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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Updated: Jun 27, 2026

Detection of Copy Number Alterations Using Single Cell Sequencing
09:45

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Published on: February 17, 2017

Quantitative analysis of single nucleotide polymorphisms within copy number variation.

Soohyun Lee1, Simon Kasif, Zhiping Weng

  • 1Bioinformatics Program, Boston University, Boston, MA, USA.

Plos One
|December 19, 2008
PubMed
Summary

Copy number variation (CNV) significantly impacts single nucleotide polymorphism (SNP) Hardy-Weinberg equilibrium (HWE) testing, especially for rare variants. This finding is crucial for genetic and epidemiological studies.

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Area of Science:

  • Genetics
  • Genomics
  • Population Genetics

Background:

  • Single nucleotide polymorphisms (SNPs) are fundamental in genetic and epidemiological studies.
  • Deviations from Hardy-Weinberg equilibrium (HWE) traditionally lead to SNP exclusion.
  • Structural variations, like copy number variations (CNVs), are increasingly recognized in the human genome.

Purpose of the Study:

  • To investigate the influence of CNVs, segmental duplications, and genotyping errors on SNP HWE.
  • To quantify the impact of these factors on HWE testing outcomes.

Main Methods:

  • Bayesian analysis was employed to model the effects of CNVs, segmental duplications, and genotyping errors.
  • The analysis focused on the behavior of SNPs under various conditions.

Main Results:

  • Copy number variation was identified as a primary driver of HWE violation for SNPs with low minor allele frequencies.
  • This effect is pronounced in large sample sizes with low genotyping error rates (0-1%).

Conclusions:

  • The study provides a probabilistic framework to assess SNP location within CNVs or segmental duplications.
  • This is based on observed allele frequency, sample size, and HWE test significance.