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

[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: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.