DNA Sequencing versus Standard Prenatal Aneuploidy Screening

Published - Written by Carla Rothaus

As every expectant woman will tell you, the foremost question on her mind is, “Will my child be healthy?” Recent advances in prenatal screening techniques may change the way that concern is addressed, particularly with regard to screening for aneuploidy.

Prenatal screening for fetal abnormalities began decades ago, limited initially to rudimentary ultrasound evaluation for determination of fetal gestational age. Today, noninvasive screening for the most common trisomy syndromes includes various combinations of maternal serum biochemical assays, and ultrasound measurement of fetal nuchal translucency. Positive screening tests require follow up invasive diagnostic tests – amniocentesis or chorionic villous sampling – both of which carry a risk of spontaneous miscarriage. The known high false positive rates of existing screening techniques have therefore fueled efforts to find better alternatives.

A new era in prenatal screening began a few years ago, with the clinical use of massively parallel DNA sequencing (MPS) of cell-free fetal DNA to screen for aneuploidy. This technique involves sequencing fragments of cell-free fetal DNA (cfDNA) shed into the maternal circulation by the placenta, and quantifying the random sequence reads of each chromosome. Sequence reads from any one specific autosomal chromosome are expected to have a 1:1 ratio with reads from other autosomal chromosomes; cases of aneuploidy, in contrast, will deviate from this 1:1 ratio. Clinical validation studies of MPS sequencing of cfDNA for aneuploidy screening in high-risk pregnant women have demonstrated high sensitivity, specificity, and negative predictive values. As a result, investigators are studying the potential role of cfDNA screening in a general/low-risk obstetric population. Available data are promising, but further investigation is needed, as relevant trials to date have been performed outside the United States, where screening practices do not match the variety of aneuploidy screening approaches used in the United States.

In this week’s NEJM, Bianchi et al. report the results of a United States trial designed to address this need. They performed a prospective, blinded, multicenter observational study of women undergoing routine obstetrical care, all of whom had already had or were planning to have standard aneuploidy screening. Eligible women (at least 18 years old, with singleton gestation of 8 weeks or more) underwent standard screening with either first trimester maternal serum measurements of PAPP-A and βhCG (or total hCG) with or without sonographic measurement of nuchal translucency, or second trimester ‘quadruple screening’ alone (maternal serum measurements of AFP, hCG, uE3, and inhibin A) or in combination with first trimester screening. On enrollment, each participant had blood drawn for cfDNA testing, although cfDNA test results were not revealed. Participants were followed through the end of their pregnancy, with note made of birth outcomes and karyotypes, the latter obtained from invasive diagnostic procedures that followed positive standard screening tests, or cytogenetic testing of products of conception in cases of nonlive births. The primary endpoint was comparison of the false positive rates of standard aneuploidy screening with those of MPS for detection of trisomies 21 and 18.

The primary analysis population included just over 1900 women, most of whom were at low risk for aneuploidy. For trisomies 21 and 18, the false positive rates of cfDNA testing were significantly lower than those of standard screening. For trisomy 21, there were false positive results in 6 versus 69 of 1909 women (0.3% vs. 3.6%, P‹0.001); for trisomy 18, there were false positive results in 3 versus 11 of 1905 women (0.2% vs. 0.6%, P=0.03). Both screening techniques detected all true cases of aneuploidy.  While positive predictive values were considerably higher for cfDNA, they were not high enough to eliminate the need for confirmatory invasive diagnostic tests. Nevertheless, the authors note that if all pregnant women in their study had undergone cfDNA testing only, the number of invasive tests required would have been significantly reduced, thus reducing the number of procedure-related miscarriages. They conclude that cfDNA testing “merits serious consideration as a primary screening method for fetal autosomal aneuploidy.”

NEJM Deputy Editor Dr. Elizabeth Phimister and Dr. Michael Greene of the Massachusetts General Hospital concluded in their accompanying editorial that the study “augurs well for pregnant women and their fetuses: a negative result on cfDNA screening obviates the need for invasive testing and thus the discomfort and risk to the pregnancy incurred by such testing.”