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WASHINGTON — Federal regulators alleged Tuesday that an Illinois-based company bought the only two medicines approved to treat premature babies born with a potentially life-threatening congenital heart defect, and then increased prices nearly 1,300 percent.

The Federal Trade Commission said in a civil lawsuit that Ovation Pharmaceuticals Inc. illegally maintained a monopoly in drug treatments for the heart defect. The commission seeks to prevent Ovation from maintaining simultaneous interest in the two drugs — NeoProfen and Indocin. Also, it seeks forfeiture of all unlawfully obtained profits.

The commission said Ovation purchased the rights to Indocin in August 2005 and then acquired the rights to NeoProfen five months later. It set the price for the two medicines at about $500. Before the second acquisition, Indocin was priced at $36.

An estimated 30,000 babies are treated with the drugs each year.

“Ovation’s profiteering on the backs of critically ill premature babies is not only immoral, it is illegal,” said FTC Commissioner Jon Leibowitz in a statement issued separately from the lawsuit.

Ovation Pharmaceuticals Inc., based in Deerfield, Ill., rejected the commission’s allegations. It said NeoProfen is superior to Indocin and is not interchangeable for most premature infants with the heart defect.

The company “welcomes the opportunity to demonstrate in court in Minneapolis that the FTC’s allegations and claims are without merit,” Ovation said in a prepared statement.

The FTC said the only alternative to treating the heart defect, known as patent ductus arteriosus, is surgery, but that option carries a risk of serious complications and costs far more than treatment with drugs.

Indocin was approved by the Food and Drug Administration to treat the heart defect in infants in 1985.

Ovation purchased the rights to Indocin from Merck and Co. Ovation purchased the U.S. rights to NeoProfen in January 2006 from Abbot Laboratories Inc.

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