A cell-based method of detecting a fetal identifier, comprising: dividing a maternal blood sample comprising a mixture of maternal and fetal cells into subsamples; performing whole genome amplification on at least one said subsample comprising a cell to provide an amplified product, wherein the chromosome copy number from the sample is preserved in the subsample following whole genome amplification such that the resulting amplified product represents the genome or transcriptome of either a maternal or fetal cell; dividing said amplified product into aliquots; screening or genotyping an aliquot for the presence of a fetal identifier, wherein said screening or genotyping comprises; providing a SNP panel to identify the presence of a non-maternal allele in said mixed sample wherein the SNP panel comprises at least one control chromosome-specific panel comprising SNPs located on a chromosome that is not susceptible to aneuploidy and a chromosome-specific panel on a chromosome that is susceptible to aneuploidy; determining whether the genetic material of a maternal cells is homozygous or heterozygous at a set of target loci in said SNP panel to determine a maternal genotype; selecting a test locus from said target loci, wherein said selection of said test locus comprises screening a sample of mixed maternal and fetal nucleic acids for a genotype differing from said maternal genotype at a target locus and selecting as said test locus a target locus with a non-maternal genotype in said sample of mixed maternal and fetal nucleic acids; screening or genotyping said aliquot for a genotype differing from said maternal genotype at said test locus, wherein the presence of said genotype differing from said maternal genotype indicates the presence of an informative paternal allele in said amplified product; and identifying the presence of at least one said fetal identifier from a fetal cell in an aliquot from at least one subsample, wherein said identifying the presence of at least one said fetal identifier comprises identifying an informative paternal allele in at least one aliquot or subsample. dividing a maternal blood sample comprising a mixture of maternal and fetal cells into subsamples; performing whole genome amplification on at least one said subsample comprising a cell to provide an amplified product, wherein the chromosome copy number from the sample is preserved in the subsample following whole genome amplification such that the resulting amplified product represents the genome or transcriptome of either a maternal or fetal cell; dividing said amplified product into aliquots; screening or genotyping an aliquot for the presence of a fetal identifier, wherein said screening or genotyping comprises; providing a SNP panel to identify the presence of a non-maternal allele in said mixed sample wherein the SNP panel comprises at least one control chromosome-specific panel comprising SNPs located on a chromosome that is not susceptible to aneuploidy and a chromosome-specific panel on a chromosome that is susceptible to aneuploidy; determining whether the genetic material of a maternal cells is homozygous or heterozygous at a set of target loci in said SNP panel to determine a maternal genotype; selecting a test locus from said target loci, wherein said selection of said test locus comprises screening a sample of mixed maternal and fetal nucleic acids for a genotype differing from said maternal genotype at a target locus and selecting as said test locus a target locus with a non-maternal genotype in said sample of mixed maternal and fetal nucleic acids; screening or genotyping said aliquot for a genotype differing from said maternal genotype at said test locus, wherein the presence of said genotype differing from said maternal genotype indicates the presence of an informative paternal allele in said amplified product; and identifying the presence of at least one said fetal identifier from a fetal cell in an aliquot from at least one subsample, wherein said identifying the presence of at least one said fetal identifier comprises identifying an informative paternal allele in at least one aliquot or subsample.