As part of the family analysis, Franklin performs a relatedness check for all family members.
In the Quality Control (QC) section, 2 metrics are being displayed:
Consanguinity Check - checking whether parents are family related and to what degree.
Family Relationship Check - checking relationships between proband and all family members and warning if one of the relationships is not as it is supposed to be.
Normal sample - no consanguinity and relatedness as expected
Abnormal sample - Related parents, and duplicated samples
Franklin’s relatedness new score method is based on KING coefficient score (Manichaikul et al. 2010). The score is calculated by a formula that takes into account the number of similar homozygotes and heterozygote variants in two samples.
Possible relatedness values are:
Duplicated sample- a score above 0.354
First-degree relatedness - score in the range [0.177, 0.354]
Second-degree relatedness - score in the range [0.0884, 0.177]
Third-degree relatedness - score in the range [0.0442, 0.0884]
No relatedness - a score below 0.0442 suggests corresponds with no relatedness.
In cases of relatedness that is lower than 3rd degree, an ROH evaluation is performed using the following logic: if there are 2 regions of homozygosity in different chromosomes larger than 4Mb, or 3 regions of homozygosity in different chromosomes larger than 3Mb a consanguinity alert will show with the text of "large regions of homozygosity detected, parents might be related".
Note - Consanguinity check is only available if both parents' samples are analyzed.
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