New chip able to sequence genome in hours!

For the discussion of the sciences. Physics problems, chemistry equations, biology weirdness, it all goes here.

Moderators: gmalivuk, Moderators General, Prelates

User avatar
Sanjuricus
Posts: 72
Joined: Tue Jun 21, 2011 10:02 am UTC

New chip able to sequence genome in hours!

Postby Sanjuricus » Wed Jun 22, 2011 10:02 am UTC

I've just read an article on Extremetech about a new chip that will be able to sequence entire genomes in just a few hours (Linky)

The article alludes to the possibilities of this new technology but I was wondering what you guys think the possible benefits of this new technology might be?

One area that springs to mind is criminal forensics...much better description of a suspect from their DNA left at a crime scene etc etc....all available within a couple of hours via an automated process.
Mostly kind of almost...ish.

User avatar
Dopefish
Posts: 855
Joined: Sun Sep 20, 2009 5:46 am UTC
Location: The Well of Wishes

Re: New chip able to sequence genome in hours!

Postby Dopefish » Wed Jun 22, 2011 12:18 pm UTC

It seems to be a bit too good to be true without looking into it too much.

It strikes me as one of those things that might possibly work in a few very specific instances in theory, but when put into practice issues might surface, or the chip itself might be a long ways off from actually being anywhere near as capable as the article suggests. I can imagine a quantum computer that can break RSA encryption in a matter of hours, but that doesn't mean that's going to happen any time soon.

If it all does work and is practically realisable, awesome. The bio-ish types who rely on genome sequencing will be able to work all sorts of magic with it and we'll all be the better for it.

qetzal
Posts: 862
Joined: Thu May 01, 2008 12:54 pm UTC

Re: New chip able to sequence genome in hours!

Postby qetzal » Wed Jun 22, 2011 3:21 pm UTC

It's real stuff, and is already commercially available. The particular platform described in the OP's link is just one of many so-called 'next-generation' sequencing platforms. Here's a recent review of a bunch of them. It's behind a pay-wall, but you can browse updated comparison tables here.

One point of info. When they say they can sequence an entire genome in just a few hours, I think that refers to instrument run-time. It ignores the much, much longer front-end time needed to prepare the samples before they ever go into the instrument, and also (I think) ignores the back-end time for data processing to actually generate the "final" sequence.

User avatar
a-wan
Posts: 5
Joined: Thu Jun 09, 2011 3:51 pm UTC

Re: New chip able to sequence genome in hours!

Postby a-wan » Wed Jun 22, 2011 5:14 pm UTC

The main reason people do whole genome sequencing is to discover rare variants that affect diseases or other outcomes of interest. Two limiting steps are time and money. If it becomes cheap and quick then this can be used in clinical studies and trials to identify genetic risk factors used in counseling patients and choosing the safest and most effective drugs. Cheap and fast whole genome sequencing could be key to provide personalized medicine that is sometimes spoken of, but that requires that genetic risk factors be actually present for a given condition, and I'm sure there are several conditions that have been deemed to be heritable that just aren't.

Common variants can currently be found (or at least the signature of common variants) using genome-wide association studies based on genotyping chips that determines a persons genotypes at what is usually between 100,000 and a little over a million points in our DNA. Whole genome sequencing can provide information for almost all of the approximately 3 billion bases.

The article you linked to also points out that we can sequence bacteria and viruses to create treatments for them.

User avatar
justaman
Posts: 498
Joined: Thu Jan 31, 2008 1:53 am UTC
Location: in ur walls eatin' ur internets

Re: New chip able to sequence genome in hours!

Postby justaman » Wed Jun 22, 2011 9:38 pm UTC

qetzal wrote:One point of info. When they say they can sequence an entire genome in just a few hours, I think that refers to instrument run-time. It ignores the much, much longer front-end time needed to prepare the samples before they ever go into the instrument, and also (I think) ignores the back-end time for data processing to actually generate the "final" sequence.

Yeah, the back-end time on these sorts of things is typically huge. From a quick scan on the Ion Torrent page, it seems that it is a short DNA sequence readout of about 200 bp, similar to the ones you get off 454 or SOLiD and Solexa sequencers. IIRC, these sorts of machines produce about 50 bytes/base-pair, and millions-billions of reads/genome. This will mean terabytes of data off the machine and usually in excess of 100 hours of processing for making contigs from the information. This sort of data processing is speeding up though, with cloud computing coming on line (see this Nature article).

Still awesome stuff, these sorts of things are. It'll only get better and faster...
Felstaff wrote:"deglove"? I think you may have just conjured the sickest image within my mind since I heard the term "testicle pop".

User avatar
iop
Posts: 930
Joined: Tue Jul 24, 2007 11:26 am UTC
Location: The ivory tower

Re: New chip able to sequence genome in hours!

Postby iop » Thu Jun 23, 2011 7:03 pm UTC

For research, these next-gen sequencing approaches are awesome. Instead of spending a lot of time trying to clone a mutant allele, you can just sequence the whole genome and you know all the possible mutations causing a phenotype (like done here). All the digestions and gels of PCR products you do when cloning? You can just sequence at every step. After you make a stable cell line, you can sequence to know exactly where you got an integration, and check whether this may be in a potentially silenced region etc.

But yes, computing is hard. For example, we needed to put servers into the same room as the sequencing machines, because it's too slow to transfer data to the servers downstairs via the network.

rflrob
Posts: 235
Joined: Wed Oct 31, 2007 6:45 pm UTC
Location: Berkeley, CA, USA, Terra, Sol
Contact:

Re: New chip able to sequence genome in hours!

Postby rflrob » Sun Jun 26, 2011 6:00 am UTC

When someone is taken ill, Ion Torrent will let us diagnose the exact strain of virus, and then treat it with specialized drugs rather than broad spectrum antibiotics.


This whole article seems much more like a glorified press release, but the above quote is just plain wrong. Antibiotics typically have zero effect against viruses, and using them inappropriately makes it much more likely that antibiotic-resistant strains of bacteria will develop. Next time someone who has a cold tells you they're taking antibiotics, slap them upside the head.
Ten is approximately infinity (It's very large)
Ten is approximately zero (It's very small)


Return to “Science”

Who is online

Users browsing this forum: No registered users and 12 guests