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  • #16
    Pixels? I didn't think the ion torrent needed pixels?

    Also, it seems like right now they've got a machine equivalent to a single hiseq lane costing slightly less if only reagents are being taken into account. Running quicker, of course. But is it better, faster, cheaper than a Miseq?

    I'm also slightly confused by the genomeweb article, where the Proton won't leave people with a mountain of data like the hiseq? And yet it still produces what should be tons of data?

    Furthermore are read lengths >4-500bp feasible, really?

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    • #17
      Yeah I wouldn't be very happy unboxing a new instrument with a planned obsolescence date of mid-2012.

      Comment


      • #18
        Originally posted by GW_OK View Post
        Also, it seems like right now they've got a machine equivalent to a single hiseq lane costing slightly less if only reagents are being taken into account. Running quicker, of course. But is it better, faster, cheaper than a Miseq?
        Right now they haven't got anything as this is just an announcement... first machines to early access customers mid-2012.

        MiSeq spec as of now is 1.5-2Gb per 27 hours (2x150bp).

        We've extrapolated that Ion is looking at maybe >20 Gb per run (3 hours?) for Proton 1 chip in Q3 2012, and >100Gb per run for Proton 2 Q1 2013. So it promises far greater throughput and faster than the MiSeq.

        Currently MiSeq is cheaper than the Proton but more than the PGM.

        Strongly expect to see Illumina announcements reacting to this!

        Furthermore are read lengths >4-500bp feasible, really?
        We don't really know!

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        • #19
          Originally posted by nickloman View Post
          Strongly expect to see Illumina announcements reacting to this!
          Obviously not a good time for Illumina to inform us that our sequencing prices are going up by 10% then.

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          • #20
            Originally posted by TonyBrooks View Post
            Obviously not a good time for Illumina to inform us that our sequencing prices are going up by 10% then.
            Hmm perhaps not, but Illumina has >90% of the sequencing market right now.

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            • #21
              JP Morgan conference at 9am PST will most likely bring Illumina's response!

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              • #22
                Originally posted by ECO View Post
                JP Morgan conference at 9am PST will most likely bring Illumina's response!
                Yep, I'm following #JPM12 and keen to see what is said! I was kind of expecting platform announcements to be made at AGBT but seems that's too far away for $ILMN and $LIFE.

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                • #23
                  Originally posted by nickloman View Post
                  Right now they haven't got anything as this is just an announcement... first machines to early access customers mid-2012.
                  They've got something or they wouldn't be announcing it. Then again, they did promise quite a bit more than the ion torrent turned out to be.. We'll see what's hype and what isn't.

                  Strongly expect to see Illumina announcements reacting to this!
                  Indeed. Anyone see the latest bit from nanopore in last months Nature Nanotechnology? Looks promising...

                  We don't really know!
                  Then I won't get excited about it....

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                  • #24
                    Woosh, here goes!

                    Illumina announces #HiSeq 2500: able to seq entire genome or 20 exomes in 24h. #JPM12 #GenomeInADay

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                    • #25
                      Man, where can I watch this thing?
                      Also, chemistry? Tech? What's the new sauce?

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                      • #26
                        Originally posted by nickloman View Post
                        BTW I would think the chip is more like 20mm^2 (old chips 9mm^2) and they will be working on near-complete loading.
                        Sorry to be pedantic, but the chip in the image clearly isn't square (measures up using the high tech method of "ruler against screen" with edge ratio of 2x1.6) that aside, back to the sensor size (I won't use "pixels" to describe them again, perhaps they should be called sexels (sensor elements)).

                        Have just been back and reworked (post coffee) some of the sensor dimensions. Using images of sensor cross-section posted previously here, the sensors on the 318 chip are ~4.1um edge-to-edge, with ~3.4 um diameter wells, and ~0.7um well to well spacing.

                        For Proton I, the sensor size (at ~170M per chip) must be ~2um2. Assuming a square sensor (not necessarily a good approximation, but let's go with it for now), the sensor width would be ~1.4um. If the ratio of well width to sensor spacing is preserved relative to the 318 chip, then the well would be ~1.16um wide, and the intersensor spacing would be ~0.25 um.

                        For Proton II, the sensor size (at ~660M per chip) must be ~0.5um2. Assuming a square sensor (still probably not the best approximation...), the sensor width would be ~0.7um. If the ratio of well width to sensor spacing is preserved relative to the 318 chip, then the well would be 0.58um wide, and the intersensor spacing would be 0.125 um.

                        This all assumes that there will be no increase in cross-talk between wells or sensors as the density increases.

                        Even with this best case scenario, the well width on the Proton II will be ~0.6um, which would require the use of 0.2-0.3um diameter beads. Perhaps that isn't so unreasonable?

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                        • #27
                          Originally posted by turnersd View Post
                          Here's the announcement from Illumina about the HiSeq 2500 "genome-in-a-day" machine http://investor.illumina.com/phoenix...757&highlight=
                          We should talk about Illumina stuff in the Illumina forum:
                          http://seqanswers.com/forums/showthread.php?t=16725

                          Comment


                          • #28
                            Originally posted by turnersd View Post
                            Yeah I wouldn't be very happy unboxing a new instrument with a planned obsolescence date of mid-2012.
                            I don't see this as making the PGM obsolete. PGM will come in at a lower price point; with all the accessories the all-in price of a PGM is going to be about 30-40% of the all-in price of the Proton. For a lot of applications, PGM will be sufficient for many researchers.

                            Comment


                            • #29
                              Originally posted by GW_OK View Post
                              We should talk about Illumina stuff in the Illumina forum:
                              http://seqanswers.com/forums/showthread.php?t=16725
                              Thanks, moved them there.

                              Comment


                              • #30
                                Someone just sent me this, claiming it was from their sales rep. Read with caution

                                Hello,
                                Today Life Technologies has announced the Ion Proton Sequencing Platform-the first benchtop sequencing system capable of completely sequencing an human genome for $1000 in one day. Many more details to come through the day but a few details to take note of below:

                                Instrument Price: $149,000 (as a current PGM or SOLiD 5500xl owner you can purchase one for $99,000 through the end of the year)
                                Ancillary Items for Proton (Ion Proton OneTouch and Proton Torrent Server): Pricing not finalized but expected to be $95,000 or less

                                Chips:

                                Ion Proton I chip: 165 million wells, run 2 full exomes per chip for $1000
                                Ion Proton II chip: 660 million wells, run full human genome for $1000 (available towards the end of 2012)
                                Also deep whole transcriptome analysis can be performed using either chip

                                Proton Torrent Server-designed to analyzed a human genome without additional servers in one day providing primary and secondary analysis

                                More details to follow in the next couple of days!

                                Also a number of additional updates to the PGM platform were announced yesterday-please take a look below and let me know if you have any questions! Look to the Ion Community for additional information also.

                                Sequencing chips:

                                318 chip (1Gb) now officially released in 4 and 8 packs. Cost per chip is $500/chip
                                316 chip-cost reduced from $500 to $299/chip. This will reduce your 316 complete run cost by ~ 40%

                                Template prep and sequencing kits:

                                Updated 200bp Template prep kits for both manual and OneTouch applications, sequencing kits with improved accuracy for more throughput. For use with all size chips.
                                Release of Ion-demonstrated protocols for 2 x 100bp paired end sequencing
                                Barcode kits availability increased from 16 to 32. Additional barcode options on Ion Community site up to 96 now available

                                AmpliSeq Updates:

                                Launch of Ion AmpliSeq Designer for custom AmpliSeq Panels in March. Rapid 48hr design turnaround, 2-4 week assay delivery. Up to 1536 targets in a single tube
                                AmpliSeq Comprehensive Cancer Panel-targets over 400 genes involved in tumor formation with 95% of targets at 500X coverage using 318 chip. Early access in Q1, full release in Q2 2012. Detailed gene list on Ion Community
                                AmpliSeq Inherited Disease Gene Panel targeting genes implicated in over 140 inherited diseases (300 genes, 10,000 amplicons) at ~30X coverage using the 316 chip. Early access in Q1, full release in Q2 2012. Detailed gene list on Ion Community
                                Protocols for barcoding of all Ion AmpliSeq custom or fixed panels available. Can do up to 4 Cancer Panel barcoded samples on a 316 chip or 6 normal/tumor pairs on the 318 chip.
                                New website available for designs: www.ampliseq.com

                                Torrent Suite and Software:

                                Version 2.0 includes updates for 318 chip, new unified variant caller to combine germline and AmpliSeq callers. Enhancements to algorithms, basecalling time (30% faster), increased INDEL calling, work with any reference
                                Launch of Torrent Circuit-central repository for download of analysis plug-ins for Torrent Suite from both Ion Torrent developers and Ion Community contributers
                                Early Access Launch of Ion Reporter-secure hosted data analysis using cloud structure. Enables simplified routine data analysis for AmpliSeq projects

                                RNA Seq:
                                Coming soon-white paper and application note describing comparison of RNA Seq on Ion Torrent to microarrays and qPCR
                                RNA How to Guide for application development, protocols, FAQ’s, etc

                                Misc upgrades and enhancements:

                                Announcing New England Biolabs NEBnext Fast Library Construction Kits-2hr protocol (12 min hands on time) for libraries up to 300bp in size
                                Availability of ELGA PURELAB flex water Purification System-simple to set up ultrapure water source and validated with the Ion PGM System

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