Separating the DNA of the fetus from the DNA of the mother is one of the main limitations of this test, as it is not entirely uncomplicated.
If the fetus is male, it is possible to identify the Y chromosome sequences unique to the male sex and therefore it is easier to distinguish fetal DNA from maternal DNA.
However, when the fetus is a girl, the diagnosis is more complicated. In this case, the methods used to separate the fetal DNA from that of the mother are based on looking for differences in the methylation of the genes or in the length of the DNA fragments, as those from the fetus are shorter.
Finally, it should be noted that the most common way to distinguish the fetal from the maternal genetic endowment is to look for genetic characteristics of the father inherited by the fetus and which are therefore not present in the mother's DNA.