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Safer Prenatal Testing

New technologies aim to reduce the risks and improve the accuracy of prenatal genetic tests.
April 23, 2008

Amniocentesis and chorionic villus sampling remain the gold standard for detecting genetic abnormalities such as Down syndrome in a developing fetus. But because these procedures are invasive and can cause miscarriage, their use is normally only advised for women with known risk factors. Now a handful of emerging tests suggest that in the near future, it may be possible to detect genetic defects with a simple blood draw from the mother.

A telltale triplet: The cell above originally belonged to a fetus, but it leaked through the placenta into its mother’s bloodstream, where it was picked up by a simple blood draw. Using sophisticated microfluidic technology and sticky antibodies, a new technology developed by Biocept plucked out this single fetal cell from among millions of maternal cells. Next, fluorescent molecular tags were used to stain the most important chromosomes: two copies of the X chromosome (light blue) mean that the fetus is female, and three copies of chromosome 21 (pink) mean that it suffers from Down syndrome. If this noninvasive test stands up to clinical validation over the next few months, it could revolutionize prenatal testing for Down syndrome.

“The holy grail all along is to give women a diagnosis without having an invasive procedure,” says Joe Leigh Simpson, executive associate dean for academic affairs at the Florida International University College of Medicine and a pioneer in the field of noninvasive prenatal testing.

While the placenta serves to separate the fetus’s circulatory system from the mother’s, a minuscule amount of free-floating fetal nucleic acid and a small number of fetal cells can be found circulating in the mother’s bloodstream. For decades, scientists have been searching for ways to isolate and characterize these potential clues to the genetic status of a developing fetus.

It’s relatively straightforward to purify circulating snippets of DNA and RNA and analyze their sequences, but distinguishing fetal nucleic acids from those of the mother remains a challenge. Particularly in the case of Down syndrome, in which the defining feature is an extra copy of chromosome 21, it’s tough to tally how many copies the fetus has without an intact fetal cell.

To get around this roadblock, Dennis Lo, professor of chemical pathology and medicine at the Chinese University of Hong Kong, takes advantage of SNPs–commonly occurring single-letter differences in a given gene. A normal fetus with two copies of chromosome 21 might have two different spellings of a particular gene on that chromosome, expressed in a one-to-one ratio. A Down syndrome fetus would have an extra copy of one version, yielding a two-to-one ratio.

By analyzing the ratios of RNA produced by SNP-containing genes, researchers can indirectly count fetal copies of chromosome 21. The more SNPs included in the analysis, the more accurate the outcome. Sequenom, a molecular diagnostics company based in San Diego, is currently working to adapt Lo’s work into a clinical test for Down syndrome.

Other genetic disorders, such as Rh incompatibility syndrome, are more readily amenable to an analysis of fetal nucleic acids from the maternal bloodstream. Rh is a protein found sticking out of the red blood cells of individuals with Rh-positive blood. If a mother is Rh-negative, her immune system may react violently to an Rh-positive fetus. In this case, scanning the mother’s bloodstream for the presence of the Rh-encoding gene or its corresponding RNA provides a simple way to determine whether preventative treatment will be necessary. Traditionally, all Rh-negative pregnant women are treated–unless the father is known to be Rh-negative as well–even though only a fraction of them carry an Rh-positive baby.

Although Rh tests based on this approach have been in use in Europe for years, the first U.S. version, developed by Lo in conjunction with Sequenom and implemented by Lenetix Medical Screening Laboratory, just hit the market last December.

Diana Bianchi, a professor of pediatrics, obstetrics, and gynecology at the Tufts University School of Medicine, says that Sequenom’s Rh test is promising but not perfect. “It will be interesting to see whether obstetricians in the United States are willing to take the risk of a false negative,” she says.

A similar technology developed by Biocept, also based in San Diego, has likewise been clinically validated, and it will launch in early May. It expands upon Sequenom’s approach by scanning for a large number of SNPs that distinguish between maternal and fetal DNA. That way, a negative result can be confidently attributed to an Rh-negative fetus rather than to a failure to detect the Rh-encoding gene.

A complementary approach to noninvasive prenatal testing involves isolating fetal cells, rather than nucleic acids, from the maternal bloodstream. This strategy is especially amenable to testing for Down syndrome and other chromosome copy number defects. With fetal cells on hand, diagnosing Down syndrome is straightforward: all it takes is a probe to fluorescently stain chromosome 21 and a microscope to count how many copies are present.

“If you can get an intact fetal cell, you have access to the entire fetal genome noninvasively,” says Bianchi. “So that’s what’s enchanted people for a long period of time.” But because a milliliter of maternal blood contains fewer than five fetal cells, this tactic presents enormous technical hurdles.”You’re on the hunt for extremely rare cells,” says Bianchi.

Biocept deals with this challenge by targeting immature, nucleated red blood cells (NRBCs), which are much more likely to come from the fetus than from the mother. NRBCs can be sorted from other cell types using antibodies that latch on to proteins unique to their surfaces, and their unusual morphology makes them easy to spot under a microscope.

“When you find an NRBC, chances are it’s going to be fetal,” says Farideh Bischoff, Biocept’s vice president of translational research and development.

The Biocept cell-based testing platform uses a microfluidic system, in which the mother’s blood is channeled across a surface studded with antibodies that capture immature red blood cells. The surface is microscopically engineered to maximize the blood’s exposure to the antibodies, dramatically upping the chances of pulling out any immature red blood cells that may be present.

Biocept will begin clinical evaluation of this platform next month as a noninvasive Down syndrome test, and it may become commercially available before the end of 2008.

Another company tackling the fetal-cell-based approach to noninvasive prenatal testing is Ikonisys, based in New Haven, CT. Instead of physically sorting NRBCs from other cell types, Ikonisys takes a brute-force computational approach. The company has developed an automated microscope that scans slide after slide of maternal blood, using cell shape to distinguish fetal cells from other nucleated cell types. The microscope includes software that compiles the locations of potentially relevant cells, obviating the need for a more subjective manual scan and thus reducing human error. A technician can then inspect those cells and make a final ruling on their status.

“Rather than mechanically filtering, we’re using a combination of visualization and artificial intelligence,” says Paul White, CFO and president of Ikonisys. “The microscope does the hard part.”

Ikonisys plans to launch its Down syndrome test in late 2008. The company is also adapting its technology for use in oncology, where the ability to identify rare cancerous cells in a sea of healthy cells could help diagnose certain cancers and monitor their response to treatment.

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