Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set
Author Information
Author(s): Nicolae Dan L, Wen Xiaoquan, Voight Benjamin F, Cox Nancy J
Primary Institution: The University of Chicago
Hypothesis
How does the Affymetrix GeneChip Human Mapping 100K SNP set compare to the HapMap SNP set in terms of SNP distribution and information content?
Conclusion
The Affymetrix 100K SNP set is undersampled from coding regions and oversampled from regions outside genes compared to the HapMap SNP set.
Supporting Evidence
- SNPs in the 100K set are undersampled from coding regions.
- The 100K set provides substantial coverage on variation in the HapMap database.
- The selection of SNPs was based on a database of more than 3 million SNPs.
Takeaway
Scientists looked at a special set of genetic markers to see if they were good at finding differences in genes that might affect diseases. They found that this set missed some important parts of genes.
Methodology
The study involved a systematic analysis of SNP distribution in the Affymetrix 100K set compared to the HapMap database, focusing on the functional classification of SNPs.
Limitations
The 100K SNP set has considerable redundancy and may not represent all genomic variation effectively.
Digital Object Identifier (DOI)
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