Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology
DNA Mutational Analysis; *Gene Dosage; Gene Duplication; Gene Frequency; Genotype; Humans; Linkage Disequilibrium; Models, Genetic; *Polymorphism, Single Nucleotide; Sample Size
Bioinformatics | Computational Biology | Genetics and Genomics | Systems Biology
BACKGROUND: Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE.
RESULTS: We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%.
CONCLUSIONS: Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.
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Citation: PLoS One. 2008;3(12):e3906. doi: 10.1371/journal.pone.0003906. Epub 2008 Dec 18. Link to article on publisher's site
Lee, Soohyun; Kasif, Simon; Weng, Zhiping; and Cantor, Charles R., "Quantitative analysis of single nucleotide polymorphisms within copy number variation" (2008). Program in Bioinformatics and Integrative Biology Publications and Presentations. 39.