1. An ex vivo method for determining a number of copies of a chromosome or chromosome segment of interest in the genome of an individual, the method comprising: using a single nucleotide polymorphism (SNP) genotyping array or high throughput DNA sequencing to measure genetic material and produce genetic data for some or all possible alleles at a plurality of at least 100 loci on the chromosome or chromosome segment of interest in the individual, wherein the genetic data is noisy due to a small amount of genetic material from the individual; and wherein the small amount of genetic material from the individual is from fifty or fewer of the individual's cells, 0.3 ng or less of the individual's DNA, extracellular DNA from the individual found in maternal blood, or combinations thereof; creating a set of one or more hypotheses specifying the number of copies of the chromosome or chromosome segment of interest in the genome of the individual; determining, on a computer, the probability of each of the hypotheses given the produced genetic data; and using the probabilities associated with each hypothesis to determine the most likely number of copies of the chromosome or chromosome segment of interest in the genome of the individual.