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Old 01-12-2010, 06:27 PM   #1
mccullou
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Default Illumina's new sequencer: HiSeq 2000

Wow GAII just came out last year, they just now got the reagents QC under control after their SNAFU and now this. . .

http://www.illumina.com/systems/hiseq_2000.ilmn

How different can this be? It uses the cBot (which I have but there are no reagents to buy yet) so I know the cluster station is more walk away, but is the sequencing chemistry and engineering so much better as to:

"obtain ~30x coverage of two human genomes in a single run for under $10,000 (USD)* per sample." (per their site)

What was the dramatic leap?
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Old 01-12-2010, 07:22 PM   #2
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There are some good blog posts that explain this; start with David Dooling's which gives a lot of details but Dan Vorhaus' & Daniel MacArthur's posts as well as GenomeWeb.

A key bit is two flowcells & 4 cameras. They also officially go to spike-in control rather than burning a lane. Flow cells also have more area. Somehow it all adds up to 1 billion good clusters per run with 2x100 reads per cluster. That doesn't quite add up to 2 x 30X coverage human genomes for me, but perhaps they're rounding up a tad or my roundoff is simply in the other direction..

It actually is spec-ed out at lower cluster density & read length (2x100) than the top centers are getting, so slurping in more data is possible (roughly 1.8X by my quick calculation). Semi-ordered arrays would push that even further -- so a future version kicking out 1-2 human genomes per flowcell (or 2-4 genomes per run) might show up later this year.

Last edited by krobison; 01-12-2010 at 07:25 PM.
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Old 01-12-2010, 11:06 PM   #3
james hadfield
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It also reads the top and bottom of a flow cell, something we thought might be possible. Think about it, we have thrown away half of each run so far!
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Old 01-12-2010, 11:13 PM   #4
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200 gene expression analyses in a single run, looks like arrays are coming closer to oblivion.

And if it does do four times the work of a GA then BGI (buying 128) will have about the same capcity as half of the world!
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Old 01-12-2010, 11:49 PM   #5
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I wonder what this means for those of us running GAIIs. Will future chemistry / pipeline improvements be backported to the older platform or is this going to be the sole focus for new development.
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Old 01-13-2010, 07:42 AM   #6
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Well that is good and bad. Good to see that the biochemistry is rather unchanged (aside from repackaging reagents for HiSeq use only). That way hopefully upstream modifications made for specific needs should translate. . . the bad is of course needing to buy another $500K+ machine!

Either way technology is as technology is, weren't we all just clamoring to get the an iPhone only to find the bigger better cheap one 6 months later. Sequencers should have a "new every two" program as well
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Old 01-15-2010, 04:59 AM   #7
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I would be a bit upset that my GAII was out of date less than a year after buying it. Seems like an upgrade to GAII rather than a whole new instrument would serve their current customers better.
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Old 01-15-2010, 05:07 AM   #8
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Looking at the Illumina site I see they are still selling the GAIIx (with a new skin on it compared to ours!) so maybe they intend to continue both lines?

If I were buying a new sequencer for our use I'd still take a GAIIx over the HiSeq. We're often stuck for finding 8 samples which want to run the same programme as it is. Having to find 16 wouldn't make our life any easier.

I suspect the HiSeq had to be a new instrument given the big changes to the optics. The underlying chemistry is still the same so maybe there's life in our existing machines yet...
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Old 01-15-2010, 07:19 AM   #9
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Well with the GAIIx sequencing itself is much cheaper. What is unfortunate this presents yet another data analysis nightmare.
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Old 01-15-2010, 07:22 AM   #10
simonandrews
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Quote:
Originally Posted by Madscientist View Post
What is unfortunate this presents yet another data analysis nightmare.
I'm getting used to those now...
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Old 01-15-2010, 11:47 AM   #11
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Illumina has also introduced a new lower priced, lower throughput version of the GAIIx.
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Old 01-15-2010, 01:04 PM   #12
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Quote:
Originally Posted by system7 View Post
Illumina has also introduced a new lower priced, lower throughput version of the GAIIx.
I think they should have called it the "GA junior".

Last edited by GW_OK; 01-18-2010 at 12:08 PM.
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Old 01-16-2010, 12:30 AM   #13
avilella
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It's been mentioned in genomeweb that the new Illumina machine can have different programs running simultaneously on the different lanes.

Quote:
Originally Posted by simonandrews View Post
Looking at the Illumina site I see they are still selling the GAIIx (with a new skin on it compared to ours!) so maybe they intend to continue both lines?

If I were buying a new sequencer for our use I'd still take a GAIIx over the HiSeq. We're often stuck for finding 8 samples which want to run the same programme as it is. Having to find 16 wouldn't make our life any easier.

I suspect the HiSeq had to be a new instrument given the big changes to the optics. The underlying chemistry is still the same so maybe there's life in our existing machines yet...
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Old 01-17-2010, 11:46 PM   #14
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Quote:
the new Illumina machine can have different programs running simultaneously on the different lanes.
Isn't it just that the machine can handle each Flow Cell indepandently and run single read on one of them and paired end on the other?
Nevertheless, it says that you don't need to complete both flow cells to launch a run: you can still run only one flow cell and you will only use the required amount of sequencing solutions.

Last edited by huguesparri; 01-17-2010 at 11:51 PM.
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Old 01-19-2010, 11:08 AM   #15
RockChalkJayhawk
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Default HiSeq 2000

Yeah, increases in throughput are nice. However, I think they are missing the boat when it comes to cost. Even if it is better than arrays and other technologies, many are resisting because it will cost $20,000 every time you turn the machine on!
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