Officials at the National Institutes of Health believe they can still obtain a patent for more than 2,400 gene fragments despite an initial rejection by the U.S. Patent and Trademark Office.
The NIH's application to patent gene sequences that it discovered a year ago was intended to protect the nation's biotechnology industry.
Instead, it has caused a contentious debate between the government and academic researchers who are trying to draw a map of the 50,000 to 100,000 genes in the human body.
The initial rejection of the patent application was for gene fragments for which no function was yet known.
The move could pressure the federal government to consider legislation or an international agreement to prohibit patenting of gene fragments, according to Bernadine Healy, director of the NIH.
But in announcing the patent rejection Tuesday before a Senate Judiciary subcommittee, Dr. Healy said that patent attorneys outside the NIH have advised her that the institutes might be able to satisfy the concerns of the patent office.
The patent office is prohibited by law from commenting on any applications before it. But a spokesman for the office said 90 percent of all patent applications are initially rejected.
"It is the exception for someone to get a patent on the first determination," said the spokesman, Gil Widenfeld.
The patent office initially rejected the application, according to Dr. Healy, because small pieces of the new gene fragments had been published in scientific journals and because they had been discovered from gene-sequencing libraries.
In addition, the office said the use for the gene fragments had not been identified.
NIH had applied for the patents because it feared that, if its scientists published the identification of thousands of gene sequences, biotechnology companies might not be able to apply for patents after a use for the genes was discovered.
Companies have no incentive to develop drugs or genetic therapies to treat illnesses if they cannot protect it with a patent. The NIH said that if it received patents on the gene fragments, it would allow companies to license the patents from the government.
Patenting genes has been allowed by the patent office when a use for the gene is known.
Not everyone agrees with the NIH position.
"I believe that one should not grant patents on natural sequences, particularly little snippets of genes, when you haven't the slightest idea of what its function is," said Victor A. McKusick, a professor of medical genetics at Johns Hopkins University and an authority on the human genome, the map of all genes in the human body. "All [the NIH] has done is determine a part of the human anatomy."
If many gene fragments were patented, it could, in fact, slow down research by scientists who are trying to identify the use of entire genes, because the scientists would not hold the patent to such genes, he said.