A method for identifying the presence or absence of an aneuploidy of a target chromosome in a subject, which comprises: a. preparing a plurality of sets of amplified nucleic acid species by amplifying a plurality of nucleotide sequence species sets from extracellular nucleic acid template of a subject, wherein: (i) the extracellular nucleic acid template comprises fetally derived and maternally derived nucleic acid, (ii) the nucleotide sequence species of a set are located in a target chromosome and one or more reference chromosomes, wherein a reference chromosome is a chromosome that is not associated with the aneuploidy to be identified, (iii) the nucleotide sequence species in a set differ by one or more mismatch nucleotides; (iv) the nucleotide sequence species of a set are reproducibly amplified relative to each other, (v) the primer hybridization sequences located in the target nucleotide sequence species and in the one or more reference nucleotide sequence species of a set share a degree of sequence similarity that allows a single pair of amplification primers to hybridize to the primer hybridization sequences such that the species of a set are co-amplified; and (vi) each amplified nucleic acid species in a set comprises a nucleotide sequence having the one or more mismatch nucleotides; b. determining the amount of each amplified nucleic acid species in each set by detecting the one or more mismatch nucleotides in each amplified nucleic acid species; c. determining a ratio between the relative amount of (i) an amplified target nucleic acid species and (ii) an amplified reference nucleic acid species, in each set; and d. identifying the presence or absence of an aneuploidy of a target chromosome based on the ratios from two or more sets. a. preparing a plurality of sets of amplified nucleic acid species by amplifying a plurality of nucleotide sequence species sets from extracellular nucleic acid template of a subject, wherein: (i) the extracellular nucleic acid template comprises fetally derived and maternally derived nucleic acid, (ii) the nucleotide sequence species of a set are located in a target chromosome and one or more reference chromosomes, wherein a reference chromosome is a chromosome that is not associated with the aneuploidy to be identified, (iii) the nucleotide sequence species in a set differ by one or more mismatch nucleotides; (iv) the nucleotide sequence species of a set are reproducibly amplified relative to each other, (v) the primer hybridization sequences located in the target nucleotide sequence species and in the one or more reference nucleotide sequence species of a set share a degree of sequence similarity that allows a single pair of amplification primers to hybridize to the primer hybridization sequences such that the species of a set are co-amplified; and (vi) each amplified nucleic acid species in a set comprises a nucleotide sequence having the one or more mismatch nucleotides; b. determining the amount of each amplified nucleic acid species in each set by detecting the one or more mismatch nucleotides in each amplified nucleic acid species; c. determining a ratio between the relative amount of (i) an amplified target nucleic acid species and (ii) an amplified reference nucleic acid species, in each set; and d. identifying the presence or absence of an aneuploidy of a target chromosome based on the ratios from two or more sets.