System and method for cleaning noisy genetic data and determining chromosome copy number

A method for determining a number of copies of a segment of a chromosome in the genome of a target individual, comprising:

• creating, on a computer, a plurality of copy number hypotheses specifying the number of copies of the chromosome segment that are present in the genome of the target individual;
• obtaining genetic data from (1) the target individual at a plurality of single nucleotide polymorphic loci on the chromosome segment which data comprises measurement errors that result from allele drop outs or allele drop ins at a subset of the plurality of loci and (2) one or more biological parents of the target individual at the plurality of loci;
• calculating, on a computer, a distribution of measurement errors for the obtained genetic data;
• creating, on a computer, for each of the hypotheses, a probability distribution of the expected genotypes of the target individual from (i) the obtained genetic data from the one or more biological parents, (ii) the probability of one or more crossovers that may have occurred during the formation of a gamete that contributed a copy of the chromosome segment to the target individual, and (iii) the distribution of measurement errors for the obtained genetic data;
• applying, on a computer, a technique selected from the group consisting of maximum a-posteriori estimation, maximum likelihood estimation, and Bayesian estimation to the obtained genetic data of the target individual and the probability distribution of the expected genotypes of the target individual to rank one or more of the hypotheses according to the data fit between the obtained genetic data of the target individual and the probability distribution of the expected genotypes of the target individual;
• and
• selecting the hypothesis that is ranked the highest, thereby determining the number of copies of the chromosome segment in the genome of a target individual.