Evaluating Commercial SNP Panels for Genetic Variation
Author Information
Author(s): Mägi Reedik, Pfeufer Arne, Nelis Mari, Montpetit Alexandre, Metspalu Andres, Remm Maido
Primary Institution: Institute of Molecular and Cell Biology, University of Tartu, Estonia
Hypothesis
How well do commercial genome-wide SNP panels capture common genetic variation in different populations?
Conclusion
Commercial SNP panels provide similar levels of coverage in a non-reference Caucasian population compared to the HapMap CEPH population sample.
Supporting Evidence
- Commercial SNP panels can capture most common SNPs from non-reference European populations.
- The HumanHap 550 panel showed the best performance among the platforms evaluated.
- Coverage levels were similar across different non-African populations.
Takeaway
This study looked at how well different genetic testing kits can find common genetic differences in people, especially in Estonians, and found they work pretty well.
Methodology
The study compared four commercial SNP panels on various population samples, including an Estonian population, using genotyping data from two 500-kb ENCODE regions.
Potential Biases
Potential bias due to the SNP selection strategies favoring certain populations.
Limitations
The analysis was limited to two genomic regions and the number of SNPs genotyped in the Estonian sample was fewer than in HapMap populations.
Participant Demographics
Estonian population sample with over 1000 individuals.
Digital Object Identifier (DOI)
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