                        • #13
                          Originally posted by gringer View Post
                          If this is a raw per-molecule error (as I assume with a "single molecule" technology), then I consider it acceptable. Illumina and SOLiD technologies use hundreds of identical sequencing reactions per cluster to generate a consensus read, and it's unlikely they would have the same accuracy with single molecules per cluster.

                          It has been mentioned that the errors are almost entirely deletion errors. It would be possible to sequence more molecules and do a fairly simple alignment process on the sequences to identify deletions and get a consensus.

                          Assuming the error is random enough (bearing in mind the press releases suggest there is some bias), multiple sequencing experiments should increase the chance of a reliable read fairly quickly. With two strands sequenced (e.g. forward and reverse) and completely random error, you double the Q value (i.e. from ~Q14 / p = 0.04 to ~Q28 / p = 0.0016). The bias would increase the chance of two strands having an error at the same location, which would probably mean there'll be some tricky regions that still can't be sequenced accurately, regardless of how many times it is done in parallel.

                          Bear in mind that tricky regions are already accepted as a fact of life with previous sequencing technology. In particular, very long highly repetitive regions, or regions that are hypervariable within individuals are a problem with current technology.

                          Excellent synopsis...thank you.

                          Comment


                          • #14
                            I too agree the error is acceptable, IF, it is indeed the typical error they see and not a 'best case' presented for effect and advertisement. I am suspicious of resolving 64 levels (3 base read) electronically considering how small the differences will be. I don't completely buy the algorithmic deconvolution either, especially if they are still using a polymerase. If it is a non-stochasitic transport, a Viterbi/HMM algorithm might give 94% accuracy.

                            The bigger unknown is the true, customer usability of their pores. I would assume they are Poisson loading the pores before they ship to users. How many pores are still active after an hour of use? I know the bilayers can be made stable and inert, I can accept the error profile can be made length independent (especially if they tether the motor to the pore, else Brownian motion of long DNA can act to pull the complex off, even against the electric field), but how many pores are sequening at a given time and how does that number drop off over time?

                            There is plenty of smoke and mirrors happening, but to give credit where it is due, kudos to them for enabling, even a semblance of, a product around nanopores, and for a dignified and sombre presence.
                            Last edited by nxgsqq; 02-18-2012, 01:15 PM.

                            Comment


                            • #15
                              My understanding is that it's not a polymerase, they are calling it a "special progressive enzyme".

                              Comment

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