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Incomplete IBD information: multipoint calculation

Consider the setting of Kruglyak and Lander and Kruglyak et al. where we have a map of genetic markers and we wish to use the partial genotype and IBD information from all markers to perform multipoint linkage analysis at any point along the genome. Let m denote the observed multipoint marker data.

The likelihood of the multipoint marker data, in terms of the IBD probabilities at a candidate locus has the general form

under Assumptions G1, G2, G3, G4 and the assumption that the candidate locus is at a DS locus. Here is the inheritance distribution at the candidate locus computed using a HMM (Lander-Green Algorithm, ... more details later ...).

Sampling assumptions are the same as in the single marker situation.



Simon Cawley
Tue May 26 19:30:26 PDT 1998