Factors affecting cell-free DNA fetal fraction and the consequences for test accuracy

J Matern Fetal Neonatal Med. 2018 Jul;31(14):1865-1872. doi: 10.1080/14767058.2017.1330881. Epub 2017 Jun 8.


Introduction: Biological factors are known to influence the fetal fraction (FF) of cell-free DNA and may also influence the accuracy of non-invasive prenatal testing.

Material and methods: NIPT from 5267 mixed risk women across three specialist clinics in Australia were analyzed. Multivariable regression analysis was used to determine whether maternal characteristics, ultrasound, and placental biomarkers affect FF and test accuracy.

Results: FF ranged from 4% to 37% (mean 11.6%). Body mass index (BMI), gestation, and placental biomarkers were found to be significant factors associated with FF. For each unit increase in BMI, the logarithmically transformed FF, (lnFF), mean value decreased by 0.027. Each week increases in gestation, lnFF increased by 0.023. Each unit increase in free BhCG, PAPPA, and PlGF, the lnFF increased by 0.065, 0.050, and 0.17, respectively. There was no significant association between FF with either maternal age or nuchal translucency. The false-positive cases and one false-negative case did not have lower FF than the true-positive cases.

Discussion: The fetal fraction in maternal plasma cfDNA increased with gestational age, serum pregnancy-associated plasma protein A (PAPP-A), β-hCG, and PlGF and decreased with increasing maternal BMI. There was no significant correlation between low FF and test accuracy, when FF was above 4%.

Keywords: Cell-free DNA; NIPT; fetal fraction; test accuracy.

MeSH terms

  • Adult
  • Aneuploidy
  • Biomarkers / blood
  • Body Mass Index
  • Cell-Free Nucleic Acids / blood*
  • Chorionic Gonadotropin, beta Subunit, Human / blood
  • Female
  • Gestational Age
  • Humans
  • Maternal Serum Screening Tests*
  • Placenta Growth Factor / blood
  • Pregnancy
  • Pregnancy-Associated Plasma Protein-A / metabolism
  • Retrospective Studies


  • Biomarkers
  • Cell-Free Nucleic Acids
  • Chorionic Gonadotropin, beta Subunit, Human
  • Placenta Growth Factor
  • Pregnancy-Associated Plasma Protein-A
  • PAPPA protein, human