[simonandrews]

So you're saying there will be a 1 flowcell version of the 2500?

I don't know if this will be sold as a separate product, but we've been told that we can apply the 2000 > 2500 update to the 1000 we're about to get and that this is a supported upgrade path. I guess they're all based on the same platform so it makes sense.

[kmcarr]

To answer my own question, there is indeed an upgrade from a 1000 to a 1500 available.

So you're saying there will be a 1 flowcell version of the 2500?

[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?

To answer my own question, there is indeed an upgrade from a 1000 to a 1500 available.

[simonandrews]

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.

The on-flowcell cluster generation only works for the 2-lane flowcell. You still need a cbot to prepare a full run.

[epistatic]

I also just learned Illumina pricing will increase 8-10% March 1. The need for speed would be good for small pilot projects people bring us at the last minute for grant applications but I'm not sure the quicker turn around time will justify making back $50K for the upgrade. Most people need weeks to months to analyze their exome and genome data.

[ScottC]

I doubt they discount a 2-lane flow cell to be equivalent to 1/4 price of the current flow cells.

No, they won't. Illumina has already said that the cost per base will be higher for the lower-yield instrument runs.

Scott.

[simonandrews]

I doubt they discount a 2-lane flow cell to be equivalent to 1/4 price of the current flow cells.

The cynic in me wonders what the QC failure rate for new flowcells is, and whether they're selling on some of the partial failures as 2 lane flowcells

From my point of view, if that's what the upgrade actually is I'm not too worried about missing it. Now if they could offer the ability to run arbitrary numbers of lanes on any flowcell so we could use partial flowcells routinely and come back later to use up the lanes we didn't use the first time, then I'm really interested, but just having a 2 lane flowcell isn't quite as exciting.

[epistatic]

The upgrade isn't as exciting as it first appeared but could be useful. I'm still figuring out if worth $50K to upgrade to make our HiSeqs fit in between our MiSeq and HiSeq. Run time of a MiSeq with the per lane output of a HiSeq.

HiSeq 2500
Speed is due to the ability to run a flow cell with only two lanes. The quick runs are due to the lack of needing to image the whole flow cell and improvements to imaging (?). With a flow cell that only has two lanes, I can see the price per lane need to increase slightly versus running all eight on the standard HiSeq. The SBS usage will scale, but I doubt they discount a 2-lane flow cell to be equivalent to 1/4 price of the current flow cells.

With Illumina's HiSeq specs combining the two flow cell positions, it appears the 120 Gb comes from running two two-lane flow cells with 60 Gb each. With PE-100, that is ~150M reads *2 per lane (less than we get now). If the 120 Gb comes from a single two-lane flow cell with ~300M reads * 2 and could run in 27 hours, that would be something.

[GenoMax]

Perhaps you can get a HiSeq2000 now (instead of the 1000 if it has not shipped) then do the 2500 upgrade after the middle of year. That may be a conservative option (if your budget permits this).

[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

[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]

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!

[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?

[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

[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