Noninvasive Prenatal DNA Test Okay for Low-Risk Pregnancies

Ricki Lewis, PhD

February 27, 2014

Analysis of cell-free fetal DNA (cffDNA) from maternal plasma to screen for elevated risk for trisomies 21 and 18 is as useful in a general obstetric population as it is in high-risk pregnancies, according to a study published in the February 27 issue of the New England Journal of Medicine.

Widening the Scope

The American College of Obstetricians and Gynecologists endorsed cffDNA testing (also called noninvasive prenatal testing [NIPT], although this also describes ultrasound) in 2011 for high-risk women. The endorsement was based on both prospective studies from women at high risk and retrospective studies on results from offspring with abnormal karyotypes.

However, it was not clear whether the test would be similarly accurate in low-risk women. "[S]omething about high-risk women might have resulted in higher levels of fetal circulating DNA, and therefore, test performance [would have been] better in the higher-risk pregnancies," lead author Diana Bianchi, MD, executive director of the Mother Infant Research Institute at Tufts Medical Center and a professor of pediatrics, obstetrics, and gynecology at the Tufts University School of Medicine in Boston, Massachusetts, told Medscape Medical News.

"It's been a question since 2011: Could NIPT perform as well in average- or low-risk pregnancies, which make up 75% of cases of chromosomal abnormalities?" said S. Bonnie Liebers, MS CGC, clinical director of services and chief executive officer of Genetic Counseling Services in Schenectady, New York, who advises clinicians on use of the tests.

Some private physicians offer cffDNA analysis to all patients for primary screening. Out-of-pocket cost is about $1500. "Since NIPT was introduced, the paradigm of prenatal testing has shifted from medical center and hospital to the doctor's office. The onus is on physicians and their clinical staff to provide informed consent and interpretation of any results, many of which are not straightforward," Liebers said.

The current study, Comparison of Aneuploidy Risk Evaluations (CARE), is the "first to compare the current standard of care of biochemical marker testing and nuchal translucency on ultrasound against cell-free DNA testing in the general obstetric population in the United States, where we use a mixture of tests to screen for aneuploidy," Dr. Bianchi explained.

The researchers analyzed 1914 blood samples from women (mean age, 29.6 years) undergoing routine screening at 21 centers. The test used massively parallel DNA sequencing to generate millions of short sequences. A chromosome type in excess of the 1:1 ratio seen relative to all other pairs indicated trisomy. The primary study endpoint was false-positives for trisomies 21 and 18, using cffDNA vs standard screening, as determined by comparison to birth outcomes or karyotypes. In addition, some tests included trisomy 13.

Fewer False-Positives

For trisomies 21 and 18, the false-positive rates with cffDNA testing were significantly lower than for standard screening (0.3% vs 3.6% for trisomy 21 [P < .001]; 0.2% vs 0.6% for trisomy 18 [P = .03]). The cffDNA test revealed all true aneuploids: 5 for trisomy 21, 2 for trisomy 18, and 1 for trisomy 13, with a negative predictive value of 100% (95% confidence interval [CI], 99.8% - 100%).

For trisomy 21, the positive predictive value was 45.5% (95% CI, 16.7% - 76.6%) with cffDNA testing vs 4.2% (95% CI, 0.9% - 11.7%) for standard screening. For trisomy 18, the positive predictive value was 40.0% (95% CI, 5.3% - 85.3%) with cffDNA testing vs 8.3% (95% CI, 0.2% - 38.5%) with standard screening.

False-positives can reflect unusual biological circumstances. "One woman was diagnosed postpartum with cancer, and the tumor was shedding the abnormal DNA. There was also a fetal trisomy 18. The baby was fine, but the mother was mosaic," Dr. Bianchi explained.

Concerns have been raised that cffDNA screening encourages pregnancy termination, but the opposite may be true. The researchers estimate that if all women have cffDNA testing and only those with positive results have invasive diagnostic procedures, the number of such risky procedures would fall by 89%.

"Four of 5 fetuses with trisomy 21 were liveborn, and one was terminated. Of the 2 fetuses with trisomy 18, 1 was liveborn and 1 was stillborn. The fetus with T13 had an in utero demise," Dr. Bianchi told Medscape Medical News.

A limitation of the study was the inability to assess sensitivity because of the small number of aneuploidies detected.

Screening, Not Diagnosis

In an accompanying editorial, Michael F. Greene, MD, from the Department of Obstetrics and Gynecology at Massachusetts General Hospital in Boston, and journal deputy editor Elizabeth Phimister, PhD, point out that cffDNA testing will not replace diagnostic procedures. "As the investigators acknowledge, women who receive a positive result on cffDNA screening must be counseled to have a diagnostic test [eg, amniocentesis or chorionic villus sampling] to determine whether their fetus is one of the approximately 60% of fetuses that are falsely identified on cffDNA screening as having a chromosome 18 or 21 trisomy," they write.

However, they add, "a negative result on cffDNA screening obviates the need for invasive testing."

"The study sets the stage for a new choice in prenatal aneuploidy screening in low-risk women who are the primary users of available screening," Luba Djurdjinovic, MS, executive director of Ferre Institute Inc, Binghamton, New York, told Medscape Medical News. "To date, screening options leave some women with the difficult choice of an invasive procedure [even] when screening results are known to have a significant false-positive rate. The DNA sequencing screening option helps to narrow the gap of uncertainty that women face as they debate invasive prenatal testing to clarify their result."

Genetic counselors are important in explaining cffDNA testing. "As DNA sequencing prenatal testing is embraced in daily obstetrical practices, there is a need for the knowledge and experience of trained genetic counselors. Patients need to be informed of the screening nature of the test despite higher detection rates," Djurdjinovic said.

Illumina sponsored the study. Dr. Bianchi serves on an advisory board for Illumina. One coauthor consults for Illumina, and 6 coauthors are employees of Illumina; 1 of these coauthors also has filed a patent application for a method to detect copy number variants, and 1 also holds patents for normalizing chromosomes to verify aneuploidies and to detect fetal abnormalities as well as pending related patents. The other authors, the editorialists, and the commentators have disclosed no relevant financial relationships.

N Engl J Med. 2014;370:799-808, 874-875. Article abstract, Editorial extract

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