Comparison of SNP Tagging Methods
Author Information
Author(s): Ellen L Goode, Brooke L Fridley, Zhifu Sun, Elizabeth J Atkinson, Alex S Nord, Shannon K McDonnell, Gail P Jarvik, Mariza de Andrade, Susan L Slager
Primary Institution: Mayo Clinic College of Medicine
Hypothesis
We sought to compare the ability of commonly used tagging SNP selection methods to detect known associations with quantitative expression phenotypes.
Conclusion
The optimal tagging SNP method depends on the true model of the genetic association, which is often unknown at the time of SNP selection.
Supporting Evidence
- Pairwise methods worked well relative to the use of all SNPs.
- Haplotype-based methods missed associations in some regions.
- SNP subsets did not substantially overlap across methods.
Takeaway
This study looked at different ways to pick genetic markers and found that some methods work better than others depending on the situation.
Methodology
We compared pairwise, multimarker, and haplotype-based tagging SNP selection methods using data from HapMap on unrelated Utah residents.
Limitations
The study was a small pilot and may not generalize to larger populations.
Participant Demographics
Unrelated Utah residents with ancestors from northern and western Europe.
Statistical Information
P-Value
< 10-6
Statistical Significance
p<0.05
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