[BBoy]

Illumina'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 a semiconductor geek I am willing to bet a good dinner that this is NOT what Oxford is looking to commercialize . The effect is interesting science, but combining silicon nanowire FETs with synthethic nanopores is well beyond the capability of even leading edge companies today with a commercially viable process. Heck, each one of these two critical ingredients by itself is out of reach for anything resembling mass production at the dimensions required for single-base resolution. I am also familiar with Lieber's body of work over the years, sometimes I kid that he has yet to see a nanowire or a nanotube he does not like. He typically publishes a few papers that utilize the high surface/volume ratio, then moves on to the next nanowire du jour. It is good science, but is invariably too far out from a technological perspective.

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.

[GenoMax]

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.

[GW_OK]

Good points.
Whatever Chemistry B is, semiconductor or no, I hope we see more of it soon.

[winegard]

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.

[scbaker]

Chemistry B

Good points.
Whatever Chemistry B is, semiconductor or no, I hope we see more of it soon.

Ok, 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."

[BBoy]

Ok, 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."

How the heck does one do SMS with their current hardware geometry just by switching chemistry? Something does not add up.

[ymc]

The throughput of HiSeq 2500 is double that of HiSeq 2000 because it can do 600Gb in 5.5 days as oppose to 11 days??

The only pluses are turbo mode and no need for cBot?

[simonandrews]

Any hints as to whether there might be an upgrade to the HiSeq 1000 to provide the sorts of improvements seen in the 2500?

[GW_OK]

How the heck does one do SMS with their current hardware geometry just by switching chemistry? Something does not add up.

I rather think it's a code name for something completely different.

[GW_OK]

Here's the (audio) recording of the JP Morgan presentation, some interesting things in there:
-Switching to Epicenter generated enzymes in the Illumina kits (I wonder where they got them previously, NEB?)
-GA going away soon
-Cheaper exome enrichment ($49?!)
-HS2000's shipped prior to mid 2011 might have lower performance levels when upgraded to 2500 than those shipped afterwords (!!?)
-2x300 PE runs on a miseq internally at Illumina
-at least 2x increase in cluster density in the next few years
-Chemistry B is SMS, but is different from the 10 second cycle time methodology (which I guess isn't SMS?)

http://jpmorgan.metameetings.com/webcasts/healthcare12/directlink.php?ticker=ILMN

[ymc]

Any hints as to whether there might be an upgrade to the HiSeq 1000 to provide the sorts of improvements seen in the 2500?

They have a product code to upgrade to HiSeq 2000. I think it is likely they will have another code to upgrade from 1000 to 2500. If not, then upgrade to 2000 and then 2500

[GenoMax]

Simon,

Apparently there are different "hardware revisions" of HiSeq2000. I heard that not all of them will behave the same after "upgrade" to 2500. Some of the early HiSeq2000 are supposed to take longer than 27h for the "turbo" mode. Anyone else has heard this?

Illumina would ultimately have to decide if it would be profitable to sell an upgrade such as the one you describe below, if it was technically feasible.

Any hints as to whether there might be an upgrade to the HiSeq 1000 to provide the sorts of improvements seen in the 2500?

[simonandrews]

They have a product code to upgrade to HiSeq 2000. I think it is likely they will have another code to upgrade from 1000 to 2500. If not, then upgrade to 2000 and then 2500

The 1000 only has a single flowcell rather than the 2 flowcells in the 2000. There won't be an in place upgrade between the 1000 and the 2000, but it might be possible to do an equivalent upgrade to get the faster turn round on the 1000.

I'm asking because we're about to buy a 1000 and I'd like to not get something which is immediately outdated!

[kmcarr]

The 1000 only has a single flowcell rather than the 2 flowcells in the 2000. There won't be an in place upgrade between the 1000 and the 2000, but it might be possible to do an equivalent upgrade to get the faster turn round on the 1000.

I'm asking because we're about to buy a 1000 and I'd like to not get something which is immediately outdated!

I thought that there was always an upgrade path available from the 1000 => 2000, basically adding the second stage and necessary fluidics. If true then I could certainly envision an upgrade bundle like 1000 => 2000 => 2500.

[simonandrews]

I thought that there was always an upgrade path available from the 1000 => 2000, basically adding the second stage and necessary fluidics. If true then I could certainly envision an upgrade bundle like 1000 => 2000 => 2500.

You're absolutely right! I hadn't realised you could do an in place upgrade from 1000 to 2000. So I wonder if you can apply the 2000 to 2500 upgrade directly on a 1000