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Old 01-11-2016, 06:40 AM   #1
GenoMax
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Default MiniSeq - a new addition?

Just got an email from Illumina for a webinar next week "introducing MiniSeq".

Looks like a new addition to the sequencer family though Illumina's website is not listing the system just yet.
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Old 01-11-2016, 06:42 AM   #2
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Wow, Keith called it, huh?
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Old 01-11-2016, 08:40 AM   #3
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So. What is the current count of Illumina sequencers?
HiSeqX
HiSeq3000/4000
NextSeq
MiSeq/MiSeqDx
and now, the "MiniSeq".
I guess that is 5.
What are we guessing here? PGM-killer?

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Old 01-11-2016, 09:16 AM   #4
Jessica_L
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I thought the PGM and the MiSeq were more along the same lines, specs-wise. My thought is the MiniSeq is going to be a low low throughput instrument, sort of like a MiSeq that only ever runs nano and micro kits. But probably two color based, like the NextSeq.

Is there really a big market for these super low throughput machines? Maybe the idea is to compete with digital PCR? A cheap way to do library QC that isn't as expensive as a MiSeq run?
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Old 01-11-2016, 12:24 PM   #5
pmiguel
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Quote:
Originally Posted by Jessica_L View Post
I thought the PGM and the MiSeq were more along the same lines, specs-wise. My thought is the MiniSeq is going to be a low low throughput instrument, sort of like a MiSeq that only ever runs nano and micro kits. But probably two color based, like the NextSeq.

Is there really a big market for these super low throughput machines? Maybe the idea is to compete with digital PCR? A cheap way to do library QC that isn't as expensive as a MiSeq run?
I haven't checked the specs in a while, but I think a MiSeq is more along the lines of a Proton as far as the amount of sequence it produces per run. An Illumina sequencer that costs about what a PGM does and has reagent cost/run in that same region would likely be successful. The problem with the Nano MiSeq reagents is that they produce about 1/10th the amount of sequence (that is fine) but cost about 1/2 as much as the full non-Nano MiSeq reagents (not fine).

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Old 01-11-2016, 12:32 PM   #6
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There's a YouTube video: https://www.youtube.com/watch?v=JBmOWNmj4Gk

From the video, the flow cell is fairly large. The sequencer screen shows a cluster density of 196K/mm2, similar to the NextSeq. 2x150 runs, about 8 GB data. This should get about 30 million clusters.
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Old 01-11-2016, 12:40 PM   #7
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Quote:
Originally Posted by pmiguel View Post
The problem with the Nano MiSeq reagents is that they produce about 1/10th the amount of sequence (that is fine) but cost about 1/2 as much as the full non-Nano MiSeq reagents (not fine).

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That is probably a pure marketing decision because they still have to make the flowcell/cartridge in the same size.

I agree that if the nano flowcells were priced right, they would be a great way to do quick check on libraries. Perhaps people can buy a MiniSeq for this purpose if the reagents would be priced right.
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Old 01-11-2016, 12:54 PM   #8
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The specs are here:
http://www.illumina.com/systems/mini...fications.html
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Old 01-11-2016, 04:42 PM   #9
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I think the only remaining question is the price per kit. Per luc's link, it looks like it'll be a smaller, cheaper MiSeq with almost exactly the same specs.

http://core-genomics.blogspot.ie/201...y-miniseq.html is reporting that the run prices will be vastly lower than the MiSeq though, which would make this a much more interesting proposition. Not sure if that'd be in Illumina's interests, though - though the markup on SBS kits is obviously gigantic, so they might have made the calculation that they'd make more money selling lots of cheaper kits for cheaper sequencers than they get from their current relatively-small-but-lucrative market.
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Old 01-19-2016, 07:05 AM   #10
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First MiniSeq webinar under way.

Single cartridge, RFID encoded.
2-channel SBS, G - uses no dye
Users only need to interact with one well.
Custom seq primers can be used (with other wells).
Everything included (run/analysis) on machine.
Local run manager - Available on local network so can setup/analyze data remotely (on local network)
Data can be streamed to network storage during run just like MiSeq.
Can use BaseSpace (local/cloud).
MiniSeq Control software - to run the sequencer (gets data from local run manager)
High-Output - 25 Million (3 run lengths supported, 2 x 150 max)
Mid-output - 8 million reads only 300 cycles.
Cancer applications - Tumor profiling, Amplicon
TruSeq Targeted RNA assays (human, mouse) - Custom panels, single amplicon per gene
TruSeq Custom Amplicon low input - (2 x 150 runs) - 32 h turn around. 10 ng input (FFPE ok), 6+ hands on time, 16 sample kit, Example data on basespace
PCR Products - sequence via Nextera XT
Datasets in BaseSpace generated using MiniSeq available.

Shortest run - 1 x 36 for microRNA, 4 hr run

Cluster density - ~ 175-200K/mm^2 (60 tiles)

Once run completes, analysis runs automatically (including DE analysis). Lot of "canned" results options for bench scientists.

$550 per run (mid-output 300 cycle kit per @misterc, post #16 below).

MiniSeq scientific challenge to go with the intro :-)

Last edited by GenoMax; 01-19-2016 at 05:00 PM.
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Old 01-19-2016, 08:23 AM   #11
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Thanks Genomax. I'm doing the webinar at 3PM EST today...
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Old 01-19-2016, 10:08 AM   #12
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Quote:
Originally Posted by pmiguel View Post
I haven't checked the specs in a while, but I think a MiSeq is more along the lines of a Proton as far as the amount of sequence it produces per run. An Illumina sequencer that costs about what a PGM does and has reagent cost/run in that same region would likely be successful. The problem with the Nano MiSeq reagents is that they produce about 1/10th the amount of sequence (that is fine) but cost about 1/2 as much as the full non-Nano MiSeq reagents (not fine).

--
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I suppose that makes sense. I always figured that a Proton could go up to 10GB but most MiSeq kits generate around 5, but that's also for 300 cycles. Looking at 500 cycle kits brings the two systems much closer to equivalency.

Also, nothing but agreement about the cost of MiSeq nano kits. We have plenty of applications where a million reads would be great but not when it costs half as much as a full kit.
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Old 01-19-2016, 01:39 PM   #13
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Quote:
Originally Posted by GenoMax View Post
$550 per run.
Is that inclusive of sample prep, and/or did they say what run length that was? If that's for the 75-cycle kit this isn't really a big change from MiSeq, but if that's 300-cycle and the others are cheaper then this could be significant.
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Old 01-19-2016, 03:15 PM   #14
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Quote:
Originally Posted by Rocketknight View Post
Is that inclusive of sample prep, and/or did they say what run length that was? If that's for the 75-cycle kit this isn't really a big change from MiSeq, but if that's 300-cycle and the others are cheaper then this could be significant.
Sorry, I missed the details on that (I think it was just the reagent cost) since the presenter went through some of the slides rather quickly.

Someone else who attended the webinar may want to chime-in.
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Old 01-19-2016, 03:58 PM   #15
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My understanding was reagent cost only.
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Old 01-19-2016, 04:33 PM   #16
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$550 is for catalog # FC-420-1004, which is a "mid output" 300 cycle kit. So up to 8 million reads. High output kits for 300 cycles and all 25M reads costs $1500 (FC-420-1003), also not counting sample prep. Costly little fella for OpEx.
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Old 01-19-2016, 05:04 PM   #17
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Quote:
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Costly little fella for OpEx.
For research labs, perhaps.

But if eventually validated for diagnostic use then 16 samples for $550/$1500?
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Old 01-19-2016, 11:42 PM   #18
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Quote:
But if eventually validated for diagnostic use then 16 samples for $550/$1500?
That question was answered in the middle seminar. It will never be validated for diagnostic use (in USA). They have another machine for that.
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Old 01-20-2016, 02:10 AM   #19
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Quote:
Originally Posted by misterc View Post
$550 is for catalog # FC-420-1004, which is a "mid output" 300 cycle kit. So up to 8 million reads. High output kits for 300 cycles and all 25M reads costs $1500 (FC-420-1003), also not counting sample prep. Costly little fella for OpEx.
Looks to me like this is going to be more expensive per base than the MiSeq. Plus the error rate in the BaseSpace examples seems higher than the MiSeq. Very disappointing.
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Old 01-20-2016, 06:17 AM   #20
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This just seems like a smaller and cheaper MiSeq with crappier 2-dye chemistry and samey runcosts then. I guess you might consider one if you didn't have a MiSeq already, but there's nothing new for any lab that already has any decent instrument on site.
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