Is a gene more like a tree trunk or more like a baseball bat? A federal court Thursday took a stand on the question, ruling that isolated DNA molecules are “not found in nature”, and are therefore more like inventions, such as baseball bats, than natural phenomenon, such as tree trunks.

Using language steeped in metaphor in a packed U.S. federal courtroom, attorneys in July debated the question in a closely-watched case on the right to patent genes that has been working its way through the courts.

At stake: the right of one company – Myriad Genetics – to patent a gene as a human invention under U.S. patent law, which allows patents on inventions but not on products of nature.

In a ruling that largely upheld the status quo in a biotech industry that has been patenting genes for decades, the U.S. Court of Appeals for the Federal Circuit ruled Thursday that “isolated” human genes are patentable. Methods of “comparing” or “analyzing” DNA sequences are, however, not patent eligible, it ruled.

In a two-to-one decision, the court affirmed Myriad’s right to claim intellectual property rights on the BRCA-1 BRCA-2 genes, genes where mutations indicate a woman has an 82 percent increased risk of developing breast cancer.

The company’s patents on the genes are the basis of a breast cancer indicator test that has been a profitable asset in the company’s portfolio of intellectual property.

The American Civil Liberties Union (ACLU), representing a group of about 20 plaintiffs, including the breast cancer patient advocates and geneticists, several years ago launched a legal challenge to Myriad’s right to patent the genes.

The plaintiffs, including patient advocacy group Breast Cancer Action, have argued that Myriad’s IP rights to the genes allow it to block others from testing for – or even looking at – the BRCA-1 and BRCA-2 genes, a right they say Myriad has exercised in the past with legal threats.

Plaintiffs have also argued the patents raise prices for testing and essentially create a market monopoly which blocks the poorest from getting tested and stifles scientists who want to look at the genes. Yale geneticist Ellen Matloff, a plaintiff in the case, told IPS last year the situation was “horrifying.”

Matloff told IPS that 95 percent of patients she recommended for Myriad’s 700-dollar supplementary BART test, which looks for mutations on the BRCA-1 and BRCA-2 genes, opted not to get it because of its high cost.

Furthermore, those who question gene patents have pointed out that patenting individual genes might even be myopic, especially in a world of whole genome sequencing where the scientific community is increasingly interested in gene interactions, the influence of the environment on genetics (called epigenetics), and other big-picture indicators to understand patient health.

The case has been working its way through the courts. A New York district court judge sided with the ACLU in 2010, but the Federal Circuit Court of Appeals overturned the ruling in July 2011.

The ACLU appealed to the Supreme Court last year, but the Court declined to issue a ruling in the case. Instead, it sent the case back to the Federal Circuit to re-examine in light of its unanimous spring decision that Prometheus Laboratories Inc. did not have a right to patent a certain blood test because the patent was based on observations about natural phenomena.

But Thursday, the Federal Circuit again ruled that genes are patentable. The court wrote, “The isolated DNA molecules before us are not found in nature. They are obtained in the laboratory and are man-made, the product of human ingenuity.”

In its majority opinion the court also highlighted that gene patenting had been standard practice for the U.S. Patent and Trademark Office (PTO) for years.

“Why hasn’t this come up in 30 years,” Circuit Judge Kimberly Moore, who sided with the majority, asked during oral arguments in the courtroom July.

Moore hinted at the biotech sector’s financial stake in gene patents, often key components of diagnostic test IP at the centre of a much-hyped personalized medicine industry. “What about the biotech sector and all the money?” Moore asked.

In his dissenting opinion, Circuit Judge William Bryson wrote, “my colleagues assign significant weight to the fact that since 2001 the PTO has had guidelines in place that have allowed patents on entire human genes… I think the PTO’s practice and guidelines are not entitled to significant weight…”

Sandra Park, an attorney with the ACLU, told IPS her team was disappointed in the Federal Circuit court’s decision, which she said she believed did not take the Supreme Court’s ruling in Prometheus adequately into consideration.

“We think that the Supreme Court’s recent decision is very clear that the Court is very concerned about how patents interfere with scientific work,” Park told IPS. “The Supreme Court has said that the interests of industry in relying on patent protection is not a factor in determining that something is patentable.”

Park said the mere fact that Prometheus argued that it needed its patents to advance its interests, in the Supreme Court’s ruling, was insufficient reason to justify patents.

If the ACLU decides, with the other plaintiffs, to appeal the Federal Circuit court’s decision, it is possible the Supreme Court might decide to hear the case. Such a scenario is not unheard of. In fact, Park said, the Supreme Court decision to overturn Prometheus’s right to its diagnostic patent came after the Federal Circuit twice upheld it.

Park said the ACLU was still deciding its next step. “We are reviewing our options, but we haven’t made any decisions yet.”