Ion Torrent and the Democratization of Sequencing

Back from my North East American trip and still jet lagged so I’ll return to the blog sphere with a non-technical post. The term “democratizing sequencing” is synonymous with the Ion Torrent. This probably doesn’t mean Life Technologies are pitching to a bunch of hippie scientist trying to relive the 70s but what does it mean instead? The definitions of “democracy” usually refers to a form of government so this general definition would be more suitable – “The practice or principles of social equality”. This post will cover the following components of social equality: Economical equality, Freedom of speech and Freedom of information. This month has seen a massive effort introducing initiatives to emphasize these components.

Economical equality

This world map shows the positions of where all the next generation sequencers are in the world. This requires the facility to self report so is not entirely accurate but is close because people like to brag :) There are two things you may notice on this map:

  1. The richer countries tend to have more sequencers. This is not surprising as they tend to have more of everything including obese people :P
  2. Within each country it tends to be the richer Institutes and Universities that have these machines. In the case of my home city, Sydney there are three sites with us way out in suburbia.

Given the correlation between high impact publications and next generation sequencing, why aren’t there more in Sydney? Simple answer, it costs at least 1 million dollars to build the infrastructure and then there is on going costs. In Australia, this would require many investigators to get together to apply for a massive grant. Too many egos involved and that’s why it rarely happens. The other alternative is to sell 2 million dollars worth of charity chocolates. This would require you to sell one chocolate to approximately every adult in Sydney. If this charity model is successful, we will have an even bigger type 2 diabetes problem :cry:

What most researchers in Australia have to settle for is sending samples to Sequencing centres such as the Ramaciotti Centre and the Australian Genome Research Facility (AGRF), which provide a great service for Australian researchers. Then why get a sequencer, most researchers ask? We got a sequencer as a way of controlling each step of the workflow and more importantly the time frames in which projects can be completed. Ever collaborated in Science before? Felt disappointed how long things take? Well you are not the only one!! Then you would understand why controlling time frames is SO important for scientist. Most have realized this but never have had the money to act upon it. The Ion Torrent marketed at $USD 50 K is the first time a lab in Australia can seriously say lets get a sequencing machine. The Illumina MiSeq and Roche Junior are also competitively priced. A carefully planned strategy aligned with local sequencing facilities will now give everyone an equal opportunity to publish in good genetics journals as economics is no longer a barrier.

Freedom of speech

The advent of the Internet has amplified the freedom of speech of everyone! Something we should not take for granted. In the past (i.e. early 90s), if I wanted to communicate information I would use the following:

  • Publish a book, journal article, TV or radio
  • Local newspaper, public notice boards and town hall meetings
  • Letter box drops
  • Tell my mom!

There would be no way a teenager would have the ability to use the first option of communication if all they wanted to say was that “they had an epic World of Warcraft Raid” or a recording of them “owning a n00b on StarCraft 2“. Unfortunately they now can, it’s called Twitter, Facebook and YouTube :P

Life Technologies has embraced the Internet and freedom of speech through the Ion Community. This site allows members to provide feedback and problems that they are having on the Ion Torrent. The comments made by members is NOT censored in any way. This allows people like me to say absolutely whatever they want. Most of the time I alternate between skeptic hater and annoying bug. Many are still afraid to speak their minds or even contribute which is a shame. It is good to say stuff but is worthless if you can not get to your targeted audience. In other words, the reason why you complain is because you want something to be done. From my experiences, Life Technologies are very fast to respond to comments and try their best to help.

In addition, Ion Torrent is providing strong support to the blogging community. This takes on the form of early access to data and resources allowing bloggers to do what they do best… review and complain :D The release of affordable sequencing technology has seen a massive explosion in technical blogging. I think there are few reasons for this:

  1. First and foremost it’s affordable, therefore a lot of people want to know more about it and want the opinion of the wise Internet. No one nowadays goes to a restaurant, hotel or buys anything without reading a review on the Internet. Next generation sequencing is no different!
  2. It may be Science but no one can wait for a suppressed report in a journal article which usually goes something like this “we suggest perhaps maybe the Ion Torrent would be good for X, however further research will be required”.
  3. The release of publicly available data set and for the first time in the history of Biotech the exact data set used to generate the application notes and brochures! This is a gold mine for reviewing and complaining :D
  4. The support of Life Technologies, Illumina and Roche. Some more than others. I think they have realized… bloggers are like good global marketers, the only difference is we pay them absolutely nothing and people tend to believe them more!

Lastly, the greatest display of freedom of speech is allowing me to present at the Ion User Group Meeting. Putting everything in context, I am only a PhD student and quite unpredictable at times. I was given carte blanche so really could have said anything I felt like during the 10 minutes. Saying “I was busting to take a piss” during my talk shows I had freedom of speech.

Freedom of information

Currently Biotech companies have two types of customers, their preferred ones and the rest of their customers. The preferred customers usually get access to technology and information that other customers will see on a later date. How do they pick these preferred customers? Who knows! but I know one thing that these customers are usually the richer ones that can afford to do field testing for them. Having this information early gives these preferred customers an unfair advantage in terms of producing preliminary data for grant applications. These are usually the institutes that DO NOT require an advantage to compete for grants. This model is extremely non-democratic and not COOL :(, although makes economical sense to Biotech companies. There are two initiatives which Ion Torrent launched recently:

  1. Ion AmpliSeq Custom Kit Developer Access
  2. Ion 318 Chip Developer Access

In each of these initiatives, all customers are treated equally and therefore will be provided information whether they are a preferred customers or not. The main emphasis is on giving back to the community, in other words sharing what you have learned while having early access to the technology. A huge difference to using it to benefit only yourself! This will definitely rock the boat amongst the preferred customers but is the only way democracy and freedom of information can be achieved. Illumina being more established in sequencing will have a very difficult time doing this assuming they actually care about democratizing sequencing.

You can put a pipette (noun) in the hand of the scientist but you can’t make them pipette (verb)!

The paradigm shift in the business model implemented by Life Technologies is contingent upon  Ion Torrent PGM purchases and the success of the Ion Community. In order to help with the steep learning curve required for sample preparation, Ion Torrent has an Application Grant Program. The emphasis again is to give back to the community what you have learned. This will greatly help small labs like ours to develop successful workflows in order for us to produce preliminary data so we can be competitive for large government grants. The grant program is a great incentive to buy a PGM over the MiSeq or Junior.

The Ion Community like all online forums and communities in general suffer from the problem of participation. It’s in human nature to be more take than give. Due to internet lurking, forums typically follow the 1% rule or the 90:9:1 rule. 1% contribute, 9% edits/moderates, 90% just view. The Ion Community despite it’s steady increase in membership suffers from this same problem. It is no surprise the most active thread is the one where you get to boast how great your chip runs are with the possibility of winning a pack of chips. Thankfully, Ion Torrent has learned from this and have introduced an initiative called RecogitION. A program which aims to reward regular contributors. This reward system was extremely successful in the Sun Java forum I used to frequent to complain on. I nearly earned myself a free T-shirt :( Some people’s problems are just too difficult! Despite it’s extremely lame name, RecogitION will make for a more successful active community.

Scientist have recognized Ion Torrent through Semi-conductors as revolutionizing sequencing. After everything is said and done, it may be recognized instead as the first Biotech to make a bold move in embracing the Internet culture and what it stands for DEMOCRACY.

Disclaimer: For the good of all mankind! This is purely my opinion and interpretations. I dedicate this post to the all you can eat mud crabs in Rock Hall, Maryland. I try to send you bankrupt by eating all the crabs… only got to number 6 :(

6 responses to “Ion Torrent and the Democratization of Sequencing

  1. Some folks would actually beg to differ. The nice thing about scientist is how they see society, the one that stands outside their labs and that they never see enough of. Life Technology is run buy one of the most overpaid CEO in the World, one of the worst manager per dollar earned (re:see article in Forbes), furthermore, their handling of original data release and IP negociation has been nothing short of Legal warfare, this is well documented.
    I will however agree that this is disruptive and indeed a massive entrepreneurship of acceptance, this is not, however in the greater culture of Life Tech (Rothberg is not a manager per say, he is a marketing guy). So you must understand that right now, Life is doing an excellent balancing act of instrument placement (against MiSeq) vs returns and revenues. Now, go back to the days of cap sequencing and you will see that Life will slowly increase the consumables required for the machines as placement become ‘democratic’ like a Big Mac going up 5% a year. Then ask yourself, how many people needed to get fired in order to keep the price of your toy low enough and pay millions in return to the CEO. Maybe then you will have a different view about democracy. When only one company offers a single product, there is no democracy…

  2. Hi John thanks for your comments and insight. My post regarding democracy is limited to customer centric point of view. How the company operates and how they deal with other companies is not the main focus. You hinted LifeTech may have a monopoly and also will increase prices of consumables, I’m more optimistic that Illumina and Roche will provide healthy competition for years to come in order to prevent this scenario. However, in Australia Invitrogen has close to a monopoly when it comes to Cell Culture consumables.

  3. I could make the argument that the Illumina HiSeq has democratized sequencing more than the Ion Torrent PGM will for a long time. The cost per useful experiment on a HiSeq (RNA-seq, Exome, Genome, etc.) is now so much lower that this type of work is not limited to big genome centers or big labs. The ownership of the sequencer is moot, technology changes so fast it is much better to have the sequencer at a service center and spend more investigator time and effort on the analysis. The PGM is also not that cheap when you factor the sample prep and analysis portion (and how many runs you need to do for counting apps or non-microbial exomes/genomes. DNA sequencing will go the route of oligo synthesis, a few big houses will send you your data and then the fun begins. Or these places will do the informatics for you, which is the value added service, not the actual sequencing. The sequencing is now part of the “sample prep” for most people. With the sequencers the data production far outpaces the time and effort to analyze, unless you have even a PGM being used by many people it will sit idle most of the time. PGM = less data, more expensive, cheaper to park the instrument in the lab = democracy? Democracy in NGS will be when people are more savvy to analyze or understand their analysis. Now most people are slaves to the tyrannical bioinformaticians! (irony here, but how democratic is data generated that 95% of the originators can’t analyze nor question the analysis due to lack of education of the process?)

  4. Hi David, thank you for writing a insightful response and taking a different perspective. I totally agree with all the points you have made. At end you make an excellent point regarding being slaves to bioinformaticians. We have this huge problem in Australia that only a handful of collaborators (=free service) can analyze exome sequencing data before it was linkage data. The wait is usually weeks to months which is extremely frustrating given these people are extremely busy and not very accessible also. But I digress…

    Thanks for taking time out from your busy schedule helping the Obama campaign :D

  5. So I’m wondering if you’ve got a particular take on the speed challenge associated with this one. I’m from a non bio background an interested in discussing what steps might be made to increase the throughput on the DNA prep process of these machines. While I understand that the protocols on these machines are locked down ( from a programmers perspective this is nuts ) I’d be really interested if you’d have suggestions as to how to speed it along.

    • Hi Carl, thanks for the interesting question. My opinion is that working on the speed challenge would require considerable experience in knowing what is important in a protocol and what can be skipped or what short cuts can be made. There will be a lot of unsuccessful attempts so a lot of time and reagents (i.e. money) would need to be invested. I think must researchers are already pulling their hair out on their own projects with experiments not working and are probably not looking for something in addition to help their hair go grey. Then again, a lab may get lucky with a sloppy research assistant or summer student taking short cuts. The only problem is that they probably would not have written the protocol down! Sorry its all hand wavy useless info.. it’s hard because I haven’t really thought that hard for the Speed Challenge.

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