Fig. 2.

Representation of the genetic pattern indicative of MI and MII non-disjunction errors and where crossovers took place. Shown on the figure are the positions that are heterozygous in the mother, here the origin of the non-disjunction event. The difference between non-disjunction occurring at MI (left panel) and at MII (right panel) lies in the location of the tracts that are NIBD, which are associated with a retention of heterozygosity (underlined in orange). Complete genotypes (triploid) represent the number of alternative alleles to the reference genome carried by the proband, while incomplete genotypes (diploid) correspond to homozygous (0 or 2) or heterozygous (1) sites in the proband. In the HMM, the hidden states are the states of the tracts: IBD (I) or not (N), and the observed values are the genotypes of the proband: heterozygous (Z) or homozygous (H). Transitions between states depend on the recombination rate r