LAMP - Background Information

Basic Assumptions

• A single disease causal variant in the region.

• Linkage equilibrium between flanking markers and candidate SNP.

• No genetic interference.

• Hardy-Weinberg equilibrium for all genetic markers.

Genetic Models

• Candidate SNP is unlinked and is in linkage equilibrium with putative disease locus (baseline).

• Candidate SNP is completely linked and is in linkage equilibrium with putative disease locus (linkage).

• Candidate SNP is completely linked and is in complete linkage disequilibrium with putative disease locus (causal).

• Candidate SNP is completely linked and can be in any level of linkage disequilibrium with putative disease locus (association).

The first model is the baseline model, and the other three models allow for linkage, direct association and inidrect association, respectively. LAMP uses the log likelihood difference between a pair of models to construct a LOD score statistic that can be used to test for linkage, or to test for association, or to decide whether there is evidence for additional linked variants (i.e. that the current SNP cannot explain the observed linkage signal). Please refer to Table 3 in Li et al. (2005) for detailed information.