Impact of Missing Parental Genotypes on Linkage Analysis
Author Information
Author(s): Douglas F Levinson, Peter Holmans
Primary Institution: University of Pennsylvania School of Medicine
Hypothesis
How does the presence of linkage disequilibrium affect linkage scores when parental genotypes are missing?
Conclusion
Missing parental genotypes can significantly inflate linkage scores in regions of high linkage disequilibrium.
Supporting Evidence
- Inflation of linkage scores was observed in regions of high LD when parental genotypes were missing.
- Trimming SNP maps to limit r2 to 0–0.05 prevents inflation of linkage scores.
- Simulation studies indicated that strong LD can inflate linkage scores in genome-wide studies.
Takeaway
If we don't have the genetic information from parents, it can make our results look better than they really are, especially in certain areas of the DNA.
Methodology
The study used simulations to analyze the effects of missing parental genotypes on linkage scores in SNP data.
Potential Biases
Potential bias due to the exclusion of certain SNPs and reliance on simulated data.
Limitations
The study focused on a small chromosomal region and may not generalize to other regions.
Participant Demographics
116 European-ancestry pedigrees from the COGA dataset.
Statistical Information
P-Value
0.0063
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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