Handling Linkage Disequilibrium in Linkage Analysis Using Dense SNPs
Author Information
Author(s): Cho Kelly, Yang Qiong, Dupuis Josée
Primary Institution: Boston University School of Public Health
Hypothesis
Can different methods effectively handle linkage disequilibrium in linkage analysis of dense SNPs?
Conclusion
The study found that properly handling linkage disequilibrium significantly reduces false-positive linkage signals in analyses with missing parental genotypes.
Supporting Evidence
- Linkage disequilibrium can lead to bias in linkage analysis when parental genotypes are missing.
- Using methods to model linkage disequilibrium significantly reduced LOD score inflation.
- MERLIN-LD showed the most reduction in LOD score inflation among the methods tested.
Takeaway
When looking for genes related to diseases, it's important to handle genetic data carefully, especially when some family information is missing, to avoid mistakes.
Methodology
The study compared three methods for handling linkage disequilibrium using simulated data from rheumatoid arthritis families.
Potential Biases
Potential bias due to missing parental genotypes and the assumptions made by the methods used.
Limitations
The results may not be generalizable to regions with high r2 values, and the methods assume no recombination within clusters.
Participant Demographics
The study involved 1500 pedigrees with 6000 individuals, focusing on rheumatoid arthritis.
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