|
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. |
