Stephen Quake's chips may revolutionize gene study

The microchip revolutionized electronics, making computations faster and cheaper. Stephen Quake says his "microfluidic chip" could help do the same for drug discovery, prenatal testing and other genetics applications.

"We think about it as the biological equivalent of the integrated circuit," says Quake, a 41-year-old bioengineering professor at Stanford University.

His chip dramatically streamlines genetic research: An experiment that would have required a week and 18,000 steps using standard lab equipment can be done in three hours and 200 steps.

Today, scientists deciphering DNA must painstakingly place samples and reagents into trays, wait for reactions, and then repeat the process over and over. Quake's chip automates this. Its key component is a series of tiny rubber valves that can be pinched closed by pressurized gas to form tiny chambers.

Quake and researchers in his lab came up with the design for the valves while he was teaching at Caltech in 1998. The following year he co-founded Fluidigm to figure out how to manipulate tens of thousands of chambers, each about the size of a dot of ink, on a patch of silicone rubber smaller than a saltine.

Instead of filling trays repeatedly, scientists load Fluidigm chips with samples and reagents, and a countertop controller automatically fills the rubber chambers with every possible combination.

The chips, which South San Francisco-based Fluidigm makes in Singapore, assist in work that requires looking for hundreds of genetic variations in hundreds of samples.

The Alaska Fish and Game Department uses them to manage salmon runs. Because salmon are genetically programmed to return to spawning spots, researchers can use gene analysis to predict where they're headed. They catch salmon on their way to breeding grounds, punch holes in their fins, treat the tissue to isolate strands of DNA, and then run the samples through Fluidigm's chips.

The technology screens samples fast enough to predict the course of whole salmon populations and guide fishing fleets.

"There's tremendous upside for this technology," says Kevin Davies, the author of "The $1,000 Genome."

Fluidigm's chips have shown promise for developing less-invasive forms of prenatal testing, for instance, by screening the minute quantities of a fetus' DNA found in the mother's blood. Fluidigm's customers - primarily universities, national labs, seed companies, fish and game managers, and drugmakers - pay $400 to $900 per chip.

Quake has made headlines for genetics technology before. In 2009 he used a machine of his own invention, the $1 million HeliScope, to analyze his DNA and become the eighth person to have his genome decoded.

As Davies puts it, Quake "has already guaranteed himself an entry in the genome history books."

This article appeared on page D - 2 of the San Francisco Chronicle