Why would I buy an Ion Torrent?

[Haiqu]

I've been looking at used Ion Torrent sequencers on eBay lovingly, then researching to ensure that I don't buy yet another gadget I can't use. So here's what I've discovered so far:

1. They need a dedicated server and several extra bits like the One Touch, so they're useless alone. The full setup is about $10k used.
2. Cost of use includes $90 for the cheapest chip, plus $300 in chemicals. That ain't cheap when you consider that I bought a WGS test on special from Dante Labs for $200
3. There's no information publicly available from Thermo Fisher Scientific. In fact when I visit their website, I'm blocked by a message that tells me these products aren't available in Australia. That, to me, seems stupid in the extreme.
4. The chips can be cleaned and reused indefinitely if you're willing to put up with minor contamination (83% clean is what I've been told.)
5. They are only really useful for small jobs. Doing a whole human genome would take forever and use about 1,000 chips.
6. Reagents have a shelf life of 3 months.
7. Sample preparation is time consuming and complex.

So the above indicates major suckage for the hobbyist.

Can anyone suggest a better alternative? I'm happy enough with a system that can only sequence a small genome but RNA profiling would also be nice too. Where is Moore's Law taking us? And is there something just around the corner that is both affordable and available for the low end of the market?

[r.rosati]

4. The chips can be cleaned and reused indefinitely if you're willing to put up with minor contamination (83% clean is what I've been told.)

Hi. Do you actually have a protocol for that? I've tried, unsuccessfully.

[Haiqu]

You'd have to ask this guy: https://hackaday.io/project/160183-d...uencer/details

[cmbetts]

Is there a reason you need your own sequencer? You're highly unlikely to ever break even vs making homebrew Illumina libraries and sending them to a service facility that will pool them onto a HiSeq/NovaSeq.

My old company hated running our PGM. It's very user unfriendly.

If you're just interested in dinking around at home, go with Oxford Nanopore.

[Haiqu]

I live in Australia. Such services don't exist here.

Oxford Nanopore was considered and rejected on two bases: 1. Cost and short life of reagents. 2. The proprietary nature of the system. Sensors need to be returned to the manufacturer after 12 weeks. i.e. You don't actually own what you pay for.

So far no-one has come up with a system that's usable for the hobbyist. Everything seems to be aimed at batch processing. It's like computing in the 70's.

BTW I don't see this as a problem, I see it as a business opportunity.

[GenoMax]

@Haiqu: You should clarify if you are looking at Ion as a hobbyist (outside of a research institution) i.e. for DIY use.

[Haiqu]

My intro in the Introductions section clearly states that I'm retired and consider this a hobby activity. Sorry if I seemed too knowledgeable for that to come through here, it's a side-effect of being smart.

But I would have thought that my being interested in eBay equipment that's almost 10 years old would have given the game away.

[Bukowski]

My intro in the Introductions section clearly states that I'm retired and consider this a hobby activity. Sorry if I seemed too knowledgeable for that to come through here, it's a side-effect of being smart.

No one digs through your post history to answer your questions.

The Ion Torrent workflow is notoriously finicky. Many people submit DNA or pre-made libraries to service providers in other countries in order to get their sequencing done. And outside of professional contexts too. The economic feasibility of this has already been outlined, let alone the issue of tying yourself to a dead platform (I'm interested in how you would source reagents to run a PGM).

Are you sure a MinION and some Flongles wouldn't be a more cost effective route? I bet there's a lot of DIYbio people floating around that would ameliorate the cost of a starter pack. And the library prep workflow is a lot less complex.

[nucacidhunter]

I live in Australia. Such services don't exist here.

There are several companies in OZ that will sequence your own prepared libraries. You can PM me if you one a list.

[Haiqu]

No one digs through your post history to answer your questions.

Sheesh, another one. From the top post in this thread:

"So the above indicates major suckage for the hobbyist."

The Ion Torrent workflow is notoriously finicky. Many people submit DNA or pre-made libraries to service providers in other countries in order to get their sequencing done. And outside of professional contexts too. The economic feasibility of this has already been outlined, let alone the issue of tying yourself to a dead platform (I'm interested in how you would source reagents to run a PGM).

All the ancillary stuff is available via eBay. But that's a Bad Idea (TM) for the same reason that outsourcing to overseas companies is a Bad Idea. Lead times are going to stretch into infinity. I'm still waiting (since February) for a WGS I did with an overseas company. Not acceptable.

Are you sure a MinION and some Flongles wouldn't be a more cost effective route? I bet there's a lot of DIYbio people floating around that would ameliorate the cost of a starter pack. And the library prep workflow is a lot less complex.

It seems to me neither option is a cost-effective route. Added to that, the MinION is very proprietary, sensors need to be returned to the manufacturer.

[Haiqu]

There are several companies in OZ that will sequence your own prepared libraries. You can PM me if you one a list.

Awesome!! Will PM you, thanks. They sure don't advertise.

Edit: Oops. Forum doesn't seem to have a PM system. I've emailed you, hope it gets through.

[nucacidhunter]

Following is the link to some OZ sequencing service providers:

http://www.agrf.org.au/contact-us

https://www.ramaciotti.unsw.edu.au/

http://dna.med.monash.edu.au/

I am sure they all will do good job.

[Haiqu]

Thanks nucacidhunter. I did also receive the email.

I've also become aware of the unreleased ONT SmidgION device. If they can get the cost of use down it may prove to be a viable alternative, although they (stupidly) haven't announced software for a PC and seem to be aiming at tethering the thing to an iPhone. They also screwed up by using the wrong gender of mini-USB connector.

The ONT technologies are of most interest so far, although I believe the costs need to come down by another order of magnitude before broad use ensues from hobbyists. They need to decouple reagents from the package so that individuals can source them locally, bring down the cost of the flow cells and forget about their enforced use of commercial data analysis services like Epi2Me. Only then will I believe their hyperbolic claim of "Anyone, anywhere, anytime" usage.

[gringer]

The MinION flow cell return to ONT is so that they can recycle them for use in training and internal research. If you contaminate the flow cells such that they are not safe for posting back, you don't need to return them. There is no return required for flongle flow cells.

There's no need to use Epi2Me; the only necessary proprietary software is the MinKNOW sequencing software (for controlling the MinION), which produces HDF5 files containing raw signal traces from the sensor arrays. You're free to design your own base-calling software (e.g. Chiron) and bypass every other part of the process. As far as I'm aware, all other sequencing companies also have proprietary software for controlling initial data acquisition.

Minimum per-sample cost via 12-sample multiplexing with the rapid barcoding kit and a flongle flow cell is about $9 USD. The only thing cheaper than that which I'm aware of (possibly excluding microarray) is a single Sanger sequence by service, or do-it-yourself Sanger.

[Haiqu]

If the cells can be recycled, that option should be available to the purchaser. It has already been discovered that cells from the older Ion Torrent machine can be used indefinitely, and I suspect ONT don't want the user experimenting with that possibility. Their official reason per their website varies from "Please return your flow cells after use." (i.e. no reason) to "It is a requirement of the contract." depending on where you read. In any case, I can't see any valid reason to be paying return shipping to the UK if the device is merely going to be disposed of.

Good to know there are options for base calling. My objection to Epi2Me was the necessity for large online data flow, which is difficult when you're mobile and expensive in general in Australia. As an example, I had to reach out to a friend who works for an ISP to merely download a 100GB BAM file, because such bandwidth isn't available to the end user at any price as yet. Being a kiwi, I'm sure you can relate.

I can't see a hobbyist needing to handle the volumes for 12-sample multiplexing, and the learning curve for barcoding would complicate an already complex procedure. A more likely scenario is use and rewash of the flow cell, where maybe 4 or 5 samples can be read at best. With single flow cells being $900 (plus reagents at several hundred bucks) the cost will be more like $300 per sample, especially when you take into account that they have a limited (12 week) shelf life.

All this just outlines the differences between commercial operation and home use, and is no criticism of ONT technology per se. There is no product for the low end of the market at present, and the one that might have fit the purpose - the SmidgION - has been stillborn, judging from the lack of progress since 2016.

I fully expect something new to eclipse ONT soon anyhow, given that it is now fairly old technology in "dog years."