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Microsatellites versus single-nucleotide polymorphisms in linkage analysis for quantitative and qualitative measures
Gerald Dunn1, Anthony L Hinrichs, Sarah Bertelsen
1Department of Psychiatry, Genetics, Washington University School of Medicine, St. Louis, Missouri, USA. dunnge@notes.wustl.edu
BMC Genetics
|February 3, 2006
Summary
Single-nucleotide polymorphisms (SNPs) offer a promising alternative to microsatellite markers for genetic linkage analysis. This study found SNPs generally yielded stronger results, especially when accounting for high linkage disequilibrium (LD).
Area of Science:
- Genetics
- Genomics
- Statistical Genetics
Background:
- Microsatellite genetic maps are being replaced by single-nucleotide polymorphism (SNP) maps.
- This study compares SNP and microsatellite maps for neurophysiology and alcohol dependence phenotypes.
Purpose of the Study:
- To compare the efficacy of SNP maps versus microsatellite maps in genetic linkage analysis.
- To investigate the impact of high linkage disequilibrium (LD) on SNP map accuracy.
Main Methods:
- Utilized two SNP maps (Illumina and Affymetrix) and a microsatellite map.
- Analyzed a "sparse" SNP map, thinned in regions of high LD, to assess LD effects.
Main Results:
- SNP maps generally produced higher LOD scores than microsatellite maps for both phenotypes.
- The alcohol dependence phenotype showed particularly strong linkage signals with SNP maps.
Conclusions:
- SNPs can be an effective substitute for microsatellites in linkage analysis for various phenotypes.
- Thinning SNP maps in high LD regions improves the accuracy of LOD scores.