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Linkage disequilibrium for different scales and applications.
1National Centre for Genetic Epidemiological Methods, Institute for Human Genetics, GSF-National Research Institute for Environment and Health, 85764 Neuherberg, Germany. jakob.mueller@gsf.de
Briefings in Bioinformatics
|December 21, 2004
Summary
Linkage disequilibrium (LD) describes genetic variation correlation within populations. This review explains various LD measures and their properties for evolutionary and medical genetics research.
Area of Science:
- Genetics
- Evolutionary Biology
- Bioinformatics
Background:
- Linkage disequilibrium (LD) analysis is crucial due to increasing DNA sequence variation data.
- LD quantifies the correlation of genetic variation at multiple genomic sites within populations.
- Understanding LD patterns is vital for evolutionary and medical genetics.
Purpose of the Study:
- To review and explain fundamental linkage disequilibrium measures.
- To discuss the properties and applications of different LD metrics.
- To highlight factors influencing LD patterns, such as recombination and marker type.
Main Methods:
- Review of traditional pairwise LD measures (e.g., D', r2).
- Exploration of advanced multi-locus and haplotype-specific LD approaches.
- Discussion of model-based LD analysis for inferring evolutionary forces like recombination.
Main Results:
- Various LD measures exist, each with specific statistical properties and applications.
- Recombination and marker type (e.g., microsatellites vs. SNPs) significantly impact observed LD patterns.
- Microsatellites show higher power for LD detection in population isolates compared to SNPs.
Conclusions:
- A comprehensive understanding of LD measures is essential for genetic research.
- LD analysis provides insights into population genetics and disease association studies.
- The choice of LD measure and marker type depends on the specific research question and population structure.