A method for determining the copy number of a chromosome of interest in a fetus, using genotypic measurements made on free floating DNA from the fetus found in maternal blood, wherein the free floating DNA of the fetus is mixed with genetic material from the mother of the fetus, the method comprising: making genotypic measurements for a set of SNPs comprising a plurality of SNPs from the chromosome of interest, and a plurality of SNPs from at least one chromosome that is expected to be disomic on the fetus on a mixed sample that comprises the free floating DNA from the fetus mixed with free floating maternal DNA, wherein measuring genetic material is done on genetic material that is amplified prior to being measured, and wherein genotypic measurements are made on 1,000 to 20,000 SNPs using high throughput sequencing; creating, on a computer, a set of ploidy state hypothesis where each ploidy state hypothesis is one possible ploidy state of the chromosome of interest in the fetus, wherein the set of ploidy state hypothesis comprises nine possible hypotheses to correspond to different ploidy states: H00 (0, 0); H01 (0, 1); H02 (0, 2); H10 (1, 0); H11 (1, 1); H12 (1, 2); H20 (2, 0); H21 (2, 1); and H22 (2, 2), wherein (m, f) refer to the hypothesis where m is the number of a given chromosome inherited from the mother, and f is the number of a given chromosome inherited from the father; determining, on the computer, the probability of each of the hypotheses given the genotypic measurements of the mixed sample; and using the determined probabilities of each hypothesis to determine the most likely copy number of the chromosome of interest in the fetus, wherein the determined probabilities are the maximum likelihood estimate of probabilities, and wherein the mixed sample is a maternal blood sample and the fetal DNA is not purified. making genotypic measurements for a set of SNPs comprising a plurality of SNPs from the chromosome of interest, and a plurality of SNPs from at least one chromosome that is expected to be disomic on the fetus on a mixed sample that comprises the free floating DNA from the fetus mixed with free floating maternal DNA, wherein measuring genetic material is done on genetic material that is amplified prior to being measured, and wherein genotypic measurements are made on 1,000 to 20,000 SNPs using high throughput sequencing; creating, on a computer, a set of ploidy state hypothesis where each ploidy state hypothesis is one possible ploidy state of the chromosome of interest in the fetus, wherein the set of ploidy state hypothesis comprises nine possible hypotheses to correspond to different ploidy states: H00 (0, 0); H01 (0, 1); H02 (0, 2); H10 (1, 0); H11 (1, 1); H12 (1, 2); H20 (2, 0); H21 (2, 1); and H22 (2, 2), wherein (m, f) refer to the hypothesis where m is the number of a given chromosome inherited from the mother, and f is the number of a given chromosome inherited from the father; determining, on the computer, the probability of each of the hypotheses given the genotypic measurements of the mixed sample; and using the determined probabilities of each hypothesis to determine the most likely copy number of the chromosome of interest in the fetus, wherein the determined probabilities are the maximum likelihood estimate of probabilities, and wherein the mixed sample is a maternal blood sample and the fetal DNA is not purified.