Ion Torrent, how much to run?

[brianlamx]

Does anyone have an idea on roughly how much an ion torrent instrument costs and how expensive it is to run?

[brianlamx]

good stuff! Thanks!

[Hiro.Protagonist]

The full cost depends on what support instrumentation you have available for the library prep and instrument prep.

From Life for the PGM and needed server plan for ~$80K

Ancillary equipment, like pH meter, water system, argon tanks, bioanalyzer, bioruptor, pippen prep, qubit, guava, thermal cycler, etc. that you may or may not need for library prep should fall into your budget and can cost more than the PGM.'

Running the instrument with the 314 chip costs ~>$1K per sample with their kits, chip, and consumables needed for the preps. Their stated run cost and run cost in that paper are for the superficial chip and reagents and not the inclusive cost you will pay.

[krobison]

$49K for the box
$16K for the required Linux server
$5K for the upcoming emPCR device (not strictly required, but probably worth spending on)

List prices on reagents:

Cost for sample prep kits
RNA-Seq kit is $1.2K for 10 rxns (it's going to be a while before the instrument has the horsepower for most RNA-Seq projects, but perhaps microRNAs can work)

Fragment library kit is $500 to produce 10 libraries


Cost for template prep kit
$1250 for 10 samples

Sequencing kit
$600 for 8 reactions

Sequencing chip
314 $2000 for 8 chips
316 $4000 for 8 chips (supposedly not out 'til next month, but I can get a price on the website)

Cost for control library kit
$500 for 3 runs
(this is something it is probably wise to run periodically, but isn't strictly required)

So, per library for fragment libraries would be
$50 for fragment library
$125 for template prep
$75 for sequencing reagents
$250 for 314 chip

Or a total of $500 for the 314 chip and $750 for the 316 chip

(by which, with great effort, I get the same value as the review linked to above!)

[Hiro.Protagonist]

With you doing your work at an outside provider, did they charge $500 sample to do the sequencing? My only point would be to plan for more cost per sample than the actual kit components from Life, as they do not give you all you need to make the libraries. If you have to account for sample prep time for a staff member, that is a big portion of the cost involved with the PGM workflow.

[krobison]

The costs I listed above would be if had an instrument on site, which is what the original question was about Yes, outside provider is $1250 (EdgeBio) for the 314 chip. And yes, the cost estimate did assume a certain level of basic laboratory setup (an argon tank is required to run the system). If someone was really starting a lab from scratch, then they would need to go through the protocols and tally up all that gear.

[SeqAA]

The full cost depends on what support instrumentation you have available for the library prep and instrument prep.

From Life for the PGM and needed server plan for ~$80K

Ancillary equipment, like pH meter, water system, argon tanks, bioanalyzer, bioruptor, pippen prep, qubit, guava, thermal cycler, etc. that you may or may not need for library prep should fall into your budget and can cost more than the PGM.'

Running the instrument with the 314 chip costs ~>$1K per sample with their kits, chip, and consumables needed for the preps. Their stated run cost and run cost in that paper are for the superficial chip and reagents and not the inclusive cost you will pay.

You must work for illumina marketing.

[ECO]

You must work for illumina marketing.

Ad hominem. Don't do it, please.

[Hiro.Protagonist]

No, I think Illumina is equally as guilty at stating run costs but not the real cost. "Reagent cost" of a genome, for example.

It is fair that I exaggerated the cost, my only point is the cost to run isn't just the kits from any manufacturer, be it PGM or MiSeq. If you need to budget, adding a factor for all the other things you need to actually do a run is fair.

I would say it is not marketing, just reality. Add a similar factor for anything Illumina or others say about cost per run.

Also a run for any is not going to be 100% successful, in library prep, emPCR, cluster generation, sequencing, etc. Average out your success rate and the cost per sample will also be a bit higher.

[larissa]

Could someone please clarify what is the referred guava for the Ion? Because I am exactly going through protocols to tally up everything needed to set up the system and do not remember reading about it. Thanks in advance!

[SeqAA]

There is no guava.. This has been replaced by an optional qubit assay.

[lek2k]

Two things to note since krobinson posted in June.

1. The Q3 price has changed, most notable the 314 chips are $100 dollars which means $800 for a pack of 8. The price for the 314 chip is exactly the same in Australia for once !!

2. Prices vary locally, thus converting it to British pounds may not be an indicator of price. krobinson I assume has quoted the US price. In Australia we pay 20% more than the US, despite the AUD being stronger for the whole year. Previously someone from the UK complained that they had to pay more than their US colleagues.

[lek2k]

Comment regarding Ancillary equipment.
You do not need a pH meter, the PGM now does all the pH for you.

Bioruptor not required. The latest library prep kit uses enzymatic digestion (Ion Shear). This is a relief since the Bioruptor is quite expensive for a sonicator. In fact, all DNA sonicators are quite expensive e.g. in Australia a Covaris S2 costs more than the Ion Torrent itself!!

We are trialing the Invitrogen E-gel size select system as a cheaper alternative to pippen prep.

[halpink]

How is the Invitrogen E-gel size select working out, lek2k?

[lek2k]

Had a go last week. Didn't go so good for the 2% size select gel
1. The gel had to be run much longer than in the instructions.
2. The water you put in the collection slots disappears quite fast. Don't puncture the gel and the bottom of the slot or there will be no collection in that slot.
3. After the selection the 260/280 ratio from the nanodrop was not so good.
4. Bioanalyzer showing size distribution result could be better.

Mind you this is the first time we have tried so we will persist cuz I like the idea and its cheap. Once we get better then we can whine about it. This was with NEB fragmentase, next try will be with the Ion Shear reagents.