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Pregnant women seeking prenatal tests for genetic defects face difficult choices. Either they accept less-than-reliable blood tests or ultrasound interpretations that leave them anxious and guessing, or they choose amniocentesis, which punctures the embryonic sac and has a small risk of causing miscarriage.

Researchers have long envisioned the day when a test of the mother’s blood or urine could conclusively detect a genetic defect in her baby. Xenomics, a New York City-based biotech firm, is now conducting the first clinical studies of a urine test that, it says, can detect Down syndrome in the fetus.

A pregnant woman’s blood and urine both contain fragments of her fetus’s DNA. Xenomics’ advance is based on its discovery of specific DNA markers, called methylation sites, that may indicate whether a fetus has a chromosome abnormality related to Down syndrome. The Xenomics test under development uses standard DNA amplification technology to spot the markers in a urine sample.

Xenomics is now conducting human clinical studies with two U.S. hospitals and hopes to submit the test for U.S. Food and Drug Administration approval in mid-2007.

The basic technique could work for certain other genetic disorders; ones that result from a mutation in a single gene are likely to have their own methylation markers, researchers say. Farideh Bischoff, a reproductive geneticist at Baylor College of Medicine in Houston, says scientists have identified the mutations that cause cystic fibrosis, Huntington’s disease, beta-thalassemia, and other ailments.

Although DNA tests for these diseases have been developed, says Bischoff, they require full strands of DNA found only in cells, not just the fragments that can be most easily found in maternal blood or urine. “Clinical trials using DNA fragments haven’t been pursued to validate [them],” she says. But Bischoff predicts clinical trials will begin within five years and lead to new prenatal tests. “I think noninvasive testing is going to take over,” she says.

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