Methods of isolating DNA of a fetus of an ongoing pregnancy are provided according to the present invention which include obtaining a maternal endocervical sample containing maternal cells and fetal extravillous trophoblast cells from a pregnant subject; isolating fetal extravillous trophoblast cells from the maternal endocervical sample, producing isolated fetal extravillous trophoblast cells contaminated with maternal DNA; lysing the isolated fetal extravillous trophoblast cells; isolating fetal nuclei from the lysed fetal extravillous trophoblast cells, producing isolated fetal nuclei, thereby removing at least a portion of the contaminating maternal DNA; and purifying genomic DNA from the isolated fetal nuclei, producing purified fetal genomic DNA. The purified fetal genomic DNA can be assayed to determine a characteristic of a genomic DNA sequence of the purified fetal genomic DNA, thereby determining a characteristic of DNA of a fetus of an ongoing pregnancy.