Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Soohyun Lee, Simon Kasif, Zhiping Weng and Charles R Cantor

PLOS ONE, 2008, vol. 3, issue 12, 1-10

Abstract: 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.

Date: 2008
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0003906

DOI: 10.1371/journal.pone.0003906

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