Gene sequencing technology, to debut in 2010, aims for $100 DNA analysis in minutes

AUGUST 3, 2009--A new technology designed to read read human genomes faster and more cost effectively than current approaches, Single Molecule Real-Time (SMRT, pronounced "smart") sequencing was presented last week at the 51st Annual Meeting of American Association of Physicists in Medicine (July 26-30, Anaheim, CA). Pacific Biosciences (Menlo Park, CA), maker of the technology, hopes to set a new benchmark with the method, which watches DNA being copied in real time. A device is being developed to sequence DNA at speeds 20,000 times faster than second-generation sequencers now available, and will ultimately have a price tag of $100 per genome. It is due for commercial release in 2010.

A decade ago, it took Celera Genomics and the Human Genome Project years to sequence complete human genomes. In 2008, James Watson's entire genetic code was read by a new generation of technology in months. SMRT sequencing aims to eventually accomplish the same feat in minutes.

The method used in the Human Genome Project, Sanger sequencing, taps into the cell's natural machinery for replicating DNA. The enzyme DNA polymerase is used to copy strands of DNA, creating billions of fragments of varying length. Each fragment--a chain of building blocks called nucleotides--ends with a tiny fluorescent molecule that identifies only the last nucleotide in the chain. By lining these fragments up according to length, their glowing tips can be read off like letters on a page.

Instead of inspecting DNA copies after polymerase has done its work, SMRT sequencing watches the enzyme in real time as it copies each individual strand stuck to the bottom of a tiny well. Every nucleotide used to make the copy is attached to its own fluorescent molecule that lights up when the nucleotide is incorporated. This light is spotted by a detector that identifies the color and the nucleotide--A, C, G, or T.

By repeating this process simultaneously in many wells, the technology hopes to bring about a substantial boost in sequencing speed. "When we reach a million separate molecules that we're able to sequence at once…we'll be able to sequence the entire human genome in less than 15 minutes," said Turner.

The speed of the reaction is currently limited by the ability of the detector to keep up with the polymerase. The first commercial instrument will operate at three to five bases per second, and Turner reports that lab tests have achieved 10 bases per second. The polymerase has the potential to go much faster, up to hundreds of bases per second. "To push past 50 bases per second, we will need brighter fluorescent reporters or more sensitive detection," says Turner.

The device also has the potential to reduce the number of errors made in DNA sequencing. Current technologies achieve an accuracy of 99.9999 percent (three thousand errors in a genome of three billion base pairs). "For cancer, you need to be able to spot a single mutation in the genome," said Turner. Because the errors made by SMRT sequencing are random--not systematically occurring at the same spot--they are more likely to disappear as the procedure is repeated.

Chief Technology Officer Stephen Turner of Pacific Biosciences discussed the technology in a presentation called "Single Molecule Real-Time DNA Sequencers," during the AAPM meeting's 2009 Industrial Physics Forum.

For more information see the page for the AAPM meeting's 2009 Industrial Physics Forum, which focused on "Frontiers in Quantitative Imaging for Cancer Detection and Treatment." See also Pacific Biosciences' web site.

Posted by Barbara G. Goode, [email protected], for BioOptics World.