kinship matrix plot

[Atoosa Samani]

Hi,

why would an individual have low degree of allele sharing with itself? 

in the plot I copied here, I have an example of what I mean. in the figure, individual 8 does show a light color when it is compared with itself. what can the reason be?

[Karl Broman]

I think that means they are unusually heterozygous. The kinship coefficient, for an individual to itself, is the probability of two alleles drawn at random at an autosomal locus being IBD. For a fully inbred inbred individual, the kinship coefficient is 1. For a non-inbred individual, it would be 1/2. 

karl

[Dan Gatti]

You might look at the degree of homozygosity in each sample. I suspect that sample 8 has lower homozygosity than the other samples.

 

I was confused by this same thing for a long time. When allele sharing within the same sample is estimated, you compare allele1 with allele2 at one locus. If they’re both ‘A’, then the locus shares an allele. If allele1 is ‘A’ and allele2 is ‘C’, then they don’t share an allele at that locus. So if you have lots of homozygous loci, your self-kinship will be closer to 1. As the number of heterozygous loci increases, you’ll see lower self-kinship numbers.

 

Does that help?

 

Dan

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[Atoosa Samani]

Thank you so much for your answers. 

this individual had a very low quality genotyping (only 41 markers were genotyped) so I dropped it from the map. 

I assume since it had a lot of NAs the degree of allele sharing with itself was low.