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Extended IBD states

When the --extended command line option is used, MERLIN calculates probabitities for 15 extended IBD states. These define all possible states of allele sharing for a pair of individuals. This page describes the labelling used by MERLIN for each possible IBD state.

Nuclear family

Consider two individuals i and j. Each of these individuals carries a maternally inherited allele im and jm and a paternally inherited allele ip and jp. For a pair of full siblings in a non-inbred family, four IBD states are possible:

StateGroupings of IBD allelesDescription
I09 {im, jm}{ip, jp} Maternal and paternal alleles are shared IBD
I10 {im, jm}{ip}{jp} Only maternal alleles are shared IBD
I11 {ip, jp}{im}{jm} Only paternal alleles are shared IBD
I15 {im}{jm}{ip}{jp} No alleles are shared IBD

Extended non-inbred pedigree

For larger pedigrees, additional IBD states are possible. For example, a maternally inherited allele for one individual may be indentical to the paternally inherited allele for another individual. In these pedigres, three additional IBD states are possible for a total of seven IBD states:

StateGroupings of IBD allelesDescription
I09 {im, jm}{ip, jp} Maternal and paternal alleles are shared IBD
I10 {im, jm}{ip}{jp} Only maternal alleles are shared IBD
I11 {ip, jp}{im}{jm} Only paternal alleles are shared IBD
I12 {im, jp}{ip, jm} i's maternal allele is IBD to j's paternal allele and vice-versa
I13 {im, jp}{ip}{jm} i's maternal allele is IBD to j's paternal allele, other alleles are not IBD
I14 {ip, jm}{im}{jp} i's paternal allele is IBD to j's maternal allele, other alleles are not IBD
I15 {im}{jm}{ip}{jp} No alleles are shared IBD

Inbred Pedigree

The two alleles carried by an inbred individual may be IBD, and this produces additional IBD states. In an inbred pedigree there are up to 15 possible IBD states for each pair of individuals:

StateGroupings of IBD allelesDescription
I01 {im, ip, jm, jp} All four alleles are identical by descent
I02 {im, ip, jm}{jp} All alleles, except jp, are identical by descent
I03 {im, ip, jp}{jm} All alleles, except jm, are identical by descent
I04 {im, jm, jp}{ip} All alleles, except ip, are identical by descent
I05 {ip, jm, jp}{im} All alleles, except im, are identical by descent
I06 {im, ip}{jm, jp} i and j are inbred and alleles are IBD within each individual
I07 {im, ip}{jm}{jp} i is inbred and carries maternal and paternal alleles that are IBD
I08 {im}{ip}{jm, jp} j is inbred and carries maternal and paternal alleles that are IBD
I09 {im, jm}{ip, jp} Maternal and paternal alleles are shared IBD
I10 {im, jm}{ip}{jp} Only maternal alleles are shared IBD
I11 {ip, jp}{im}{jm} Only paternal alleles are shared IBD
I12 {im, jp}{ip, jm} i's maternal allele is IBD to j's paternal allele and vice-versa
I13 {im, jp}{ip}{jm} i's maternal allele is IBD to j's paternal allele, other alleles are not IBD
I14 {ip, jm}{im}{jp} i's paternal allele is IBD to j's maternal allele, other alleles are not IBD
I15 {im}{jm}{ip}{jp} No alleles are shared IBD

References

For more information on extended IBD states, see the excellent book by Ken Lange, Mathematical and statistical methods for genetic analysis (1997).

 
 

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