Further evidence for the increased power of LOD scores compared with nonparametric methods

Article Abstract:

More evidence has been found for the power of LOD scores versus nonparametric methods. Genetic analysis of diseases where the underlying model is not known, model-free methods, among them affected sib pair (ASP) tests, are often preferred over LOD-score methods, though LOD-score methods under the correct or even nearly correct model are more powerful than ASP tests. Whether or not certain models do set up a situation in which ASP tests are more powerful than LOD scores has been investigated. Sl analysis performed twice and corrected for the type I-error increase coming from multiple testing gives almost as much linkage information as an analysis under the correct 2L model does and is more powerful than the NPL method or the ASP method. Even for complex genetic models, the most important condition for linkage analysis is that the assumed mode of inheritance (MOI) at the disease locus tested is approximately correct, not that the inheritance of the disease itself is specified correctly.

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A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting

Article Abstract:

A log-linear approach to case-parent-triad data can be effective in assessment of effects of disease genes that act directly through maternal effects or directly and that may be affected by parental imprinting. Estimates of association parameters can be found through use of this method. With one allele being studied, the method can yield powerful tests for detection of linkage disequilibrium. It is applicable to a broader range of causative scenarios than transmission/disequilibrium tests (TDT).

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Replication of linkage studies of complex traits: an examination of variation in location estimates

Article Abstract:

Replication of linkage studies of complex traits is discussed. The distance at which to reject the hypothesis that two location estimates in a genomic region represent the same gene is addressed. For conditions studied the standard error of a location estimate is a function of the magnitude of the expected LOD score.

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