The latest chapter in the legal battle over gene patenting unfolded this week during oral arguments (MP3) made in a Washington, D.C., courtroom. A year after a somewhat surprising victory in a New York federal district court, a group of plaintiffs led by the American Civil Liberties Union (ACLU) and Public Patent Foundation (PUBPAT) now hopes the U.S. Court of Appeals for the Federal Circuit (pdf) will uphold the earlier ruling that invalidated patents on BRCA1 and BRCA2—two genes commonly tested to determine risk for breast and ovarian cancers.

Lawyers for BRCA1 and BRCA2's patent holders—Myriad Genetics, Inc., in Salt Lake City and the University of Utah Research Foundation—led off Monday's proceedings before a three-judge panel by challenging the timing of the plaintiff's original lawsuit in May 2009 and their targeting of the defendants' work on the BRCA genes in particular. But the crux of the case rests on whether the work and expense that Myriad or any other biotech company invests in isolating DNA and sequencing genes should be patentable, or whether these companies are simply cashing in on something readily found in nature.

The appellate judges on Monday drew an analogy between isolating DNA and extracting a mineral from the ground, noting that, despite the effort and technology required to mine diamonds, diamonds are not a patentable product. The defense chose to frame the argument differently. If the discovery of some mineral taken from a mine would not have been possible without "human intervention and human invention," then the result of that discovery should be protected by a patent, lead defense attorney Gregory Castanias, a partner with the Jones Day law firm in Washington, D.C., said during his opening argument.

The lawsuit's plaintiffs claim to represent about 150,00 researchers, pathologists and laboratory professionals as well as breast cancer and women's health groups. Their position is that a gene patent gives its owner the right to prevent anyone from studying or testing that gene. As a result, scientific research and genetic testing has been delayed, limited or even shut down due to concerns about gene patents.

BRCA1 and BRCA2 are of particular concern because of the role they play as tumor suppressors. Women with BRCA1 or BRCA2 mutations are at increased risk of breast, ovarian and other cancers (men with the mutations are at increased risk of breast and other cancers). As a result, diagnostic tests that can detect such mutations are in demand. According to the National Cancer Institute (NCI), about 12 percent of women in the general population will develop breast cancer sometime during their lives compared with about 60 percent of women who have inherited a harmful mutation in BRCA1 or BRCA2. Lifetime risk estimates for ovarian cancer among women in the general population indicate that 1.4 percent will be diagnosed with ovarian cancer compared with 15 to 40 percent of women who have a harmful BRCA1 or BRCA2 mutation.

U.S. District Court for the Southern District of New York Judge Robert Sweet ruled last April (pdf) that copies of DNA isolated by biotech companies are not that different from non-isolated DNA found in the body and therefore cannot be protected by patents.

Nearly 58,000 DNA-based patents have been issued since 1971, according to the DNA Patent Database. A 2005 study published in the journal Science indicated that 4,000, or 20 percent, of the almost 24,000 human genes, have been claimed in U.S. patents.

Although it will be months before the federal appeals court makes a ruling, and that ruling could be subject to further appeal all the way up to the U.S. Supreme Court, the biotech industry eagerly awaits the judges' decision. If the appeals court favors Myriad's right to patent BRCA, thus reversing Sweet's district-level decision, other companies would not be able to offer therapeutics made with the help of that isolated DNA. In the context of gene testing Myriad's ability to hold exclusive patent rights continues to be a way for the company to eliminate its competition, says Bob Cook-Deegan, director of the Institute for Genome Sciences and Policy's Center for Genome Ethics, Law and Policy at Duke University. No one is going to enter the market with a product related to BRCA as long as there is a risk that Myriad can successfully sue them, he adds.

If the appellate court stands by Sweet's decision, something Cook-Deegan thinks is unlikely, the broader biotech industry gets a vote of confidence to pursue work using BRCA1 and BRCA2. Of course, Myriad already has a big head start in this market and its diagnostic tools for hereditary breast and ovarian cancer have been very successful, Cook-Deegan says. The company reported more than $152 million in profits (pdf) for its most recent fiscal year, which ended in June 30, 2010. BRACAnalysis, Myriad's products that provide users with an analysis of their BRCA1 and BRCA2 genes, accounted for $82.5 million of total revenues for the fourth fiscal quarter alone.