Several relevant examples are presented in Peirce et al. (2007, 2008), and the respective authors provide evidence for the consideration of linkage as a possible causal factor of location bias.
As the SNPs selected for Stage 1 were chosen without consideration of linkage disequilibrium (LD), there are a number of SNPs with P-values ≤0.0001 that are in relatively strong LD with each other and therefore the significant SNPs do not represent 85 independent loci.
Closed-form expressions for its motion and the rotation of the double Cardan joint are derived by consideration of spherical linkage kinematics, and presented in this work.
However, there are at least three points to be methodologically improved: 1) there is no consideration of LD (Linkage Disequilibrium) blocks which can cause bias of variants, 2) statistical tests need be improved to evaluate the level of confidence, and 3) users are required to manipulate large data sets step-by-step to obtain a phylogenetic tree.
Ideally, such a framework would include consideration of X-linkage of causal variants, the contribution of cis by trans interactions, sex-biased expression, breadth of expression/tissue-specificity, and sex-specific fitness effects.
The relationship within and between files and the level of confidence in existing links/relationships are important considerations in the design and optimisation of linkage strategies.
A parameter worth consideration during variant selection is the likely extent of linkage disequilibrium (LD) between variants in either pool.
Three steps were taken into consideration: (1) determination of significance thresholds for association, (2) identification of linkage disequilibrium (LD) regions for significant association signal and (3) positive control of association.
This special issue provides an overview of innovative research approaches that are specifically designed to promote a deeper ecological understanding of the effects of human-induced global change by explicitly addressing linkages between broad considerations of life on earth to biologically relevant responses from other organizational levels and spatial scales.
Patterns of linkage disequilibrium between associated SNPs in different studies will have to be taken into consideration before either claiming replication or the lack of it.
