The $30 genome is coming soon

Dozens of companies are racing to sequence the entire genome with their next generation machines, charging anywhere from a few thousand to a tens of thousands of dollars. David Weitz has figured out a cheaper way to sequence the entire genome: It would only cost $30.

Harvard's physicist Weitz announced at the Consumer Genetics Conference in Boston the world's first "affordable" DNA sequencing machine. The trick was minimizing the amount of chemicals used in sequencing.

Before you get excited about this, there's a slight disclaimer: The machine is being developed to sequence the entire genome and will be available in about two years. There will be a machine that does a fraction of the genome available in less than a year.

Still, Weitz's sequencing method could popularize personal medicine, make consumer genetics more affordable, and democratize genetic research. Weitz recognized the commercial potential of his laboratory experiment, so he co-founded a startup called GnuBio.

Weitz worked on the technique for 7 years to improve the technology that allowed them to manipulate the drops to make them function as tiny test tubes. He has already used drops made with microfluidics to create a product to protect active ingredients in cosmetics and has used the drops as test tubes for selective amplification of genomic DNA.

"A colleague of mine suggested we do sequencing years ago. I didn't pay attention to him until two to three years ago. I didn't appreciate how inexpensive and fast it would be," said Weitz. "I realized our way was much faster and much cheaper. It's a totally different use of microfluidics, but it's basically the same technology."

Essentially, water droplets will act like a test tube. By placing a piece of DNA in with appropriate chemicals in each drop, the genome can react and sort itself out. According to GenomeWeb:

"What we have done in my lab is learned how to control and manipulate these drops, so we can fill them, let the reaction take place, and read them at rates of something like a million drops a second," he said.

By filling small droplets with reagents and tagging them with labels, the water droplets are dished out on the microfluidic chip and then the DNA organizes itself into a readable form. The Boston Globe reported:

“It’s the size of the test tube’’ that makes the difference, Weitz said. “We’re just doing tiny volumes . . . We use known methods, proven methods. We just scale it down and use a lot less material and [do it] a lot faster.’’

The genome can be sequenced 30 times for a more accurate read. According to Technology Review, Weitz's sequencing genius would ideally work like this:

• take short strands of DNA and put them in drops
• put an optical bar code in drops for identification of the known strands
• mix the known strand with an unknown strand
• if the bases can bind together, the color of the drop will change
• use a microscope and camera to see the color of the drop (like looking at glare on a window)

So far, Weitz's team has completed only some of these steps. Pretty soon, GnuBio will sell the machines for $45,000: The first two customers are Ignite Institute and the University of Montreal's Beauleiu-Saucier Pharmacogenomics Centre.

"The instruments that we deliver would look for mutations in known genes and would do this very rapidly and very cheaply," said Weitz.

In the future, the database will be open for researchers to use. For instance, cancer research could benefit tremendously. Scientists could sequence entire tumor genomes cheaply, which would allow them to find rare variants in the tumor.

But it's not exactly smooth sailing from here. Harvard geneticist George Church told Technology Review, "the biggest hurdles will be integrating the different steps of sequencing, such as sample preparation, and creating good, user-friendly software."

Weitz is quite confident he will solve all the problems to get an instrument out by the end of the year.

"We are not inventing new science to do this, the technology we are using is all known technology — we are doing it with much smaller containers. We've demonstrated all the proof of principle, there's just a lot of detail in the engineering that needs to be worked out," said Weitz.

Photo: ynse / flickr

Updated

This post was originally published on Smartplanet.com