What is it about?

Fetal fraction, the proportion of cell-free DNA in maternal plasma which is of fetal origin, is one of the most important quality control measures in NIPT. We have thoroughly studied how the total number of sequencing reads influence the estimation of fetal fraction in NIPT samples, which to the best of our knowledge had not been considered before. Our data show that fetal fraction estimation is highly affected by the number of reads. Contrary to common hypothesis in the field, we also show that fetal fraction estimation is not dependent on the level of cell-free fetal DNA in the sample. Finally, in this manuscript, we provide suggestions on the read count thresholds to be considered for NIPT screens in clinical setting.

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Why is it important?

NIPT is widely used in prenatal screening, however, the methods should be developed further to provide the most reliable results. Accurate and precise estimation of fetal fraction (FF) is crucial for the development of NIPT and the interpretation of NIPT results. Our study shows that total read count highly affects the bioinformatic FF estimation in NIPT. Insufficient number of reads will affect estimation of FF, introducing the possibility of false positive or false negative results in NIPT report, which could in turn lead to a missed diagnosis.


The awareness of all factors important for the quality of NIPT provides more knowledge on how to work with cell-free-DNA-based methods, and aids in further development of non-invasive prenatal diagnostics.

Ieva Miceikaite
Syddansk Universitet

Read the Original

This page is a summary of: Total number of reads affects the accuracy of fetal fraction estimates in NIPT, Molecular Genetics & Genomic Medicine, March 2021, Wiley, DOI: 10.1002/mgg3.1653.
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