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By Moore R. L.

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The plus sign indicates the individual with the actual genotype error; and the triangle points to the individual identified by PedCheck as most likely to have an erroneous genotype. and Weeks implemented an odds-ratio statistic based on single-locus likelihoods for the pedigree. We would first like to bring to the users’ attention that the authors restrict the genotypes to contain only alleles appearing in the pedigree under consideration. Because “untyping” an individual with a critical genotype results in a consistent pedigree, one recognizes that after genotype elimination the individual must have at least one alternative genotype that is equally valid in a statistical sense.

4 3 8 9 2 1 5 5 0 0 6 6 7 8 ... 4 8 0 0 1 0 5 5 0 0 3 6 7 7 ... 4 9 5 6 2 1 5 7 0 0 0 0 5 8 ... 4 5 0 0 1 0 0 0 0 0 0 0 0 0 ... 4 6 0 0 2 0 0 0 0 0 0 0 0 0 ... 2. Likelihood-Based Statistic: MLRT The likelihood for a relationship type R is LðRÞ ¼ PR ðG1 ; G2 ; :::; Gm ; :::; GM Þ: Due to the linkage correlation between markers, this probability calculation is nontrivial and is typically executed via the hidden Markov model (HMM) (11) assumed for the underlying IBD process, {Dm} (see Chapters 14–17 for more details).

We refer readers to (7) and (12) for technical details of the calculation. 4. Relationship Estimation M M 1 X 1 X ER0 ½Xm Š ¼ ER ER ½Dm jGm Š M m¼1 M m¼1 0 0 M 1 X ER ½Dm Š ¼ p1 þ 2p2 ¼ 4fR0 : M m¼1 0 When strong evidence against the hypothesized null relationship, H0 : R ¼ R0 has been found, it is very helpful to know the alternative relationship(s) that are compatible to the genotype data observed for the pair of individuals. McPeek and Sun (7) proposed a simple strategy that estimates the most likely IBD distribution, p ¼ ðp0 ; p1 ; p2 Þ; by obtaining ^p ¼ ð^p0 ; ^p1 ; ^p2 Þ that maximizes the following quantity !

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