Hyseq Inc. said it has filed more than 63,500 patents on gene discoveries — many of them rarely expressed genes — found by massive high throughput sequencing.

About 12,000 gene patent filings were disclosed late last year. The rest have been made since then, and were made public in the company's annual report.

"We routinely do a half million samples per tissue," said Lewis Gruber, president and CEO of Sunnyvale, Calif.-based Hyseq. "Finding copies of rarely expressed genes is a matter of statistics, and by doing more samples, we're more likely to find them."

By comparison, companies such as Incyte Pharmaceuticals Inc., of Palo Alto, Calif., and Human Genome Sciences Inc., of Rockville, Md., "routinely [sequence] a few thousand per tissue sample, or 5,000, or in rare cases 20,000," Gruber said.

Among the rarely expressed genes, about 45 percent are new, he said.

Top-selling drugs such as erythropoietin (EPO) and tissue plasminogen activator (tPA) are made from rarely expressed genes. "Either the genes are expressed at low levels and act at low levels or they are found in very few cells of a tissue," Gruber said.

EPO, an anti-anemia drug, is marketed by Amgen Inc., of Thousand Oaks, Calif., and Ortho Pharmaceutical Corp., a division of New Brunswick, N.J.-based Johnson & Johnson. South San Francisco-based Genentech Inc. sells tPA, a thrombolytic used to treat heart attacks.

"We're trying to get as many as we can find functions for initially, and have some sort of utility to support a filing," Gruber said. "We don't want to let anything slip through our net."

Hyseq's stock (NASDAQ:HYSQ) closed Thursday at $10.625, up $0.50. — Randall Osborne