Chris Anderson

Genetic testing of cell-free fetal DNA moves the bar on screening accuracy.

Prenatal screening for Down syndrome first became available for expectant mothers with the advent, in the late 1960s, of a diagnostic test employing amniocentesis and fetal karyotyping. At the time, only one risk factor was considered—the age of the mother.

In the ensuing years, discoveries showing the correlation between over- and under-expression of specific biomarkers in the mother’s blood, such as alpha-fetoprotein (AFP), human chorionic gonadotropin (hCG), estriol, and inhibin A, led to new prenatal screening tests that could indicate the likelihood of not only Down syndrome but other potential birth defects.

While these tests are still widely used and continue to serve a valuable function in helping physicians screen high-risk patients for potential abnormalities, these screening tools also have a relatively high incidence of false positives and false negatives. Women with a normal pregnancy are often referred for unnecessary invasive procedures such as amniocentesis or chorionic villus sampling, both of which carry a risk of miscarriage.

So it is not surprising that there has been a search for new, more accurate screening technologies and it is equally unsurprising that these methods have been found by analyzing cell-free fetal DNA that circulates readily in a pregnant mother’s bloodstream. While new to the market in the last couple of years, this new generation of noninvasive prenatal tests (NIPT) is making inroads in doctors’ offices across the country.

“The tests before were marker screen tests where you were looking for analytes that are correlated with specific conditions,” said Zachary Demko, senior director of R&D at Natera, a San Carlos, CA-based genetic testing company that markets the Panorama prenatal test. “With NIPT, we are detecting the actual DNA that is fetal in nature.”

Discovery to Screening Tool

The development of the new NIPT screens has occurred rapidly over the past five years, with the first product, MaterniT21, brought to market nearly two years ago. Development was fed by both new research findings and rapid technology advances.

“First and foremost it came with the biological insights that a good portion of the cell-free DNA that floats in the maternal blood stream—anywhere from 2 to 20 percent—comes from fetal origin.” said Vance Vanier, M.D., vp, global marketing for reproductive and genetic health at Illumina, which sells the verifi® prenatal test.

The availability of fetal DNA coincided with the rapidly increasing power—and concomitant decreasing costs—of gene sequencing, which spurred growth.

While tradition serum-based methods screened for such genetic defects as trisomies 21, 18, and neural tube defects, NIPT, using cell-free fetal DNA, has the potential to screen for a much broader array of genetic defects. “Given that there is enough cell-free DNA to be able to identify the SNPs on the DNA—we analyze 19,488 of those individual SNPs per sample—that allows us to, in a way, read the fetal DNA,” said Melissa Stosic, certified genetic counselor and director of medical education at Natera. “We are not then limited by what analytes tend to correspond with specific trisomies.”

Because of this, companies say they plan to expand the screens beyond the most common trisomy defects to also look for other less common defects such as DiGeorge, Angelman, and Prader-Willi syndromes.

“It is important to realize that all of these tests today assess for a set of conditions that comprise about 86 percent of all chromosomal conditions,” said Dr. Vanier. “Thereafter, in that remaining 14 percent, you have a long tail of relatively rare conditions. To date, the only way to assess those has been through an invasive procedure and putting a sample on a microarray. I think the next wave of innovations is companies beginning to offer screens for some of those rarer conditions that you can only get (today) on an array.”

Clinical Implications

The primary clinical vale for NIPT, vendors of the tests say, is derived from their high specificity and sensitivity, which for the most common defects can exceed 90 and 95 percent. That, coupled with significant reductions in false positives, allows clinicians to have much more definitive conversations with their patients about the risks in their pregnancies. Further, while some traditional screenings have moved into the first trimester of pregnancy, the bulk of these tests are conducted during the second trimester. Cell-free fetal DNA tests are typical effective in the first trimester, as early as 10 weeks.

“Screening has come a long way,” noted Stosic. “We used to think of screening as using a test to identify which women are at increased risk of having a baby with a specific problem, most probably Down syndrome, and the screening test would have sensitivity of 80 to 90 percent. Inherent in that, there is also a five percent false rate. With the advent of noninvasive prenatal testing or screening, we have made screening such that it walks a much closer line to diagnostic testing.”

Yet while many see NIPT taking its place on the diagnostics line, clinicians and the test developers themselves are clear they are not definitive. “I think it has to be emphasized to patients that these are still screening tests and don’t replace diagnostics,” said Nancy Rose, M.D., director of reproductive genetics at Intermountain Healthcare in Salt Lake City. As a screening tool, explained Dr. Rose, “they are certainly a better screening test in women at high risk” than traditional methods.

One influence on increased uptake by OB-GYNs in the use of the genetic screens arises from recommendations by medical societies which issue standard-of-care guidelines for practitioners. In December 2012, the American College of Obstetricians and Gynecologists (ACOG) added noninvasive prenatal testing that uses cell-free fetal DNA from the plasma of pregnant women as a method that “offers tremendous potential as a screening tool for fetal aneuploidy.”

Dr. Rose, who was the chair of the ACOG genetics committee that issued the opinion, noted that the recommendation was only for those women with high-risk pregnancies and not a recommendation that all women, regardless of risk profile, have NIPT.

But companies developing the screens also want to tap into the market of low-risk pregnancies with these tests to broaden their market. To that end, test developers are currently conducting clinical trials, or releasing new data on trials, in an attempt to show the tests also work with the low and normal risk cohort. If they can show efficacy and an improvement in care, the hopes are that ACOG will issue another opinion that expands the standard of care.

“Typically what happens is the societies come out with clinical guidelines, which can drive adoption, but more important is when health plans decide to pay for a new technology and they often wait to take their lead off of clinical society guidelines,” said Dr. Vanier. “That is the pattern. (Societies) set guidelines, reimbursement happens and then physicians begin to feel more comfortable prescribing the test.”

Prenatal Diagnostics

With NIPT highly accurate, but not up to diagnostic standards, a market does exist for sequencing-based prenatal diagnostics that can confirm screening results. One provider of array-based diagnostics is Irvine, California-based CombiMatrix via its CombiSNP microarray-based test, which does require an invasive procedure like amniocentesis to obtain a sample.

As Mark McDonough, CombiMatrix’ CEO, sees it, noninvasive screens play an important role in prenatal care, but should only be considered a first step. “If you are a believer in NIPT, which you should be because it is a better screen than what was available, and if the screen comes back positive, you simply have to follow ACOGs recommendation and reflex to an invasive procedure to confirm it,” he said. “And if you are going to do an invasive procedure you should be doing microarray.”

That is not to say that the CombiSNP diagnostic is dependent on NIPT to generate business. McDonough noted that more than 100,000 women who are high risk based on factors such as an abnormal ultrasound, family history, or age have amniotic fluid drawn each year. “If a doctor sees something they don’t like, even if the patient gets NIPT, they are likely going to go back for amniocentesis anyway,” McDonough noted. “So why not get the answer from the outset?”

Looking ahead, industry observers think the genetic screens and diagnostics will only gain more traction and detect an ever-expanding list of genetic disorders. That will only be to the benefit of mothers and their babies, especially as more rare disorders are identified by their genetic signatures.

“One of the values that is emerging for NIPT, as well as one-day sequencing the DNA of newborns, is babies born with rare conditions go through these hugely expensive, long, heartbreaking diagnostic odysseys,” said Dr. Vanier. “These days, no one knows what is wrong with them. They are in the ICU, and every kind of test is applied. In the future, early testing can be valuable, because if you know what their condition is, you can intervene early avoid all these tests and have a significant impact on their care and the cost of care.”

Chris Anderson ([email protected]) is the former chief editor of Drug Discovery News, which he helped launch in 2005.

This article was originally published in the September 10 issue of Clinical OMICs. For more content like this and details on how to get a free subscription to this digital publication, go to

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