A DNA Sequencer Cheap Enough For (Some) Doctors' Offices

cylonlover writes "Until recently, DNA decoding machines — fitting in the US$500,000 to $750,000 price range — would take weeks or even months to sequence a human genome, and the whole procedure would cost $5,000 to $10,000. That could be about to change, however, as Life Technologies introduces the Benchtop Ion Proton Sequencer — a machine that may finally deliver the power of genetics into the hands of ordinary doctors thanks to its $149,000 price tag and ability to decode a human genome in one day at a cost of $1,000."

Comments

Unforeseen consequences

[bonch]

Warning--side effects may occur.

Re:Unforeseen consequences

[justforgetme]

omg, the days of GATTACA are finally here! Now I'll never fly to mars ${sadface}

Re:Unforeseen consequences

[zippthorne]

Half of what was happening in Gattaca. Not even the interesting half.

Messing with genes was the logical response to the first half, though, which was gene discrimination. Or did you not notice that the main character was smart enough and driven enough to become a rocket engineer, but because of a chance of a flaw in other areas was relegated to menial labor.

It's not just that they wouldn't let him be an astronaut, either. They wouldn't even hire him as an engineer at all, as a "bad risk." And his love-life was implied to have suffered as well, with the matchmaking sequencers on every street corner....

The movie was about the horrors of discrimination, and the virtue of overcoming them, not gene manipulation, which is not a necessary precondition to gene discrimination. Regardless, I think it was probably supposed to be an allegory to present-day race discrimination, but with a narrative trick to make the character white, so white people wouldn't have any preconceived notions getting in the way of the message, rather than a direct prediction of the future, however prescient it may appear to have been.

Don't believe the hype

[Anonymous Coward]

There are two unfortunate challenges that the Ion Proton approach hasn't yet solved. The first is that the steps required to get the DNA out of human cells and into the sequencer (DNA extraction and especially library preparation) are still frustratingly complex. Their OneTouch device simplifies parts of the library prep but there are still many steps that require highly skilled people doing hours to days of work.
The second major issue is that the genome is being read out in fragments of 200-400 nucleotides, then needs to be assembled. The human genome is full of repetitive regions that are much longer than 200-400nt and when one gets a sequence read from one of these regions, it's can be very difficult to determine which of the copies of the repeat region that sequence came from. Better statistical models and algorithms for genome assembly may solve this to some extent, but there are fundamental limits to what can be done with short sequence reads. Other sequencing technologies don't suffer the short read problem, Pacific Biosciences' hardware for example can read several thousand nucleotide fragments. Mate pairing strategies might be used on the Ion instrument but the library prep for these involves considerably more challenging and manual lab work.

Re:Don't believe the hype

[Samantha Wright]

Pacbio promises a trillion unicorn farts per second. It's hard to take them seriously. As far as medical applications are concerned, the read length in the Ion Torrent system is ten times the size it needs to be, since most (known) diseases occur due to mutations in the very specific and non-repetitive exome, or in its close vicinity. No one (that I know of) has ever seriously proposed using this hardware for de novo sequencing of large eukaryotes, especially since the machine currently on offer doesn't have the well capacity to sequence the whole human genome!

That being said, there's always paired-end reads. I'm guessing the protocol for doing so with this system doesn't exist yet, but they tend to solve most of the repetitiveness problems for shorter read lengths.

Re:Don't believe the hype

[Samantha Wright]

You archive it until you need it. A situation-specific microarray might cost a hundred dollars; those tend to stack up with every hospital visit. With whole exome sequencing like this, you pay the fee once, and have all* the data medical science will ever need about you.

* Not counting repetitive elements, promoter regions, UTRs, spacer DNA, or the epigenome, all of which are known to describe at least a few diseases.

Re:How does that compare to X-ray machines?

[ColdWetDog]

"Ah, I see you have the machine that goes ping. This is my favorite. You see we lease it back from the company we sold it to and that way it comes under the monthly current budget and not the capital account. "

Re:Hospitals

[Samantha Wright]

Gene hacking already is the next nerd occupation (I should know; I'm in the middle of it. Mozilla even funds projects for it.) Here's one starting place if you're really interested.

About the read/write thing: synthesizing large amounts of DNA from scratch still costs ungodly amounts of money. Further, the ABI IonTorrent system being advertised here is a destructive read; you have to treat a blood sample with a large number of chemicals and then stuff it in a big machine. It's no Star Trek scanner.

Hands of ordinary doctors

[nbauman]

Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

"What am I supposed to do with that?"

Years ago, people thought that we could find Mendelian genes for all the important things in health and disease. Now it turns out that most of the important things we want to know are controlled by hundreds or thousands of genes, each of which increases the risk by 1%, sometimes less. That's for things like cholesterol, autoimmune diseases, cancer susceptibility, etc.

For the most part, your family history is a better predictor than any genome screening. Gene tests usually aren't useful unless you have a particular gene in your family and you want to find out whether you have it, like the BRCA genes for breast cancer. If your mother died of breast cancer at age 40 because of the BRCA1 gene, and you don't have the BRCA1 gene, you don't have to worry.

Re:Hospitals

[Samantha Wright]

Yes, but it's fraught with errors, and making a single molecule longer than a few thousand bases costs a great deal. A bacterial genome is 0.4-3 million bases; humans are 3.1 billion in total. That's why only the Venter Institute has done it.

Re:Hospitals

[bill_mcgonigle]

It needs to drop a bit more before seeing it at your local pediatrician's.

And I'm not sure that it ever will. How long has generating a CBC been a solved science? But the pediatrician will still send you over to the hospital's phlebotomy lab to get one.

I guess they do do instant strep tests in the office. When a DNA sequence costs $15 including equipment perhaps they'll do it.

Re: Your sig

[srussia]

I am a biologist. Ask me questions in my journal. I'll give car/computer analogies if possible!

No need for the invite. This is Slashdot. You had us at "Samantha".