Counsyl Release: New Study Finds Non-Invasive Prenatal Screening Using Whole-Genome Sequencing Detects More Chromosomal Abnormalities At Low Fetal Fraction, Minimizes Unnecessary Invasive Procedures

SOUTH SAN FRANCISCO, Calif.--(BUSINESS WIRE)--Counsyl, a DNA testing and genetic counseling service company, today reported the results from a new study published in Prenatal Diagnosis, titled “Noninvasive Prenatal Screening at Low Fetal Fraction: Comparing Whole-Genome Sequencing and Single-Nucleotide Polymorphism Methods.”1

The study examines the two most common genome sequencing methods used for noninvasive prenatal screening (NIPS), which can detect certain fetal chromosomal abnormalities by measuring fetal DNA fragments in a sample of the mother’s blood.

In general, two methodologies for NIPS - Whole Genome Sequencing (WGS) and Single-Nucleotide Polymorphism (SNP) - perform well when the percent of fetal DNA found in the mother’s blood (i.e., the “fetal fraction”) is high. However, for samples with low fetal fraction, the performance and clinical consequences of the two methods were not well-established prior to this study.

To ensure a fair comparison between methods, the authors developed computational simulations drawn directly from recent published reports, such as peer-reviewed manuscripts and patents. To further provide transparency, all computer code has been made publicly available2.

By directly comparing the WGS and SNP methodologies, the analysis revealed the following with respect to detection of certain common aneuploidies:

  • The WGS method has high analytical sensitivity for low fetal fraction samples.
  • Analytical sensitivity of the SNP method falls off sharply at 3% fetal fraction, consistent with the published threshold at which laboratories using the SNP method do not provide results (known as a ‘no-call’).
  • WGS leads to fewer no-calls at low fetal fraction, fewer false negatives, and fewer invasive procedures in low fetal fraction samples when modeled in the context of clinical practices and medical guidelines.

“Our research illuminates the mechanism and math behind why there are disparities in the no-call rates of WGS- and SNP-based labs,” said Yuval Yaron, MD, Director, Prenatal Genetic Diagnosis Unit, Tel-Aviv Sourasky Medical Center & Tel Aviv University. “In the broader clinical context in which it is performed, the results of this simulation suggest that the WGS method will offer a simpler workflow - fewer no-calls and blood redraws - than the SNP method, when the maternal blood sample has a low fetal fraction.”

“NIPS is incredibly useful in identifying more pregnancies potentially impacted by common chromosomal abnormalities, but not all NIPS methodologies are created equal,” said James Goldberg, MD, chief medical officer of Counsyl. “We were encouraged to find that using WGS for all patients allows a provider to avoid a large number of invasive procedures and undiagnosed aneuploidies.”

About Counsyl

Counsyl provides a DNA testing and genetic counseling service. We're committed to helping patients understand their DNA and how this knowledge can inform important health decisions. Whether it’s starting a family or evaluating risk for cancer, Counsyl's DNA tests provide patients with early awareness about genetic conditions, so they can live informed and prepare for the future. Counsyl has screened more than 750,000 patients and served more than 10,000 healthcare professionals. For more information, visit Sign up to receive Counsyl news notifications at

1 Authors of the study include Carlo G. Artieri, Carrie Haverty, Eric Evans, PhD, James Goldberg, MD (Departments of Medical Affairs and Research, Counsyl), Imran Haque, PhD, Yuval Yaron, and Dale Muzzey. All authors other than Yuval Yaron are current or former employees of Counsyl. The study was funded by Counsyl.

2 Code required to reproduce the results of the study can be found online at:

Donelle M. Gregory

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