tag:blogger.com,1999:blog-36768584.post6974323799873428042..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Has Ion Torrent Taken A 318-Sized Lead over MiSeq?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-36768584.post-37141257344119976912011-09-08T10:18:01.850-04:002011-09-08T10:18:01.850-04:00Sanger got a 1.6 Gb out of their very first Run on...Sanger got a 1.6 Gb out of their very first Run on their spanking new Miseq, just after it was installed, on time and tested, successfully. So using the glitches Hiseq had at launch knowing that nothing out there ever matched its throughput in highly unfair.<br /><br />Furthermore I can't see where LEDs could be a problem. On the contrary, being less aggressive on clusters one can hope the polymerase survives longer and yields reads longer that 150bp. Which would solve once and for all Solexa's "short read" issue.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-18472084367634252692011-04-13T18:22:27.864-04:002011-04-13T18:22:27.864-04:00Ion Torrent is doing a good job of promoting and s...Ion Torrent is doing a good job of promoting and selling the trajectory....but where's the beef? Just because one lab is able to achieve something doesn't mean it should be on the Ion torrent spec sheet.<br />I think IT/Life is following the same path as Solid--they never did meet their specs, and continue to overpromise and underdeliver. Plus the IT is very much like a 454, but uses a PH meter rather than a light for detection. IT and 454 are both bead based technologies, and there are inherent problems with bead based technologies. Solid, too.<br /><br />Wait and see...is the best approach for me. <br />On the LEDs--in real time PCR--they outperformed laser technology consistently in accuracy and sensitivity and are easier to maintain- far better technology in my opinion. If I were to place a bet--<br />I would bet Illumina.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-24166990916206703302011-03-01T12:14:54.826-05:002011-03-01T12:14:54.826-05:00When "IT's confidence they can bring thes...When "IT's confidence they can bring these improvements to market" depends on their receiving $350M, everything they say without data to back it up is suspect. This is the biggest conflict of interest I have seen in the genomics field.<br /><br />The media should be reporting on published data, not treating their crafted press releases as gospel truth. Whether they get the $350M or not, I bet the reports come back to reality when real versus press release data is shown. What ever happened to peer review?<br /><br /><br />"Over the past few years, Life Technologies (LIFE - Analyst Report) has been expanding its product portfolio through acquisitions; the latest being privately held Ion Torrent, a DNA sequencing company, for $375 million in cash and stock. In addition, Life is also liable to pay $350 million if certain milestones are met through 2012."Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-86510818803551315652011-02-25T11:19:38.110-05:002011-02-25T11:19:38.110-05:00I am sorry, but the data quality shown at AGBT was...I am sorry, but the data quality shown at AGBT wasn't that great and same for accuracy. I can certainly agree with you on Illumina but your claim as far as AGBT dataset is pure fiction... In fact I saw one slide that specifically showed a cell below signal specifications (understandable, early adopter). If it was so good, Life would have data files of any simple model organism. I guess I cannot condemn anon marketing input in a blog because it would simply decrease the flow of information, but we are scientists here, data doesn't lie... I am sure PGM will be great, just show us how. I am mature enough to understand why early data is not so great, IT was mostly a technology driven company with little chemistry, now Life will likely change that... Let's stick to facts.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-54182910056796677532011-02-25T07:17:12.184-05:002011-02-25T07:17:12.184-05:00I‘m not convinced by the MiSeq. 'Proven techno...I‘m not convinced by the MiSeq. 'Proven technology': I can see a lot of potential issues by not using a laser, but LEDs. Looking at track records as was mentioned before. Look at 2010 and the HiSeq promises. Many labs are faced now with an expensive (late delivered) machine that doesn't perform as was promised, lots of issues with the flowcells , reproducible runs, reagent delivery, support, not to speak about the poor accuracy compared to other platforms. Even the GA, which is supposed to be the same 'proven' technology has better quality reads: not mentioning the HiSeq's poor data quality over 70bp. Doesn’t look good for the ‘new’ MiSeq… At AGBT the Ion Torrent was seen as a great tool, presented by a number of early access labs. Good quality data, 3 to 4 fold higher output than the specified 10Mb with quite amazing accuracy at such an early stage. The best reason for me to go for the Ion Torrent (PGM) is the fact that it I available now, bearing in mind the delivery times on the HiSeq: Who knows when a (viable) MiSeq would be available? 2012? No contest for me here: Ion Torrent all the way!!!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-16330043448410792982011-02-24T11:59:44.117-05:002011-02-24T11:59:44.117-05:00Your comparison of the daily workflow is a bit dis...Your comparison of the daily workflow is a bit disingenuous. No matter what LIFE says, they will not get ePCR and enrichment under 6 hours (or if they do, their insert lengths will not be longer than ~100bp), nor will it be efficiently automated by a device whose cost is remotely compatible with being an accessory to a $50k PGM. (maybe 10 of them). <br /><br />The comparison here also neglects to really appreciate the cost of having a skilled tech banging through ePCRs CONSTANTLY (and not cross contaminating, etc). LIFE has tried to pull the classic marketing tactic of convincing people that their greatest weakness is actually a strength. Assuming the library prep sides are equal (which again, they're not with Nextera but...), the ePCR vs. drop-library-into-MiSeq is a no-brainer. What else could your frazzled grad student be doing with their time?<br /><br />Also, while I can only guess what it would be, ILMN is certainly not going to be content with "maturing".<br /><br />Time will tell, I suppose, however given the track record of the ePCR workflow vs. cluster generation...my money is on ILMN.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-15814470391501102872011-02-24T05:12:45.980-05:002011-02-24T05:12:45.980-05:00This PGM system will be superceded before it has c...This PGM system will be superceded before it has chance to gain significant market traction in exactly the same way the 454 system was pushed out by Solexa. Poor Jonathan, he will end up with egg on his face.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-8600231360487696452011-02-23T21:06:54.090-05:002011-02-23T21:06:54.090-05:00The current 1.5M well chip gives <100K reads wi...The current 1.5M well chip gives <100K reads with <50% mapping. Why would a 15M well chip be expected to give >1M reads? Have they explained why the current chip performance hasn't increased, they just keep promising more and more wells. If 7% sequence and 3% have quality data, they need a lot more wells to compete with MiSeq and never with a HiSeq.<br /><br />There are a lot of reasons amplicon size is limited, just think back to 454 without the amplification of signal with the enzyme cascade. How many large templates fit on a bead?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-32944295283760392992011-02-23T18:16:37.780-05:002011-02-23T18:16:37.780-05:00The entry price (1 PGM, 1 server) in China is bein...The entry price (1 PGM, 1 server) in China is being quoted at 135K USD, almost twice the US price. Why? They won't explain. Also, it's not clear that their emPCR process is able to accept amplicons of over 100 bp length, or at least that is what their slides are saying. This obviously must be changing, since they are claiming longer read lengths, but my lab wants to use amplicons of 707bp length (we only need a few hundred to be read, but that's our amplicon). Will that be possible? Not clear at all.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-67794445832467155282011-02-23T16:37:12.053-05:002011-02-23T16:37:12.053-05:00I am never surprised about the implication that Il...I am never surprised about the implication that Illumina has reached its peak and now some new technology is going to take over. As a researcher it comes across as a marketing tactic rather than a scientific truth. All one had to do was attend AGBT to see the real truth on the Ion Torrent and that was there wasn't much to see. Their claims are based on their internal data and not coming from the researchers.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-56484578406932392092011-02-23T15:19:10.375-05:002011-02-23T15:19:10.375-05:00I have to agree with Rick, a killer move would be ...I have to agree with Rick, a killer move would be to announce the chip well before it is anticipated and deliver it the following week. I still like he PGM approach, the issue however is that Life Tech has had a dreadful track record at execution (you may argue not so much with Solid but reading all the single molecule PR is truly scary). Also, multiple sample work and quick turn around is definitely an important need out there. A lot of behemoth centers might just get in trouble by massive approaches, yet the simple chemistry approach on the PGM doesn't give a lot of room for MID usage right now... So there are still challenges, I'm all for PGM because I think this is how next gen should truly be, it just needs to be more sophisticated and less corporate mumbo jumbo.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-7234476412774852562011-02-23T13:04:56.883-05:002011-02-23T13:04:56.883-05:00Can't say that I am too excited about the 318 ...Can't say that I am too excited about the 318 chip. Oh, the chip itself is fine. But announcing now (Feb) that the chip will be available in 7 months (Sep) and only then for "early access" seems to me to be grasping at straws in order to make the Ion Torrent seem to be useful and productive. So much can change in those 7+ months. Might as well announce the arrival of the iPad3 in September -- vapor is vapor.Rickhttps://www.blogger.com/profile/09945270829932237628noreply@blogger.com