Concurrent with efforts to use fetal-cell isolation to perform NIPS was the discovery, in the late 1990s by Dr. Dennis Lo, upon whose work next-generation sequencing for NIPS is based, of the presence of circulating cell-free fetal DNA in maternal plasma. The concentration of cell-free fetal DNA may be as much as 5%-8% of the total circulating cell-free DNA in maternal plasma, making free fetal DNA a promising source of fetal genetic material for noninvasive prenatal investigation.
The first high-quality trials on the use of free fetal DNA measurement for detection of trisomy 21 were published in the fall of 2011, and demonstrated up to a 99% detection rate for Down syndrome (less for trisomies 18 and 13). Companies subsequently began to manufacture free fetal DNA tests as off-label products, The tests were initially designated as "noninvasive prenatal diagnosis" tools, but experts around the world objected to the "diagnosis" label, and the terminology shifted to "noninvasive prenatal testing" and finally to "noninvasive prenatal screening"– a designation that I believe accurately reflects its current role.
The uptake in utilization of NIPS has been faster than anyone could have predicted: In just over 2 years, several hundred thousand screening tests have been performed. With 98% to 99% sensitivity, NIPS is an excellent screening test for Down syndrome. However, 99% sensitivity does not equate to 99% positive predictive value, that is, the risk that a patient with a positive screen actually has Down syndrome is much lower.
The published studies of NIPS cite false positive rates of 0.2%-1.0%, but this rate will increase as more disorders are screened. Positive predictive value is directly proportional to the underlying risk. For example, a test with 99% sensitivity and 99% specificity (1% false positive rate) means that a 26-year-old woman who has a positive free fetal DNA test actually has as low as an 11% chance of having a baby with Down syndrome. In older women, who have a higher incidence of having a baby with Down syndrome, a positive NIPS result will have a higher positive predictive value of giving birth to a baby with Down syndrome. However, at the current time, NIPS is an excellent screening test for Down syndrome, but it is not ready for universal primary screening in younger women.
Falsely reassuring are the hyped marketing claims in the United States that NIPS "replaces amnio" and eliminates the need for a nuchal translucency (NT) test. When clinicians abandon performing or referring for a high-quality NT measurement, they can miss or significantly delay the diagnosis of twins/zygosity, growth abnormalities and placentation, cardiac defects, and numerous other anomalies. Similarly, when patients who otherwise would have opted to have CVS or amniocentesis forego having the procedure and have NIPS performed instead, they may regret this decision.
The danger that overreliance on screening tests may paradoxically increase the number of births of babies with otherwise detectable problems was raised in a study led by the late Dr. George Henry, an obstetrician-geneticist in Denver. Curious about declining rates of diagnostic testing in his own practice, Dr. Henry examined trends in his state and found that while the utilization of diagnostic tests had plummeted by 70% over about 15 years, the birth rate of babies born with Down syndrome during this time had doubled among mothers over age 35, and stayed the same among mothers under age 35.
A sociologist-researcher examined the trend that Dr. Henry identified and found that the rise in Down syndrome births was not due to an increase in women electing to keep these pregnancies, but to the fact that the abnormality was not detected in the first place (Fetal Diagn. Ther. 2008;23:308-15). The same risk of screening tests replacing definitive diagnosis exists today with the uptake of NIPS.
The impact of microarray
Microarray technologies have been developed over the past decade. The National Institutes of Health study on chromosomal microarray versus karyotyping, published a year ago, is a game changer. The microarray is analogous to a 15-fold magnifying glass on the karyotype. While the smallest piece of a chromosome that can be evaluated by karyotype analysis is about 5 million base pairs, microarray analysis zooms in on about 200,000 base pairs, allowing us to see small genomic deletions and duplications (copy number variants) that we’ve never seen before.
The trial looked at upward of 4,000 women undergoing CVS or amniocentesis at one of 29 centers. Each diagnostic sample was split in two, with standard karyotyping performed on one portion and chromosomal microarray on the other (N. Engl. J. Med. 2012;367:2175-84).