Originally posted by BBoy
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Any hints as to whether there might be an upgrade to the HiSeq 1000 to provide the sorts of improvements seen in the 2500?
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Originally posted by scbaker View PostOk, so this isn't a LOT of new info, but here's something from the latest William Blair report (https://www.rdocs.com/GetRDocNoLogin...40&zID=34808):
"Although not too much detail was provided, we get the idea that
one chemistry features a fast cycle time (10 seconds per cycle) and long read length, while the other chemistry, code
named “Chemistry B,” features single molecular sequencing, which, according to Mr. Flatley, has high accuracy rate
and low cost, and could become a backbone of a low‐cost machine."
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Chemistry B
Originally posted by GW_OK View PostGood points.
Whatever Chemistry B is, semiconductor or no, I hope we see more of it soon.
"Although not too much detail was provided, we get the idea that
one chemistry features a fast cycle time (10 seconds per cycle) and long read length, while the other chemistry, code
named “Chemistry B,” features single molecular sequencing, which, according to Mr. Flatley, has high accuracy rate
and low cost, and could become a backbone of a low‐cost machine."
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Just heard from our rep. Another interesting tidbit is no more need for a c-bot. Cluster generation is done on the system a la the miSeq with the 2500.
If you were thinking of buying a 2000 plus a c-bot, a 2500 looks like a pretty good deal with a $50k price differential.
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Good points.
Whatever Chemistry B is, semiconductor or no, I hope we see more of it soon.
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There is a big gap between doing "cool" science and ultimately fabricating a viable instrument that can survive rigors of use in less than perfect conditions.
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Originally posted by GW_OK View PostIllumina's optioned whatever Oxford Nanopore can come up with. Oxford Nanopore has licensed stuff that Golovchenko and Lieber have come up with. Lieber has recently published an interesting paper on nanopore sequencing in Nature Nanotechnology.
I think things might be further along than people imagine.
As the same semiconductor geek I hope I am wrong, this would be exciting stuff if I am wrong. I read on some blog that there is an expectation that Oxford will soon come out with a statement that they have been able to sequence a genome. We shall know soon enough, exciting times for us gearheads.
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Originally posted by BBoy View PostYeah, this is what I am interested in too, don't have a pro subscription to Genomeweb and they seem to be the only ones that have commented on the SMS thing.
...
Illumina's SMS strategy is probably closely linked to whatever progress Oxford Nanopore is making, Illumina is an investor there.
I think things might be further along than people imagine.
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So what is the latest per genome reagent cost for this new HiSeq 2500 machine?? Finally sub $1000??
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Originally posted by westerman View PostI don't think that there will be much more in reagent costs on a per-run basis. On the other hand perhaps the machines would be run more frequently. Most of our runs are multiple-sample projects. We often have 6 PIs spread across the lanes all with multiple samples. This can be hard because all of the sample arrivals and sample prep need to be in, more-or-less, in lock step. If some samples don't arrive or don't pass QC then the entire run get puts on hold. Or we eat the costs and do a partial run. On the other hand if we could just do a 120 GB at the same cost and with shorter turn around then we would put fewer samples in the run thus having fewer problems.
The SOLID 5500 allows for partial running -- the flowcell can be partially used and then wait around for the next batch of work to be prepared. That flexibility with a high-end machine is very nice.
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Originally posted by scbaker View PostI've not heard anyone else talk about "chemistry B" or single molecule sequencing from ILMN. Can you share more?
GW_OK, I seriously doubt this is related to the article you linked to. Much of the work at Harvard (Gene Golovchenko?) historically has been around sensing with tunneling currents. The translocation speed of DNA through the pore needs to be slowed down substantially to have a hope of single-base detection. This can probably achieved with appropriate biasing. Even then the vertical extent of solid state nanopores that can be fabricated in mass quantities with practical means today is such that stray fields above/below the nanopore average over as much as 10 bases, which makes it hopeless to deconvolute the original signal. The envisioned workaround is to use nanoelectrodes with nearly atomically sharp tips. However, this makes them susceptible to the spatial orientation of the DNA as it translocates. Furthermore the currents that the electrodes need to sustain are such that they are destroyed in relatively short times. None of this is to say that at some point in the future this technology will not become viable, but at the present time it is far away from commercialization, I belelive.
Illumina's SMS strategy is probably closely linked to whatever progress Oxford Nanopore is making, Illumina is an investor there.
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Originally posted by ECO View Post+1 krobison.
I will be very interested to see the per base pricing on the "Turbo" mode versus the "standard" longer run times. Clearly ILMN needs to get people stuffing more reagents into these big boxes...10-25 runs per year (as probably happens with most HiSeqs now) can't support a high growth business.
The SOLID 5500 allows for partial running -- the flowcell can be partially used and then wait around for the next batch of work to be prepared. That flexibility with a high-end machine is very nice.
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Chemistry B?
Originally posted by GW_OK View PostFor those of you who haven't been monitoring the latest thread over in the Ion Torrent forum. From Twitter:
Illumina announces #HiSeq 2500: able to seq entire genome or 20 exomes in 24h. #JPM12 #GenomeInADay
Illumina introduces #MiSeq enhanced performance w/ 3-fold throughput increase (7 Gb), faster cycles & 250 bp PE reads. #JPM12
How exciting!
Edit:
@illumina is working on new chemistry. "chemistry B" which is their stab at single molecule detection. #JPM12
I wonder if this has something to do with this:
http://news.harvard.edu/gazette/stor...ilding-blocks/
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