Personal DNA Sequencing Machine One Step Closer

oxide7 writes "A new, low cost semiconductor-based gene sequencing machine has been developed and may unlock the door to advanced medicines and life itself. A team led by Jonathan Rothberg of Ion Torrent in Guilford, Conn is working on a system which uses semiconductors to decode DNA, dramatically reducing costs and taking them closer to being able to reach the goal of a $1000 human genome test. The current optical based system costs around $49000 and is already on the market and being used in over 40 countries."

Comments

Essentially a Proprietary Hydrogen Ion Sensor

[eldavojohn]

From the short video on their site (youtube alternate), it appears that this technology relies on a DNA template across thousands or millions of wells on a chip that emits hydrogen ions every time a base is incorporated into a DNA strand by a polymerase. I'm not a biologist but it looks like a pretty neat idea and I certainly hope it works as well as they say it does. I guess even if your sensor isn't that great at classifying between A, G, C or T then you can just build more wells on the chip and look at the statistics. I'm not sure how they ensure that one process is going on in each cell but I'm hoping this yields some cheap and fast accuracy. This would be a huge boon for research -- hell you could start up some hobby work very quickly and (relatively) cheaply since it's such a straight forward process.

Re:Essentially a Proprietary Hydrogen Ion Sensor

[fuzzyfuzzyfungus]

You can already do most paternity and forensics stuff, to a quite usable degree of confidence, with much smaller snippets. Trying to do so on the very cheap might well get you results from a lab that can't be bothered with minor stuff like negative controls or not fucking up on a regular basis(luckily, this never, ever, ever happens at crime labs); but you can get it today, cheap. Here's an over-the-counter option for $150(no particular endorsement implied, of course, just an example of what you can find in totally mainstream shops with 30 seconds of searching...)

Whole-organism sequencing will likely remain a research tool for quite some time. The snippet-based stuff is already as or more accurate than the people doing it, and whole-organism for medical purposes will be largely snake oil(although there will certainly be people selling it) until we actually have the knowledge necessary to make meaningful inferences from those sequences.

Re:Essentially a Proprietary Hydrogen Ion Sensor

[fusellovirus]

Each well is just large enough to allow one microsphere in it. This microshpere has copies of the DNA to be sequenced attached to it. Each of the 4 bases are then added to the chip one at that time and the pH is measured. When a nucleotide is incorporated it changes the pH and the signal is recorded. The $50K pricetag is a little decieving, you also need the machinery to produce the DNA coated microspheres and a hefty server to process the millions of ~100 base reads form the machine and assemble them into a useful file. I'm not sure of the specs on our server but I believe it has 12 cores and around 20 gigs of ram, and takes 2-8 hours of processing for each run. There is also the consumables to think about. The DNA oligonucleotides that server as primers and the chemicals. All tolled it is more like $150K for the parts adn 500-1500 per run.

Re:G, A, T, C

[chemicaldave]

Already covered with the Genetic Information Nondiscrimination Act.

Re:G, A, T, C

[TaoPhoenix]

Valiant attempt sir.
Too bad we don't bother to follow laws anymore.
We're 7 days from economically blowing up our country, so a little "ethics" law won't stop anyone.

Re:Sounds great?

[ColdWetDog]

What will having your genome sequenced actually do for you, today, right now? Why should I pay $1k or even $50k for something like this?

Virtually nothing. There have been several companies that have tried to cash in on the 'personal genomics' craze (23andMe comes to mind) that actually didn't do a whole sequence, just SNP (single nucleotide polymorphisms) that purported to help you determine your risk of various diseases. Except that they found precious few diseases that had clear links to SNPs. Whole genome sequencing will be even harder to figure out.

So other than bragging rights, it does you little good. For research purposes, getting fast, accurate (and see the AC's post above concerning the Sanger Method and accuracy) and cheap sequences will be very useful. For personal use, not so much.

the dawn of hype itself!

[tverbeek]

"...may unlock the door to ...life itself"

Well, it's about time! The universe has been sitting lifeless for so long, and here we sit, unable to make any!

Re:23andMe

[Scubaraf]

There is an open source DNA sequencing project out there: http://www.polonator.org/

But the fact is that it is still expensive as a hobby.

Personal DNA Machine

[hyades1]

For the love of god, don't let one of those machines find its way into the southern United States. Can you imagine what damage it would do to the family trees if they had ironclad proof of how many hillbillies didn't understand that even if they got divorced, they're still brother and sister?

Gattaca

[Chuby007]

Gattaca, Gattaca, Gattaca !