title: Quantitative analysis of single nucleotide polymorphisms within copy number variation.
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.
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA, USA.
authors.forename: Soohyun
authors.initials: S
authors.lastname: Lee
authors.forename: Simon
authors.initials: S
authors.lastname: Kasif
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
authors.forename: Charles R
authors.initials: CR
authors.lastname: Cantor
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D018628:Gene Dosage; D020440:Gene Duplication; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D018401:Sample Size