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 - determine whether parents are blood relatives and to what degree.
Family Relationship Check - verify relationships between the proband and all family members, and alert if any relationship is not as expected.
Normal case - no consanguinity, relatedness as expected
Abnormal case - Related parents, duplicated samples
Relatedness score
Franklin’s relatedness new scoring method is based on the KING coefficient score (Manichaikul et al. 2010). The score is calculated using a formula that considers the number of similar homozygotes and heterozygote variants found 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 indicates no relatedness.
ROH analysis
In cases where relatedness is less than a third degree, an ROH evaluation is performed using the following logic: if there are two regions of homozygosity on different chromosomes larger than 4 Mb, or three regions of homozygosity on different chromosomes larger than 3 Mb, a consanguinity alert will appear with the message "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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