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Old 05-13-2011, 06:16 AM   #1
razibus
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Default Ion Torrent vs MiSeq vs GS Junior

Hi,

We already sequenced several human exomes by using Illumina GAIIx. To confirm found mutations in complete families, we need a cheaper and faster sequencer.

Which sequencer is the best for our application? Ion Torrent, MiSeq or GS Junior?

Any thought will be greatly appreciated.
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Old 05-13-2011, 06:50 AM   #2
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None, use Sanger sequencing and a 3130 or just send the PCR products out for Sanger sequencing.
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Old 05-13-2011, 07:27 AM   #3
razibus
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We already tested some mutations by Sanger sequencing but it's definitely not the fastest technique when you have a lot of mutations.

Maybe you are right and the 3 sequencers I asked for are not the best solution but which one would you pick up for other applications on human?
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Old 05-13-2011, 11:35 AM   #4
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Obviously if you are doing this in the near future, it's Ion or GSjr, as MiSeq won't be out until the end of year. You could, of course, generate Illumina products & then find a spare lane, but that can be hard to get scheduled.

For this sort of application, GSjr is a more proven system but with a 4X-ish higher cost per run, and if Ion's most recent dataset is to be believed Ion has already passed GSjr on reads/run. So you pay more to get less, but you'll be more confident in that data. Probably for your application you'll be grossly oversampling, so that confidence can be built from very deep data.

At the end of the year, it all depends on if MiSeq comes out on time & on spec and whether Ion can really push the 316 & 318 chips out on time and on spec. The fact you already have a GAIIx might skew things towards MiSeq (since all your libraries will be compatible).
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Old 05-13-2011, 01:56 PM   #5
razibus
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Thanks for your answer.

So to your opinion :
- if we want to buy one now, PGM seems to be the most relevant because of actual results and future evolution
- if we want to buy one at the end of the year, we must wait and see the specs of PGM and MiSeq

Where did you read MiSeq will be out at the end of the year? I believed the first sales were planned for this summer.

We also planned to buy one or two HiSeq. Will the libraries be compatible too?

Last question : I read in publications people using 454 to confirm mutations from GAIIx or other sequencers but I did not read anything using PGM or GSjr for this purpose. Do you think like NextGenSeq that these devices are inappropriate?
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Old 05-14-2011, 06:34 AM   #6
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According to an In Sequence piece, MiSeq's start shipping 3rd quarter with substantial shipments in 4th quarter; perhaps end-of-year is being a bit pessimistic, but it does seem like most of these companies are aggressive about quarters (i.e. if they plan to start shipping on September 30th, that counts as 3rd quarter)
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Old 05-17-2011, 08:45 AM   #7
aleferna
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Default MiSeq vs IonTorrent

So I attended an Illumina conference, 2 weeks ago and of course I asked the obvious question... how is MiSeq better than PGM?
The answer was not as clear/black and white as I wanted, they said
1. PGM has lower quality, lots of Q20 bases??
2. Unproven technology
3. No Paired End sequencing

Well, other except for the PE, the other answers were kind of ambiguous. I'm trying to compile a comparison between the 2 devices as we are probably going to buy one of these machines next year. It would be nice to have the following raster:
1. Throughput/Hands On Time/Running Time per run
2. Quality of base 25, 50, 75, 100
3. Cost:
Equipment (PGM $50k, MiSeq $150k??)
Cost per run?
Cost per sample prep? (they said $750 for the MiSeq sequencing run, but didn't mention the sample prep.
4. Read length ?
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Old 05-18-2011, 10:43 AM   #8
wraithnot
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We're also trying to decide between these two instruments. I think most of the information you're after can be found here:
http://www.thestreet.com/story/10970...ng-system.html
http://www.illumina.com/systems/mise...workflow_specs
http://www.iontorrent.com/lib/images...rmation%20.pdf
http://www.iontorrent.com/lib/images...ote_041211.pdf

The last link shows actual data for the PGM "314" chip, but it looks like the performance characteristics for their other chips are estimates/speculation. If the PGM of today doesn't meet your needs, you'll need to do a bit of speculation of your own to decide how the two instruments will match up when you plan to actually buy one.

Quote:
Originally Posted by aleferna View Post
So I attended an Illumina conference, 2 weeks ago and of course I asked the obvious question... how is MiSeq better than PGM?
The answer was not as clear/black and white as I wanted, they said
1. PGM has lower quality, lots of Q20 bases??
2. Unproven technology
3. No Paired End sequencing

Well, other except for the PE, the other answers were kind of ambiguous. I'm trying to compile a comparison between the 2 devices as we are probably going to buy one of these machines next year. It would be nice to have the following raster:
1. Throughput/Hands On Time/Running Time per run
2. Quality of base 25, 50, 75, 100
3. Cost:
Equipment (PGM $50k, MiSeq $150k??)
Cost per run?
Cost per sample prep? (they said $750 for the MiSeq sequencing run, but didn't mention the sample prep.
4. Read length ?
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Old 05-19-2011, 07:04 AM   #9
razibus
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Quote:
1. Running Time per run
- PGM : 2 hours (0.1 Gb)
- MiSeq : 4 hours (1x35), 19 hours (2x100), 27 hours (2x150)
- GS Junior : 9 hours

Quote:
3. Cost
These are just indicative prices :
- PGM : 78k€ and 820€ (316 and 318 chip) for the cost per run
- MiSeq : 105k€ and 600€ for the cost per run
- GS Junior : 120k€ and 1000€ for the cost per run

Quote:
4. Read length ?
- PGM : 10Mb (314 chip), 100Mb (316 chip), 1Gb (318 chip)
- MiSeq : 680Mb (2X100), 1Gb (2X150)
- GS Junior : 1Gb, 500bp max by amplicon

I think each of this technology meets specific needs. I think you should also take into account : required quantity of DNA, automatisation cost (oneTouch, Fluidigm), technical support, availability (machine and kits), how old the machine is (GS Junior is the older one so its protocol is pretty stable), and how proven the technology is.

Last edited by razibus; 05-19-2011 at 07:07 AM.
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Old 06-15-2011, 08:06 AM   #10
aleferna
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Thanks so much for the info, looks like the PGM has a huge lead on the other 2 (particularly since its a new tech, expecting exponential growth)... I wonder if the device quality/warranty also holds. Also we talked to an Illumina rep and he was short selling the GAIIx, I think they realized they can't compete with the miseq?
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Old 06-15-2011, 08:07 AM   #11
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Also we've been using the Nextera kit and we are delighted with it, anybody know's if you can use it for PGM?
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Old 06-15-2011, 08:16 AM   #12
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Finally:
you say PGM is $109k(78k€)? Thought it was $50k what happen, is this because of the ridiculous server spec? Can't you run it with a PC or use an existing server? (I've seen people try to make money selling you a huge server to align and store but we already have that)

Also it says PGM 2 hours times 0.1Gb, I guess this is for the 314?? For the 318 is it 2 hours for 1GB?
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Old 06-15-2011, 02:36 PM   #13
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PGM $50k
Server ~$15k, can run 2 PGM's.

I've heard the runs times will be relatively the same for 200bp, and for 316/318.
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Old 06-15-2011, 04:53 PM   #14
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Nextera cannot be directly used with PGM. With PGM's long read lengths, it would certainly be possible to design a "cheater" primer set to convert a Nextera library to a PGM library, but you would read through the Nextera primer on each read (and thereby waste some read length).

Also, at this time PGM libraries cannot have inserts longer than 150 nt; if your Nextera library is bigger than that it wouldn't currently be convertable.
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Old 06-16-2011, 02:55 AM   #15
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I gave prices for europe only and as you know prices are always higher here...

About PGM I can't remember if the run time is changed with 318 chip. Ask in PGM forum.

Whatever sequencer you chose, keep in mind that :
- ion torrent is very young and even if it seems to have a huge potential a lot of optimisations and improvements need to be done
- GS Junior has a good support and a well-developped protocol ; also the read size of amplicon is higher than the other ones
- MiSeq : No one really knows if it's real or not (just kidding) but to be serious we need to wait for an availability on the market and true specifications (miniaturization is not so easy)
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Old 06-16-2011, 09:01 PM   #16
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"I've heard the runs times will be relatively the same for 200bp, and for 316/318."

I thought the 318 was already out? Does anybody has some data on the 318? Does it really give you 200bp?
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Old 06-16-2011, 11:23 PM   #17
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As stated by Mr Robison, because of primers and specific key sequences your inserts can't be longer than 150bp.

Ion 316 chip is just available to order in Europe. Ion 318 Chip should be available in September and the read lenght associated with this chip is 300bp.
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Old 06-17-2011, 04:42 AM   #18
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- PGM : 10Mb (314 chip), 100Mb (316 chip), 1Gb (318 chip)
- MiSeq : 680Mb (2X100), 1Gb (2X150)
- GS Junior : 1Gb, 500bp max by amplicon

I have to correct your GS Junior statement:

The instrument produces on average 100.000 reads and 35 Mb per run. But I heard if you really have an extremely good library you can push it to almost 50 Mb... I got with 80k reads 38 Mb out once...

But I think that is the maximum of the GS Junior. The longer read lengths announced for 454 sequencing (700-1000) will only be available with a hardware upgrade to the big version.

I think you have to be careful when setting "read length" == "total output". Especially for de novo the read length is very important as you will need more coverage with shorter reads (e.g. Sanger =>7X, 454 =>20X, Illumina =>30X). Increases in read length will shift the numbers left... I am also not sure if you can really solve all problems of de novo assemblies using mate pair/paired end sequencing of short reads...
But for standard stuff like amplicons or short read mapping or experiments where you really need coverage you should go for PGM or MiSeq... probably PGM...
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Old 06-17-2011, 05:02 AM   #19
razibus
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Thank you Mucku for this relevant answer.

I did not notice my mistake and you are absolutely right : total output of GS Junior is 40Mb (specification from Roche) and it will be 80Mb at the beginning of 2012.

I agree with you, PGM looks good on the paper but we need more comparative scientific papers to have a better view of advantages/drawbacks of each machine.
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Old 06-17-2011, 08:11 AM   #20
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PGM ~50 Mb 314 chip and 170 Mb 316 chip @ Broad, data presented at ESHG. ~1.8 M reads with Q > 17 if I am not mistaken.
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