| |
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:
| State | Groupings of IBD alleles | Description |
| 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:
| State | Groupings of IBD alleles | Description |
| 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:
| State | Groupings of IBD alleles | Description |
| 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).
| |
