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Consanguinity and Relatedness check
Consanguinity and Relatedness check

Relatedness, consanguinity, and paternity tests in a family analysis

Yaron Einhorn avatar
Written by Yaron Einhorn
Updated over a year ago

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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