Ion Torrent vs MiSeq vs GS Junior

[razibus]

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.

[NextGenSeq]

None, use Sanger sequencing and a 3130 or just send the PCR products out for Sanger sequencing.

[razibus]

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?

[krobison]

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).

[razibus]

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?

[krobison]

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)

[aleferna]

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 ?

[wraithnot]

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/10970808/illumina-announces-miseq8482-personal-sequencing-system.html

http://www.illumina.com/systems/miseq.ilmn#workflow_specs

http://www.iontorrent.com/lib/images/PDFs/ion%20torrent%20product%20information%20.pdf

http://www.iontorrent.com/lib/images/PDFs/performance_overview_application_note_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.

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 ?

[razibus]

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

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

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.

[aleferna]

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?

[aleferna]

Also we've been using the Nextera kit and we are delighted with it, anybody know's if you can use it for PGM?

[aleferna]

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?

[SeqAA]

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.

[krobison]

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.

[razibus]

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)