Family relations check

Owned by Sara Haers
Last updated: Dec 14, 2020 by Cyrielle Kint

When performing a family analysis, Moon automatically conducts a family relations check to confirm the indicated relationships between the family members. The result is shown on the Shortlist screen, and reduces the risk of misattributed relations which could in turn impact Moon’s results.

To confirm a family relation, Moon calculates the genetic data overlap between the family members based on the uploaded VCF files. First, it determines the fraction of shared rare variants on autosomes between two VCF samples (# shared variants / # total variants in the smallest VCF file). Subsequently, the fraction of shared variants among these samples is compared to predefined threshold values (shown below).

Moreover, based on the Gender prediction feature, Moon verifies whether the predicted gender of the family sample matches the assigned relationship (e.g. a sample predicted by Moon to be male, assigned to a male relation such as father or brother, and not to mother or sister).

Based on this, for each relation, Moon shows:

  • Green checkbox: the predicted gender of the sample matches the assigned relationship and the family relation is confirmed.

    • First-degree family relations (father, mother, brother, sister) are confirmed if the fraction of shared variants is >50%

    • Second-degree family relations (aunt, uncle, grandfather, grandmother) are confirmed if the fraction of shared variants is >25%

  • Red warning sign: the predicted gender of the sample does not match the assigned relationship and/or the family relation is not confirmed.

If the gender of a sample can not be stablished by Moon, only relatedness is checked

Hovering over the checkbox or warning icons brings up a tooltip that provides more information and indicates the calculated VCF overlap between the corresponding family member and the proband

Clicking the name of the sample of each family member, refers you to the Patient info page of each linked family member.

Low quality of input VCFs can impact the calculated fractions and therefore the family relations check result. To verify the data quality of your VCF, access the quality page through the drop-down menu next to the sample name on top of the screen.