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  • #31
    Originally posted by pmiguel View Post
    The other major claim is that no library construction (or even DNA purification) is required. That would immediately put these devices in their own league. That makes HiSeqs and Torrents niche instruments.

    ....

    --
    Phillip
    I think ECO can probably comment on this better. All I know is once you go to single molecule world, any impurity can kill the sequencing mechanism / basecalling accuracy easily. Any "single molecule" impurities including any ion that one does not anticipate during engineering phase is the enemy, so, good luck for the "no sample preparation" claim. (Not saying it can not be simple, but sequencing DNA in blood with zero sample-prep to get high throughput results? one can judge that with common sense...)

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    • #32
      The grand scheme of things of for-profit sector is targeted resequencing for diagnostic. The only thing ONT are proposing that could be useful to them is the no sample prep at all. And I am having a hard time believing that.

      While a $100 disposable cartridge would be nice too, especially to forensic and DTC providers, a Q14 isn't useful for any of them.

      I agree with other people prediction that ONT will be the next PacBio. It's noble to claim that they will delay their launch until they get Q30, but they need investors, and the current ones will eventually want to cash in. PacBio was able to hype and overhype for 5 years. How much longer is it going to be for ONT?

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      • #33
        Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.
        Last edited by seqnextgen; 11-16-2012, 09:11 PM.

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        • #34
          Originally posted by seqnextgen View Post
          Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.
          Well said...

          Comment


          • #35
            Originally posted by TonyBrooks View Post
            The problem is that scaffold runs for de novo are so niche in the grand scheme of things.
            Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

            I wonder what updates will come out next week at AGBT...
            Paul Krzyzanowski
            Blog: www.checkmatescientist.net

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            • #36
              Originally posted by paulk View Post
              Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

              I wonder what updates will come out next week at AGBT...
              AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar

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              • #37
                Originally posted by seqnextgen View Post
                AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar
                What? You weren't out on the strand digging through sand like a madman?

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                • #38
                  Originally posted by krobison View Post
                  Apparently we have all been asleep at the wheel. The minion has been out for decades, the first model has even made it to a museum:
                  http://core-genomics.blogspot.com/20...announced.html

                  Comment


                  • #39
                    Originally posted by krobison View Post
                    I confess that I did stroll through the beach area around the suites (on my way to my next meeting! I was going through there anyway, honest!) looking for disturbed sand patches.

                    I should have been stalking the bar, apparently.

                    Comment


                    • #40
                      Originally posted by krobison View Post
                      I thought it was a joke originally, obviously, pathogenomics did find a MiniIon in AGBT. This is probably more comprehensive non-update one can find now
                      http://pathogenomics.bham.ac.uk/blog...-at-agbt-2013/

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                      • #41
                        Originally posted by Clive
                        ([url
                        http://pathogenomics.bham.ac.uk/blog/2013/03/a-chat-with-oxford-nanopores-clive-brown-at-agbt-2013[/url])
                        “We didn’t even know that long reads were so important to people until after that AGBT presentation.”
                        Really? I find that hard to believe.
                        Last edited by Jeremy; 03-06-2013, 05:41 PM.

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                        • #42
                          Waaaaaa we made promises we couldn't keep to get attention and funding...and now people expect us to keep them!

                          <tiny violin playing>

                          Seriously though, having been through the bring up of a single molecule sequencer...if the CTO is opining in a bar to a blogger about improving consensus accuracy by throwing in multiple types of pores...they are a LONG way from finalizing a chemistry, let alone stabilizing and commercializing it.

                          Happy to eat words. Actually I love having my pessimism proven wrong.

                          And I hope I'm not off Clive's list. I could do some long range clinical haplotyping pretty easily!

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                          • #43
                            Originally posted by ECO View Post
                            And I hope I'm not off Clive's list.
                            Perhaps not before this post.

                            But now you can't be sure

                            Comment


                            • #44
                              Originally posted by ECO View Post
                              Seriously though, having been through the bring up of a single molecule sequencer...if the CTO is opining in a bar to a blogger about improving consensus accuracy by throwing in multiple types of pores...they are a LONG way from finalizing a chemistry, let alone stabilizing and commercializing it.
                              Just to note I added a clarification from Clive at the bottom of the post on that particular point...

                              Given that they are continuously screening new and better pores and that is in fact one of the cool things about a biological nanopore (just like other sequencing companies regularly screen for new polymerases), I didn't necessarily see that as reflective of where they are in the product development pipeline.

                              Comment


                              • #45
                                Originally posted by nickloman View Post
                                Given that they are continuously screening new and better pores and that is in fact one of the cool things about a biological nanopore (just like other sequencing companies regularly screen for new polymerases), I didn't necessarily see that as reflective of where they are in the product development pipeline.
                                No argument there.

                                We all hope they will stop the screening at some point and release the first product we can use.

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