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Comparing Copy Number Variations and SNPs

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%...

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Single Nucleotide Polymorphisms-SNPs

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 18, 2026

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Variability in interpreting and reporting copy number changes detected by array-based technology in clinical

Karen D Tsuchiya¹, Lisa G Shaffer, Swaroop Aradhya

¹Department of Laboratories, Seattle Children's Hospital, Seattle, Washington, USA. karen.tsuchiya@seattlechildrens.org

Genetics in Medicine : Official Journal of the American College of Medical Genetics

|November 12, 2009

Summary

Clinical laboratories show significant variability in interpreting and reporting copy number changes detected by array comparative genomic hybridization. This inconsistency highlights the need for standardized guidelines to ensure clear communication of genetic findings.

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Area of Science:

Genomic Medicine
Clinical Diagnostics
Molecular Pathology

Background:

Array-based technologies, such as array comparative genomic hybridization (aCGH), are widely used in clinical laboratories for detecting copy number variations (CNVs).
Interpreting the clinical significance of CNVs, especially those without clear phenotypic associations, presents a challenge in routine diagnostics.

Purpose of the Study:

To evaluate the inter-laboratory variability in the interpretation and reporting of copy number changes identified by array-based technologies.
To identify inconsistencies in how clinical laboratories assess the significance of detected genetic variations.

Main Methods:

Thirteen distinct copy number changes, identified via aCGH and lacking established phenotypic correlations, were presented to 11 clinical laboratory directors.
Participants were asked to interpret and report on the clinical significance of these specific genetic findings.

Main Results:

Complete agreement on the interpretation of clinical significance was not achieved for any of the thirteen copy number changes evaluated.
Interpretations varied widely, with some cases being classified as normal while others were deemed abnormal by different laboratories.

Conclusions:

There is a critical need for the development of more specific guidelines for the interpretation and reporting of CNVs detected through array-based methods.
Standardized guidelines are essential for consistent and clear communication of the clinical significance of these genetic findings to healthcare providers.