Isolation of Cell-Free DNA from Maternal Plasma Using Manual and Automated Systems

Cell-free fetal DNA present in the maternal circulation holds great potential for noninvasive prenatal diagnosis and analysis of fetal genetic traits. However, only approximately 3–6% of total DNA in the maternal plasma is of fetal origin. Because of its scarcity in the maternal circulation, various methods have been developed and tested to optimize the extraction of this rare material from plasma. Here, we first describe the commonly used protocol for separating plasma from whole blood samples. We also describe two commercially available methods for the extraction of cell-free DNA from maternal plasma, which we have found particularly straightforward and easy to use: a manual method using the High Pure PCR Template Preparation kit (Roche Diagnostics) and an automated system using the MagNA Pure LC instrument (Roche Diagnostics). Use of the methods described here will help to ensure maximum yield and purity of cell-free fetal DNA extracted from maternal plasma samples for downstream analyses.