Linkage Disequilibrium in SNP Genome Scans
Author Information
Author(s): Juan Manuel Peralta, Thomas Dyer, Diane M. Warren, John Blangero, Laura Almasy
Primary Institution: Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica
Hypothesis
What is the extent of linkage disequilibrium (LD) present in SNP genome scans and its effect on LOD scores?
Conclusion
Considerable linkage disequilibrium exists between markers in both Affymetrix and Illumina SNP genotyping sets, with more pronounced effects in Affymetrix's denser map.
Supporting Evidence
- Extensive linkage disequilibrium was observed throughout both marker sets.
- SNP density did not solely account for the higher linkage disequilibrium in Affymetrix's map.
- Caution is advised when using high-density SNP maps with many non-genotyped founders.
Takeaway
This study looked at how closely related genetic markers are in two different types of DNA tests, finding that one type had more closely spaced markers than the other.
Methodology
SNP genotypes from Affymetrix and Illumina datasets were analyzed for linkage disequilibrium using pairwise measures.
Potential Biases
Potential bias due to the assumption of linkage equilibrium in MIBD estimation.
Limitations
The study's findings may not apply to studies with many non-genotyped founder individuals.
Participant Demographics
505 pedigree founder individuals, with 240 genotyped and 265 not genotyped.
Statistical Information
P-Value
p < 0.0001
Statistical Significance
p < 0.0001
Digital Object Identifier (DOI)
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