Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    Hmm so so, I usually keep my glass topped up ;-)

    So Tony what do you disagree with?

    I believe like you that Illumina has continued to execute improvements, borne out by the 1Gb>1Tb per run progression from GA>HiSeq. I haven't seen Roche manage anything similar nor would I expect them to start.

    I would however expect serious management changes, and I dont think that would be good. Initially, say 12-18months, it would be Ok, as Illumina have a lot of stuff in the pipeline that they can dish out when they want to e.g. when there is actually some competition. But as that runs out and the bets people leave...?

    Comment


    • #17
      Originally posted by TonyBrooks View Post
      I would disagree here.
      Dont think we disagree here. Illumina sequencing is awesome, has improved a great deal and is clearly the best choice for most applications right now!

      All that I am saying is that its not 1000$ genome awsome and probably wont be in the forseable future.

      Comment


      • #18
        I'm not saying it's a good thing either. I hope Illumina can remain out of the Roche's reach too.
        It's taken Roche 4 years to go from 500bp to 700bp (and not too robustly if any of the XL posts on here are anything to go by). In the same time frame Illumina have increased their throughput approximately 1000 fold while a the same time driving down the costs.

        Comment


        • #19
          Originally posted by matholomew View Post
          ... IonTorrent/Proton will not compete $/bp with Illumina ... The killer tech that Illumina have is clusters, it scales so much faster and better than emPCR - thats why IonTorrent can't win and will remain for smaller centers.
          Think that this is the point were you are wrong. Clusters are not Illuminas killer tech. Its heir most serious limitation! Scanning billions of clusters is slow and takes expensive optics that are prone to failure.

          Semi conductors are the killer tech here. They are much faster, scalable and so chap that you just trow your chip away after using it. Sure, we are not quite there yet. But you have to consider that Rothberg has kept all of his promises so far, shown us the machine and chips and will be shiping them to ealy access customers this spring. Ion Torrent will make the current illumina tech obsolete.

          Comment


          • #20
            Originally posted by steinmann View Post
            Dont think we disagree here. Illumina sequencing is awesome, has improved a great deal and is clearly the best choice for most applications right now!

            All that I am saying is that its not 1000$ genome awsome and probably wont be in the forseable future.
            For research the $1000 genome is great. For clinical applications, you need to be looking at the $100 genome or maybe even the $10 genome if you have a public health service and are a trillion dollars in debt (like the UK is).

            My experiences working in research is that the cost of sequencing is fine at the moment when using our Illumina machines. I'm not sure how many researchers would want to routinely do whole genomes as the analysis would be a bit challenging.

            About 10-15% of the cost of any project we undertake comprise of sequencing. The remainder are split between staff and sample prep.
            Bottom line: We need cheaper scientists and cheaper library prep kits!

            Comment


            • #21
              Originally posted by steinmann View Post
              Think that this is the point were you are wrong. Clusters are not Illuminas killer tech. Its heir most serious limitation! Scanning billions of clusters is slow and takes expensive optics that are prone to failure.

              Semi conductors are the killer tech here. They are much faster, scalable and so chap that you just trow your chip away after using it. Sure, we are not quite there yet. But you have to consider that Rothberg has kept all of his promises so far, shown us the machine and chips and will be shipping them to ealy access customers this spring. Ion Torrent will make the current illumina tech obsolete.
              Optics: MiSeq & HiSeq2500.
              Improved chemistry and optics, faster sequencing, still cheaper than IonTorrent, cheaper than it will be and better quality values.

              Clusters: I'd rather cluster than emPCR and select, or rely on poison distribution for PacBio.

              I do agree semiconductors are better, but thats not using 454 tech (IonTorrent) it's the nanopores that will take advantage and win with this.

              Re IonTorrent keeping its promises on improvements. Yes true, but that's pretty easy at the moment, they are well within the proven 454 technologies envelope of several years ago! When they get closer to what 454 can do in read lengths etc. NOW then see them slow down.

              Also as chips go from e6 to e8+ picowells the price will get higher per chip. And what happens to the quality values as they drop from 3 field-effect transistors to just 2 or even 1 just to squeeze more in?

              Comment


              • #22
                I also agree with Tony, sample and library prep are killers.
                But here again Illumina have a killer - Nextera since the bought EpiCenter, and it's automatable so lower personnel requirements.

                That leaves informatics, thats still slow, but for diagnostics maybe they have less genome variation to look at and call.

                Comment


                • #23
                  I work at a big medical center and totally agree. The doctors have little genetic training and most can't interpret a simple amplicon test, whole genome or exome no way.

                  The sequencing portion per sample is now the smallest, labor, prep, service contracts, etc. are higher. But to get to fastq is probably the cheapest portion. The highest cost is storage of the data, processing, analysis, and interpretation.

                  Comment


                  • #24
                    Originally posted by steinmann View Post
                    Think that this is the point were you are wrong. Clusters are not Illuminas killer tech. Its heir most serious limitation! Scanning billions of clusters is slow and takes expensive optics that are prone to failure.

                    Semi conductors are the killer tech here. They are much faster, scalable and so chap that you just trow your chip away after using it. Sure, we are not quite there yet. But you have to consider that Rothberg has kept all of his promises so far, shown us the machine and chips and will be shiping them to ealy access customers this spring. Ion Torrent will make the current illumina tech obsolete.
                    Hmm.. what is your opinion on the inefficiency of emPCR and the wells?

                    Note that when they claim something like 11 million wells, only 50% of them will contain all the reagents needed to carry out the reaction. They will have to scale enormously to catch up. Quality scores also don't look so good on the published runs.

                    Let's hope they can improve, otherwise I don't see Ion Torrent catching up.

                    Comment


                    • #25
                      The ion torrent is a 454 with a different sensor, and try as it might it's still going to run into the same problems and still going to be unable to compete with SBS.

                      That being said, I really don't think having a $1k genome is going to be more than a technological milestone. No doctor is going to have somebodies genome sequenced except for some rare congenital syndrome. MAYBE cancer genomics, but still, it's not going to be that widespread.

                      The new big thing in sequencing is going to be clinical sequencing, I think we can all agree on that, but it's going to be custom gene panels or amplicon sequencing. A $1k test followed by a $10k analysis.

                      Getting us back on track, I shall cast in with those who oppose the merger on general principle, having grown up on a 454 before graduating to an Illumina system, and having seen the ponderous nature of the Roche R&D group.


                      Edit:
                      And has anyone seen ILMN's stock price since the announcement, up 44% to $53, Roche is going to have to ante up...
                      Last edited by GW_OK; 01-25-2012, 08:04 AM. Reason: business news

                      Comment


                      • #26
                        I'm not that familiar with Ion, but doesn't the Proton currently only work with human samples? Correct me if I am wrong. While the PGM does not have near the output of the Illumina.

                        While the market for human genome sequencing is without a doubt the largest, keep in mind that there are a lot of other species that are worked on besides humans. I work with plants and for us Ion is not something we even consider when its time to do a next-gen experiment.

                        It seems to me that until Ion becomes a more viable option for other Eukaryotic species besides humans, there will still be a significant market for Illumina.

                        Comment


                        • #27
                          Originally posted by chadn737 View Post
                          I'm not that familiar with Ion, but doesn't the Proton currently only work with human samples? Correct me if I am wrong. While the PGM does not have near the output of the Illumina.
                          That's definitely wrong in that any of the available sequencers will sequence DNA from any organism (even arsenic-life ). But their marketing pitch is human exomes and human WGS, and any added value software might be tailored for those applications, and obviously exome capture kits will be for human samples.

                          Comment


                          • #28
                            Originally posted by nickloman View Post
                            That's definitely wrong in that any of the available sequencers will sequence DNA from any organism (even arsenic-life ). But their marketing pitch is human exomes and human WGS, and any added value software might be tailored for those applications, and obviously exome capture kits will be for human samples.
                            Thanks for the correction. Like I said I am unfamiliar with their technology, our core does not have an Ion.That and the marketing for the Proton has been so biased towards human samples that I can't even really find mention of its use in anything else on their website. This mistakenly led me to believe that the chip was tailored for human sequencing only. I knew the PGM can do any sample, but it has a far lower output.

                            Discount my argument then.
                            Last edited by chadn737; 01-25-2012, 09:16 AM.

                            Comment


                            • #29
                              Originally posted by NGSfan View Post
                              Hmm.. what is your opinion on the inefficiency of emPCR and the wells?
                              One should expect that between 30 and 50 % of the wells provide reads that pass the quality filter.

                              Quality values appear pretty good actually for existing chips. You have to consider that Ion Torrent underestimates Q values, while Illumina overestimate them. Someone from this forum did an independent analysis on this (PGM vs. MiSeq).

                              What will be really interesting to see is how making the wells smaller will affect signal to noise ratio and Q values. Thats really hard to predict.

                              Comment


                              • #30
                                Originally posted by GW_OK View Post
                                The ion torrent is a 454 with a different sensor, and try as it might it's still going to run into the same problems and still going to be unable to compete with SBS.
                                You are not making any sense whatsoever. Both IonTorrent and 454 do sequencing by synthesis (SBS)! The major problems with 454 sequencing are the optics required for detection and limited throughput. The IonTorrent chips were explicitly designed to address these limitation.

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Techniques and Challenges in Conservation Genomics
                                  by seqadmin



                                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                  Avian Conservation
                                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                  03-08-2024, 10:41 AM
                                • seqadmin
                                  The Impact of AI in Genomic Medicine
                                  by seqadmin



                                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                                  02-26-2024, 02:07 PM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 03-14-2024, 06:13 AM
                                0 responses
                                33 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-08-2024, 08:03 AM
                                0 responses
                                72 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-07-2024, 08:13 AM
                                0 responses
                                81 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-06-2024, 09:51 AM
                                0 responses
                                68 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X