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. Genetic material from the target individual is acquired, amplified and the
genetic data is measured using known methods. 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 of the invention, 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 of the invention, the
chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of
embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.