Gene Sequencing

If someone brought you an odd piece of electronic hardware and you wanted to identify it, you’d probably look for markings on the outside first. If that didn’t work out, you might look under the cover and read some markings on the board or key components. However, in a tough case, you might dump the firmware and try to guess what the device is or what it does by examining the code that makes it run. That’s kind of what [Ciro] did. Wanting to determine the bacteria in a water sample led to using relatively inexpensive DNA sequencing hardware to look at the DNA present in the samples. This would have been a huge undertaking for a well-funded lab just a few short years ago. Now it just takes a USB device and some software.

Of course, inexpensive is in the eye of the beholder. The micropore sequencer costs about $500 and has a one-time use consumable cost of about $500, although that’s enough to process about 10 human genomes. The technology depends on using a small pore only large enough to pass one strand of DNA at a time. Blocks of nucelotides cause different amounts of electrical current to flow through the pore.

Continue reading “Sequencing DNA For Metagenomics” →

Hitting the electronic surplus shop is probably old hat to most of our readership. Somewhere, everyone’s got that little festering pile of hardware they’re definitely going to use some day. An old fax is one thing, but how would your partner feel if you took home an entire pallet-sized gene sequencing rig? Our friend [kaspar] sent along an interesting note that the folks at Swiss hackerspace Hackteria got their hands on an Illumina HiSeq 2000 last year (see funny “look what we got!” photo at top) and have generated a huge amount of open documentation about whats inside and how to use it.

Okay first off, what the heck is this machine anyway? The HiSeq is designed to automatically perform the sequencing step of Illumina’s proprietary multi step gene sequencing process (see manufacturer’s glossy for more), and to do so with minimal human intervention. That means that the unit contains a microfluidics system to manipulate samples, an extremely high performance optical scan system complete with controllable stage, imager, fluorescence modes, etc, and lots of other things this author isn’t sufficiently trained to guess at.

The folks at Hackteria have done a pretty thorough teardown of the system and produced block diagrams of most of its modules. They’ve also run some of the tools and recorded logs of what they were up to, including the serial commands sent to and from the machine to control certain subsystems. Of course a tool like this was meant to be driven by Illumina’s specific software, but unusually those are available and surprisingly usable which is how the aforementioned logs were captured. Right now it looks like Hackteria has put together tools to use the system as a fluorescent microscope.

Oddly the most interesting thing here might be how available these systems are. It appears that they’re being replaced en masse and have become easily available in the range of thousands of dollars on the secondary market. At that price point they’re almost worth snapping up for the enclosure and parts! But we prefer Hackteria’s goal of enabling the Citizen Scientist to make use of these incredible machines for their intended purpose. Who knows what exciting projects we’ll find when hackers start sequencing their cats!

Thanks for the tip [kaspar]!