Linkage Disequilibrium in Genic Regions of the Human Genome
Author Information
Author(s): Eberle Michael A, Rieder Mark J, Kruglyak Leonid, Nickerson Deborah A
Primary Institution: University of Washington
Hypothesis
Does matching SNPs by allele frequency provide a more accurate measure of linkage disequilibrium in the human genome?
Conclusion
The study found that matching SNPs by allele frequency significantly increases the observed linkage disequilibrium in genic regions compared to intergenic regions.
Supporting Evidence
- Frequency matching of SNP pairs provides a more sensitive measure for assessing the average decay of linkage disequilibrium.
- Genic regions showed a significantly larger fraction of perfectly correlated SNPs compared to intergenic regions.
- Perfectly correlated SNP pairs exhibited a clear excess of high-frequency derived alleles in both genic and intergenic regions.
Takeaway
When scientists compare genetic markers, they should match them by how common they are to get better results. This study shows that markers near genes are more likely to be linked than those farther away.
Methodology
The study analyzed 1.58 million SNPs genotyped by Perlegen, comparing linkage disequilibrium using both unmatched and frequency-matched SNP pairs.
Potential Biases
Potential biases may arise from the ascertainment scheme of the SNP dataset.
Limitations
The study's findings may be influenced by the specific SNP dataset used and the sample sizes for different populations.
Participant Demographics
The study included individuals of European, Han Chinese, and African-American descent.
Statistical Information
P-Value
p<0.001
Confidence Interval
90% confidence interval of approximately 143 kb
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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