Two studies published online, ahead of the April issue of the American Journal of Obstetrics & Gynecology (AJOG), show that the risk of a fetus having chromosomal abnormalities that cause Down syndrome, and a genetic disorder known as Edwards syndrome, can now be almost precisely be identified by using a noninvasive test on maternal blood that involves a novel biochemical assay and a new algorithm for analysis.

Apart from being more scalable, compared with other recently developed genetic screening tests, this test is also able to potentially reduce unnecessary amniocentesis or CVS.

Diagnosing fetal chromosomal abnormalities, or aneuploidies, requires invasive tests that consist of chorionic villous sampling or amniocentesis in pregnancies that are known to be of high-risk, and even though these tests are accurate, they are costly and carry a risk of miscarriage.

Massively parallel shotgun sequencing (MPSS), a technique that examines cell-free DNA (cfDNA) from the mother’s plasma for fetal conditions has been used to identify trisomy 21 (T21) pregnancies, i.e. pregnancies with an extra copy of chromosome 21, which leads to Down syndrome, and trisomy 18 (T18), the chromosomal defect underlying Edwards syndrome. Although MPSS can accurately detect these conditions by analyzing the entire genome, it requires DNA sequencing large amounts and therefore its clinical usefulness is limited.

A novel assay, called Digital Analysis of Selected Regions (DANSR™), has recently been developed by scientists at Aria Diagnostics in San Jose, CA, which sequences loci from only those chromosomes under investigation, which requires 10 times less DNA sequencing as compared with MPSS.

The current study describes a novel statistical algorithm, the Fetal-fraction Optimized Risk of Trisomy Evaluation (FORTE™), which takes age-related risks and the percentage of fetal DNA in the sample into account, in order to provide an individualized risk score for trisomy. Lead researcher Dr. Ken Song, MD, explains:

“The higher the fraction of fetal cfDNA, the greater the difference in the number of cfDNA fragments originating from trisomic versus disomic [normal] chromosomes and hence the easier it is to detect trisomy. The FORTE algorithm explicitly accounts for fetal fraction in calculating trisomy risk.”

Dr. Song and his team set out to assess 123 normal pregnancies, 36 T21, and 8 T18 pregnancies to assess the performance of the DANSR/FORTE assay. They referenced all samples for FORTE odd scores of chromosome 18 and chromosome 21 and discovered in a blinded analysis that the combination of DANSR and FORTE managed to correctly identify all 36 cases of T21 and 8 cases of T18 as having a risk of more than 99% for each trisomy. The separations in risk score between trisomic and disomic samples were at least a 1,000-fold magnitude.

In an associated study, researchers from the Harris Birthright Research Centre for Fetal Medicine at Kings College Hospital in London and the University College London Hospital provided 400 maternal plasma samples to Aria for a DANSR analysis with the FORTE algorithm. All subjects were at risk for aneuploidies and had been tested by chorionic villous sampling.

According to the analysis results, all cases of T21 and 98% of T18 cases from euploid pregnancies were identified, showing that all cases of T21 had an estimated risk for this aneuploidy of ≥ 99%, whilst all normal pregnancies and those with T18 had a risk score for T21 of ≤ 0.01%.

Dr. Song explains:

“Combining the DANSR assay with the FORTE algorithm provides a robust and accurate assessment of fetal trisomy risk. Because DANSR allows analysis of specific genomic regions, it could be potentially used to evaluate genetic conditions other than trisomy. The incorporation of additional risk information, such as from ultrasonography, into the FORTE algorithm warrants investigation.”

Lead researcher Kypros H. Nicolaides, MD, of the University of London study believes that fetal trisomy evaluation with cfDNA testing will be introduced into clinical practice sooner or later, saying:

“It would be useful as a secondary test contingent upon the results of a more universally applicable primary method of screening. The extent to which it could be applied as a universal screening tool depends on whether the cost becomes comparable to that of current methods of sonographic and biochemical testing.”

Dr. Nicolaides highlights that the plasma samples were taken from high-risk pregnancies that showed some evidence of impaired placental function, and adds that it would require further tests to confirm that the observed accuracy with cfDNA testing from the investigation of pregnancies at high-risk for aneuploidies also applies to the general population, in which prevalence of fetal trisomy 21 is significantly lower.

He concludes:

“This may well prove to be the case because the ability to detect aneuploidy with cfDNA is dependent upon assay precision and fetal DNA percentage in the sample rather than the prevalence of the disease in the study population.”

Written by Petra Rattue