Sequenom Inc.’s best-known product is designed to test for Down syndrome, but the genetic testing products company said Tuesday that there may be an even larger market is other kinds of prenatal testing.

San Diego-based Sequenom hopes to begin marketing its SEQureDx test in early 2009. Speaking at a health care conference, Chief Executive Harry Stylli said the market for testing for prenatal chromosomal disorders like Down syndrome could be $3 billion to $5 billion worldwide. But a larger opportunity may exist in testing for tiny variations in the genetic code that can cause inherited diseases like autism, heart ailments, cystic fibrosis and birth defects.

“We expect this opportunity … to actually grow and dwarf chromosomal disorders over time,” Stylli said. “It represents the greatest number of disorders, even though some of them are very rare.” He added that the field has “immense growth potential.”

The genetic variations are called single nucleotide polymorphisms, or “snips.” Over time, the company hopes to find the genetic markers associated with many other birth defects, allowing for testing that will determine if a fetus will be born with them.

Speaking at the annual Lazard Capital Markets health care conference, Stylli said there are already multibillion-dollar markets for many inherited diseases. About 6 percent of all babies have a birth defect, Stylli said, and 30 percent of those are due to an inherited condition.

“There are many other things that you’d like to be able to test for,” Charles Cantor, Sequenom’s chief scientific officer, said in a telephone interview. “Down’s is the single most common fetal defect, but it’s the tip of the iceberg

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