17 months ago by
Republic of Ireland
Allelic matching is an important parameter to consider when determining relatedness via runs of homozygosity (ROH). The general threshold (for relateness or identity by descent) in any defined genomic region is that > 95% of all homozygous calls in the region should have the same call in the 2 or more individuals being studied (i.e., the homozygous calls should match allelically). If only 10% match, then it's not strong evidence that the region of DNA in question was inherited equally amongst the individuals being studied, even if it's a ROH, and implies genetic inheritance outside of those being studied.
However, as you can imagine, the metric is heavily dependent on the size of the region in question, SNP genotyping density, the number of heterozygous calls permitted (and assumed to be sequencing errors), and the number of missing calls.
If you have 2 individuals with long (>1Mbp?) ROH that allelically match, then it's evidence (but not proof) that they exhibit relatedness. I studied a family once in which one offspring was homozygous for a very rare variant (0.0002% frequency in 1000 Genomes). A check of ROH in the family revealed that the parents were possibly closely related by descent.