Evaluating the Effectiveness of HapMap SNPs in Capturing Untyped SNPs
Author Information
Author(s): Tantoso Erwin, Yang Yuchen, Li Kuo-Bin
Primary Institution: Bioinformatics Institute, Singapore
Hypothesis
Are HapMap SNPs sufficient to capture most of the variation and untyped SNPs in human genes?
Conclusion
HapMap SNPs are transferable to NIEHS SNPs, but they cannot capture all untyped SNPs, indicating that resequencing may be necessary.
Supporting Evidence
- HapMap SNPs were found to be transferable to NIEHS SNPs with over 95% coverage.
- The performance of HapMap SNPs in capturing untyped variants was approximately 55% for European and Asian populations.
- HapMap SNPs showed the lowest performance in the African population, capturing only about 30% of untyped variants.
Takeaway
This study looked at whether a set of genetic markers called HapMap SNPs can find other genetic variations that weren't directly tested. It found that while they work well in some cases, they miss a lot of others.
Methodology
The study analyzed genotype data from the HapMap project and NIEHS EGP SNPs to assess the transferability and robustness of HapMap SNPs in capturing untyped variants.
Limitations
The study's findings may not apply universally across all populations, particularly in regions with low SNP density.
Participant Demographics
The study included European, Asian, and African populations.
Digital Object Identifier (DOI)
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