1. A method of distinguishing the presence or absence of a fetal aneuploidy by analysis of a blood sample comprising a mixture of fetal and maternal genomic DNA, the method comprising: a) obtaining a blood sample comprising a mixture of fetal and maternal genomic DNA; b) isolating the mixture of fetal and maternal genomic DNA from the blood sample; c) distributing the isolated mixture of fetal and maternal DNA into a plurality of at least 500 discrete reaction samples at discrete locations; d) at each discrete location, tagging any genomic DNA by amplification; e) analyzing the tagged genomic DNA of step d to detect a presence of any amplified fetal or maternal genomic DNA at the discrete locations; f) generating data corresponding to the presence or absence of amplified fetal and maternal genomic DNA at each discrete location; and g) distinguishing the presence or absence of a fetal aneuploidy from the data of step f).