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Linkage disequilibrium across two different single-nucleotide polymorphism genome scans
Juan Manuel Peralta1, Thomas D Dyer, Diane M Warren
1Centro de Investigación en Biología Celular y Molecular, Ciudad de la Investigación, Universidad de Costa Rica, San José, Costa Rica. jperalta@darwin.sfbr.org
BMC Genetics
|February 3, 2006
Summary
Linkage disequilibrium (LD) was analyzed in genetic scans, revealing higher levels in denser SNP maps. LD had a minor impact on LOD scores when many founders were genotyped, suggesting caution with dense maps and ungenotyped individuals.
Area of Science:
- Genetics
- Statistical Genetics
- Bioinformatics
Background:
- Linkage disequilibrium (LD) is crucial for genetic association studies.
- Accurate genetic analysis requires accounting for LD, especially with dense single-nucleotide polymorphism (SNP) maps.
- The Collaborative Study on the Genetics of Alcoholism (COGA) provides valuable sample data.
Purpose of the Study:
- To calculate LD content for Affymetrix and Illumina SNP genome scans in COGA samples.
- To assess the impact of LD on multipoint identity by descent (MIBD) calculations and LOD scores.
- To provide recommendations for using dense SNP maps in genetic studies with pedigree founders.
Main Methods:
- Pair-wise LD was measured using D' and r2 on 505 pedigree founders.
- r2 estimates corrected MIBD calculations for LD.
- LOD scores were calculated for an electrophysiological trait on chromosomes 3 and 18 using corrected MIBDs.
Main Results:
- Extensive LD was observed in both Affymetrix and Illumina SNP sets.
- Higher LD was noted in the denser Affymetrix SNP map, though density alone didn't fully explain it.
- LD correction had a minor impact on LOD scores when a significant portion of founders were genotyped.
Conclusions:
- SNP density influences LD levels, but other factors also contribute.
- MIBD procedures assuming linkage equilibrium may be affected by LD in dense SNP maps.
- Caution is advised when using high-density SNP maps in pedigrees with numerous non-genotyped founders.