High Speed Sequencing of Single DNA

The MIT Technology Review reports about an innovative Massachusetts company’s efforts to develop a system for cheap and efficient DNA sample analysis and comparison:

The sequencing of the human genome is one of biotech’s greatest technical achievements to date. But some biomedical researchers argue that they won’t truly understand how genes contribute to health and disease–and so won’t be able to turn genomic knowledge into new cures and treatments–until they can compare, letter by letter, the DNA sequences of thousands of sick and healthy people. And that is just not possible with today’s technology; using about 100 state-of-the-art sequencing machines to fully sequence the 3.2 billion DNA letters that make up one person’s genome would take six months and cost $20 million to $30 million…
Helicos’s technology eliminates many of the expensive and time–consuming steps that are central to conventional DNA sequencing. The machine works, in essence, by photographing the process of DNA replication.
Technicians chop up the DNA to be sequenced into short pieces just a few hundred letters long and split each piece into single strands, which will serve as templates for new DNA copies. They take about 1.2 billion of those templates and chemically anchor them side by side, like tiny bristles, on a glass slide. The Helicos machine then washes the slide with DNA-synthesizing enzymes and fluorescently tagged versions of the DNA bases-the molecular building blocks represented by the familiar DNA letters. It introduces copies of just one base at a time; wherever a template strand calls for that letter in the next open position, the enzymes incorporate it into the growing DNA copy. The machine then washes out the extra, unincorporated bases and takes a picture that reveals the newly incorporated bases as dots of lights. Once it has captured an image, the device pumps in chemicals that stop the new bases from glowing, in preparation for another cycle of washes and photos.
The Helicos machine repeats the whole process over and over, building up the new DNA copies one letter at a time. A computer analyzes all the captured images to determine the sequence of each short strand; then, using the published human genome sequence as a guide, it pieces all the short sequences together into a single complete one. When Helicos’s commercial machine is released, says Lapidus, it will sequence a whole genome start to finish in three days and for a cost of $5,000.
Helicos’s basic approach to sequencing, called “sequencing by synthesis,” is not unique. But what makes the company’s system different from others under development is that it doesn’t require that the sample DNA be copied many thousands of times before sequencing. Skipping the copying step translates into easier preparation of samples and lower costs…

The company is planning to “place the device in an academic lab for testing by the end of the year. Helicos’s first commercial sequencing machines will be ready for sale by the end of 2006 or early 2007, says president and CEO Stan Lapidus.”
The technology…
More at Helicos BioSciences…