# Pedigree section

The Pedigree section displays relatedness metrics and the results of relationship validation for each pair of samples in the family tree.

## **Included metrics**

**Relatedness coefficient (observed)**

Shows the observed coefficient of relatedness between sample pairs. The **expected coefficient** is available via hover tooltip for quick comparison.

**IBS0**

Identity by state 0—a number of genomic loci where two individuals share zero alleles. This occurs when the two individuals are opposite homozygotes for a biallelic SNP.

This metric is calculated across a set of biallelic SNPs and is inversely related to the degree of genetic similarity between the individuals. A low IBS0 count suggests a higher degree of overall genetic similarity, but it is an indirect and limited measure of genetic relatedness that requires interpretation alongside other metrics.

**Relationship validation result**

Summarizes the outcome of the relationship validation, confirming whether the observed data aligns with the expected pedigree structure.

<figure><img src="https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-9075ade69d95ac09f71e2bb2373a8b72c5c324be%2Fimage%20(92).png?alt=media" alt=""><figcaption></figcaption></figure>

## **Relationship validation calculation**

Relationship validation is done by [Peddy](https://pubmed.ncbi.nlm.nih.gov/28190455/) based on:

* **Relatedness coefficient (𝑟)**—a measure of how much two individuals share alleles from a common ancestor, indicating the probability that alleles at the same genome location are identical by descent
* **IBS0 (Identity by state 0)**—a number of genomic loci where two individuals share zero alleles, ie, they are opposite homozygotes
* **IBS2 (Identity by state 2)**—a number of genomic loci where two individuals share two alleles, meaning they have the exact same genotype

Peddy takes the inferred relationships from the genetic data and cross-references them against the declared relationships. For every pair of individuals in a cohort, Peddy calculates a coefficient of relatedness from the genotypes observed at the sampled sites.

For each possible pair of samples in a pedigree, the expected relatedness coefficient based on declared family relation is compared with the observed relatedness coefficient (![](data:image/gif;base64,R0lGODlhAQABAIAAAP///wAAACH5BAEAAAAALAAAAAABAAEAAAICRAEAOw==)𝑟). IBS0 value helps to differentiate between sibling and parent–child relationships, both expected to have \~50% relatedness coefficient (see table).

<table><thead><tr><th width="122.9091796875">Inferred relationship</th><th width="182">Expected IBS0 number</th><th width="142.727294921875">Expected 𝑟 (%)</th><th width="341.54541015625">Observed 𝑟 (%) and interpretation</th></tr></thead><tbody><tr><td>Unrelated</td><td>Relatively high</td><td>0</td><td><p>&#x3C; 0.2 Pass<br>0.2–4 Shared ancestry<br>4–15 Consanguinity</p><p>> 15 Consanguinity + Failed validation</p></td></tr><tr><td>Parent–child</td><td>0 or close to 0. Any IBS0 sites—due to genotyping errors</td><td>50</td><td>&#x3C; 40 Failed validation<br>40–60 Pass<br>> 60 Failed validation</td></tr><tr><td><br>Full siblings</td><td>Small but detectable number</td><td>50</td><td>&#x3C; 40 Failed validation<br>40–60 Pass<br>> 60 Failed validation</td></tr></tbody></table>