Silicone chipmaker fights for patent rights, IPO

Biochips, or silicone (not silicon) microchips that speed up the process of traditional lab tests, can help researchers track the migration of wild salmon. Or analyze the genetic makeup of an unborn child.

They can also spark drama in the courts.

This week, South San Francisco-based Fluidigm filed a request for declaratory judgment in a U.S. District Court of New York on patents involving its BioMark system for genetic analysis, a rubber chip that can be used to analyze liquids on a nano-scale. According to the filing, Fluidigm rival Applied Biosystems had charged the company with violating its patent and asked Fluidigm to "cease and desist" from selling BioMark technology. Fluidigm is asking a court to decide.

The legal tussle comes nearly two months after Fluidigm filed to raise as much as $86 million in a public offering. The company, founded in 1991, isn't yet profitable. It has recorded a deficit of $133.8 million as of December 29, 2007, because of research and development of its technology, according to its prospectus.

But the company has recently updated its so-called integrated fluidic circuit system so that it can allow for even more finite research. Fluidigm has devised a lab-on-a-chip array with approximately 25,000 valves and 18,000 chambers, along with a computer to control and analyze biological samples piped into the chip. The new chip, which is capable of conducting more than 9,000 biochemical experiments, is about 1.5 inches on either side and is enclosed in a 4x6-inch housing.

Effectively, the BioMark system can replace more traditional, and more costly, lab equipment used by drug researchers, hospitals, or even wildlife scientists.

The Alaska Fish and Game Department, for example, has used the biochip to perform genetic analysis on migrating fish. Salmon return to where they were born to breed, and the populations from various locations are slightly genetically different, so a gene scan can tell a scientist where a fish was born and where it's headed during breeding time. With the data, the Fish and Game Department was able to determine what fishing grounds to open.

Gajus Worthington, Fluidigm's CEO, said that with its newest chip, the Fish and Game Department can conduct analysis for about 5 cents per data point, versus about 20 cents per data point for conventional stacks of test tubes.

The company's technology is also being tested for use in geno-typing, or analyzing the composition of genetically modified food seeds. And its arrays are so tiny that researchers can use it to detect the DNA of a fetus at only 11 weeks from the blood sample of the mother, according to Worthington.