Fig. 5

Usage of the criteria for “shared” and “homozygous” variants in a trio case. Diamonds indicate different hypotheses that can be made. For instance, if we hypothesize a recessive homozygous variant in the child we should set two criteria: 1) shared variants by child and both parents and 2) homozygous variants only in the child. Whereas, for a compound heterozygosity we would expect that the child shares the variants, but we do not know which variant is in which parent; furthermore, the variant should not be homozygous in the parents. Compound heterozygosities are generally difficult to find and criteria based only on sharing and homozygosity would not be selective enough. In this case the “Gene Analysis tool” described in the text could help in the selection of genes carrying different mutations. Sometimes it may be useful to set criteria that may appear useless, like homozygosity on a X chromosome; however this may help to reduce false positives