Patricia F. Fitzpatrick Dimond Ph.D. Technical Editor of Clinical OMICs President of BioInsight Communications

Growing market expected to reach $3.6 billion by 2019.

Prenatal screening for detection of a wide range of monogenic disorders and chromosomal abnormalities has been available to prospective parents for over 40 years. But these screening techniques, including seroscreening and ultrasound, have false positive rates of 5% and 10–15%, respectively, requiring that 1 in 20 women face a decision of whether to undergo invasive testing that may include amniocentesis, chorionic villus sampling, or, rarely, cordocentesis.

All of these procedures involve some risk with fetal loss rates of approximately 1 in 300 procedures, according to the American College of Obstetricians and Gynecologists (ACOG).

But the discovery of circulating fetal DNA (cfDNA) in the maternal circulation and the development of advanced sequencing technologies have led some scientists and clinicians to predict that antenatal diagnosis will become a predominately noninvasive process that will usher in the era of noninvasive prenatal testing (NIPT).

All of the currently available NIPTs for fetal aneuploidies target cell-free DNA (cfDNA) in the maternal blood. But only about 10% of the total circulating cfDNA is of fetal origin, whereas approximately 90% is derived from maternal sources. While the relative scarcity of cfDNA has proven challenging, the medical community has cited the broad use of NIPT as “remarkable,” e.g., Sequenom says it sold more than 150,000 tests in 2013. However, professional societies, including the ACOG, continue to recommend limitation of NIPT to high-risk pregnancies.

Currently, the Society for Maternal-Fetal Medicine (SMFM) recommends that NIPT is most appropriate for high-risk patients. The five high-risk criteria currently include maternal age 35 years or older at delivery, sonographic findings indicating an increased risk of aneuploidy, history of a prior pregnancy with a trisomy, positive screening results for aneuploidy (including first trimester, sequential, integrated, or quadruple screen) or a specific type parental balanced translocation with increased risk for trisomy 13 or 21.

Fetal aneuploidy such as Trisomy 21 (Down syndrome) is typically detected through karyotyping, a process in which a sample of fetal cells is fixed and stained to create the typical light and dark chromosomal banding pattern followed by analysis. Other techniques include fluorescence in situ hybridization (FISH), quantitative PCR of short tandem repeats, quantitative fluorescence PCR (QF-PCR), quantitative PCR dosage analysis, quantitative mass spectrometry of single nucleotide polymorphisms, (SNP analysis) and comparative genomic hybridization (CGH).

The introduction of technologies such as digital PCR and next-generation sequencing (NGS) or massively parallel sequencing (MPS) have enabled accurate estimation of very small differences in chromosome-specific sequences in maternal blood, thus providing an approach to NIPT that can be used in clinical practice.

Identification of cell free fetal DNA (cffDNA) in maternal plasma could transform prenatal screening and diagnosis of trisomy 21, with a prevalence of about 14.2 per 10,000 live births as well as detection of other, aneuploidies. MPS has enabled the development of tests that accurately predict the presence of fetal trisomies by analysis of cell-free DNA in maternal blood from as early as 10 weeks of gestation.

Four companies in the U.S. offer NIPT tests to pregnant women. Sequenom, first to market with its 2011 introduction of its MaterniT21™ test, uses MPS to identify an increased representation of chromosome 21, and its MaterniT21 Plus Test, chromosomes 21, 18, and 13.

The verifi™ prenatal test marketed by Illumina’s Verinata Health relies on MPS to identify an increased representation of chromosomes 21, 18, and 13. Ariosa’s (formerly Aria Diagnostics) Harmony Prenatal Test™ employs direct analysis of cfDNA fragments. This test couples digital analysis of selected regions and a proprietary algorithm, FORTE™, to selectively analyze cfDNA in maternal blood for trisomy 21, 18, and 13.

Natera says its SNP-based test Panorama™ provides 99% combined accuracy for trisomies 13, 18, and 21, fetal sex, and triploidy. Panorama targets 19,488 SNPs covering chromosomes 21, 18, 13, X, and Y, employing a patented algorithm called Next-Generation Aneuploidy Test Using SNPs to screen for whole chromosomal fetal aneuploidy and fetal sex.

Taking NIPT one step further, in June 2012, Kitzman and colleagues reported in Science that they combined genome sequencing of two parents, genome-wide maternal haplotyping, and deep sequencing of maternal plasma DNA to noninvasively determine the genome sequence of a human fetus at 18.5 weeks of gestation. Inheritance was predicted at 2.8 × 106 parental heterozygous sites with 98.1% accuracy. Furthermore they noted 39 of 44 de novo point mutations in the fetal genome were detected, “albeit with limited specificity.”


The Women’s Health and Education Organization said this study took the technology “beyond detection of chromosomal or single-gene disorders to contemplation of genome-wide prenatal diagnosis of both recessive and dominant Mendelian disorders,” moving the science of prenatal genetic diagnostics “at a pace that would have seemed unimaginable just a few years ago.”

Current questions about whether NIPT tests should be generally used as prenatal screening tests notwithstanding, pharma companies and diagnostic companies are putting large stakes in the ground to own pieces of this growing market. The prenatal diagnostics industry, analysts estimate, will reach $3.6 billion by 2019 and demand for prenatal tests could, they say, triple over the next six years. The industry has spawned acquisitions and a lot of litigation, as companies fight to protect their claims.

Illustrative of the competitive climate for these tests are ongoing patent fights. In January 2012, Sequenom filed a lawsuit against Ariosa for patent infringement, and then requested a preliminary injunction to stop the company from using its test. As a result, Ariosa, Natera, and Verinata, together with Stanford University, which was involved in Verinata’s patent, have all sued Sequenom, arguing that that slight differences in their testing methods do not constitute infringement.

Illumina and Sequenom reported that they had settled their patent and intellectual property disputes on December 4, 2014, agreeing to pool their patents regarding noninvasive prenatal testing. Illumina will pay Sequenom $50 million upfront, in addition to other payments to Sequenom for the pooled patent agreement through 2020.

Roche entered the prenatal diagnostics market through its December 2, 2014 announcement that it had acquired Ariosa and its Harmony test. The acquisition gives Roche rights to Ariosa’s Harmony test that assesses the risk of trisomies 13, 18, and 21.

Ariosa offers the Harmony test as an alternative to traditional screening methods, which reportedly return false-positive results up to 5% of the time, versus the Harmony test’s false-positive rate of less than 0.1%. All the contender companies in the NIPT space claim low false positive rates.

“Our view is that NIPT is a prenatal screening test that has clinical utility for the general pregnancy population. Any pregnant women should be eligible for the test, Ken Song, M.D., Ariosa’s CEO, told Clinical OMICs. “Prenatal screening for Down syndrome is the standard of care and NIPT represents such a dramatic improvement over traditional screening methods, it should at least be an option for any pregnant woman, regardless of age or risk.”

Traditional screening tests fail to identify about 30% of Down syndrome cases in addition to the 5% false positive rate. “NIPT testing as a class,” said Dr. Song, “is significantly superior to traditional screening tests. [It’s] a step function improvement in prenatal care that identifies 99% of Down syndrome cases with false positive results less than 0.1%, thus significantly fewer women are getting false alarms. That’s where the power of NIPT lies, i.e., in reducing false positives.”

But innovation remains costly, with NIPT tests still costing near $1,000 although Ariosa’s test, the company claims, is the most affordable and its mission is to continue to broaden access as much as possible.

Ariosa’s test does come in at $795 compared to $2,762 (for Sequenom’s, although out-of-pocket costs are capped at $235 for women who have health insurance). In California, Ariosa’s test is covered by Medi-Cal, a state program that pays for prenatal health care for low-income women; Sequenom’s and Verinata’s tests are not.

And as much as companies offering tests would like to see NIPT used in a prenatal screening context, SMFM stood by current practice recommendations, saying that recent research results aren’t sufficient to change its mind.

New technologies are moving the science of prenatal genetic diagnostics at a pace that would have been unimaginable just a few years ago. [Andresr/Deposit Photos]

Patricia Fitzpatrick Dimond, Ph.D., has been a long-time contributor to GEN and currently serves as the publication’s Technical Editor. She is also president of BioInsight Communications. During her career in the biotechnology industry, she was VP of strategic development and corporate communications at Coley Pharmaceutical Group (now Pfizer), where she developed and managed the company’s investor relations and communications programs. ([email protected])

This article was originally published in the January 2015 issue of Clinical OMICs. For more content like this and details on how to get a free subscription to this digital publication, go to

Previous articleGilead to Acquire Phenex’s FXR Program for Up-to-$470M
Next articleNanobiotechnology: Putting Molecular Machines to Work