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I have a question about IBD. Please see the figure below. How many pairs of alleles are IBD for X and Y, or what is the IBD value for X and Y. Is it four (4)? I have seen it to be maximally 2, but then we assume that no inbreeding occurs, right?

Pedigree

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An Identical-By-Descent (IBD) value is the number of alleles which are the same because of descent from a common ancestor. Since each (diploid) individual has two alleles for a given (autosomal) gene, the number of them that are IBD with another individual can only be 0, 1, or 2.

In your example, X and Y inherit each of their alleles from A2, so their IBD value is 2. Inbreeding is just an extreme form of descent from a common ancestor; it causes on average greater probability of high IBD values than when comparing less-inbred individuals. See the passage here for more detail.

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  • $\begingroup$ Thanks for answer @mgkrebbs. I am still a little bit confused. This is due to the following excerpt from Thompson: Pedigree Analysis in Human Genetics, 1986, The Johns Hopkins University Press, page 28: "Consider now a pair of relatives, neither of whom are inbred, although their parents may be. Since neither of the two individuals can carry two identical genes, there are only three possibilities of gene identity (figure 11): the individuals have two genes in common, or one or neither." Does the IBD value relate to only one person or to the two individuals under consideration. $\endgroup$ – FredikLAa Sep 8 '15 at 9:36
  • $\begingroup$ Hmm. I see three possible solutions: 1) the individuals share 1 allele IBD, the a allele 2) the individuals share both of their alleles IBD so that IBD=2 3) all the alles are IBD, so that IBD=4 (you can make 4 different pairs of IBD alleles). It looks Thompson and the excerpt you provide look at the two persons at the same time; i.e how many alleles do two persons share . It looks like they do not look on the individual level (i.e how many of the alleles of.one person does the individual share with the other.) $\endgroup$ – FredikLAa Sep 8 '15 at 11:33
  • $\begingroup$ If we assume that @mgkrebbs' solution is correct, what would the IBD-value be between R and X if R had genotype ca instead of cd? Now R has one allele in common with X, but X has two alleles in common with R. $\endgroup$ – FredikLAa Sep 8 '15 at 14:08
  • $\begingroup$ IBD (and IBS) is a characteristic of the relationship of two persons' genes, not a characteristic of a gene or allele itself. So the only possible relationships are: no alleles are the same, one pair of alleles are the same and one different, or both pairs of alleles are the same. If R' is ca, then R' and X have IBD (and IBS) value of 1 -- they have one pair the same. The alleles are unordered - you choose the pairings between individuals' alleles so as to maximize the IBD count, having chosen one pair, the other pair is also determined, being the only pairing that can then exist. $\endgroup$ – mgkrebbs Sep 8 '15 at 15:18

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