Disclosed herein is a
system and method for increasing the fidelity of measured
genetic data, for making
allele calls, and for determining the state of
aneuploidy, in one or a small set of cells, or from fragmentary
DNA, where a limited quantity of
genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target
genome and the
genome of genetically related individuals. In accordance with one embodiment, incomplete
genetic data from an embryonic
cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of
diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the
chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.