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Updated: Jan 3, 2026
Methylation Specific Multiplex Droplet PCR using Polymer Droplet Generator Device for Hematological Diagnostics
Published on: June 29, 2020
Precision of Fetal DNA Fraction Estimation by Quantitative Polymerase Chain Reaction Quantification of a Differently
Jonatan Blais1,2,3, Sylvie Giroux3, André Caron3
1Medical Biochemistry Service, Department of Laboratory Medicine, CHU (Centre hospitalier universitaire) de Québec-Université Laval, Quebec City, Quebec, Canada.
Background:
The performance of noninvasive prenatal testing (NIPT) assays is critically determined by the proportion of fetal DNA or fetal fraction (FF). Fetomaternal differential methylation of certain genomic regions has been proposed as a universal marker of fetal origin, and previous reports have suggested the use of methylation-sensitive restriction enzyme (MSRE) assays to estimate FF.
Methods:
We analyzed the performance of FF estimation using an MSRE assay with duplex quantitative polymerase chain reaction (qPCR). Mixtures of genomic DNA from placental cells and from adult women were digested with 2 MSRE and FF estimates obtained, for a total of 221 pairwise treatment/control comparisons.
Results:
The coefficient of variance (CV) of the MSRE assays was high, ranging from 24% to 60%. An alternative in silico FF estimation algorithm, SeqFF, displayed slightly lower variability, with a CV of 22%.
Conclusion:
These results cast doubts on the usefulness of the MSRE-based assay of differentially methylated markers for FF estimation. The lack of a universal method capable of precisely estimating FF remains an incompletely solved issue.
