Comparison of SNP Tagging Programs
Author Information
Author(s): Duggal Priya, Gillanders Elizabeth M, Mathias Rasika A, Ibay Grace P, Klein Alison P, Baffoe-Bonnie Agnes B, Ou Liang, Dusenberry Ian P, Tsai Ya-Yu, Chines Peter S, Doan Betty Q, Bailey-Wilson Joan E
Primary Institution: Inherited Disease Research Branch, NHGRI/NIH, Baltimore, MD, USA
Hypothesis
Does the amount of linkage disequilibrium or the size of the region influence the selection of tagging SNPs?
Conclusion
Different tagging SNP programs perform similarly in regions with moderate to strong linkage disequilibrium despite using different parameters and algorithms.
Supporting Evidence
- The study compared seven different tagging SNP programs in 10 regions with varied amounts of linkage disequilibrium.
- In regions with moderate to strong LD, the programs showed consistency in SNP selection.
- As the number of selected SNPs increased, the LOD score and mean information content also increased.
Takeaway
The study looked at different ways to pick important genetic markers and found that they mostly agree on which markers to choose, especially in certain areas of the genome.
Methodology
The study compared seven SNP tagging programs using data from the Collaborative Studies on the Genetics of Alcoholism, focusing on regions with varying linkage disequilibrium.
Potential Biases
The analysis was restricted to White, non-Hispanic individuals, which may introduce bias in allele frequency and linkage disequilibrium measurements.
Limitations
The study was limited to one ethnicity to reduce bias, which may affect the generalizability of the results.
Participant Demographics
All individuals classified as White, non-Hispanic (n = 1,074).
Statistical Information
P-Value
p = 0.02
Confidence Interval
0.70 - 0.98
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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