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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%...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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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Related Experiment Video

Updated: Apr 17, 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

Genome-wide copy number profiling using high-density SNP array in chickens.

G Yi¹, L Qu, S Chen

¹National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

Animal Genetics

|February 10, 2015

Summary

This summary is machine-generated.

Copy number variations (CNVs) significantly contribute to chicken genetic diversity and disease susceptibility. This study identified 231 CNV regions in chickens, revealing their role in immune responses and providing insights into chicken genome variation.

Keywords:

600 K SNP chip chicken copy number variation genetic diversity

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Area of Science:

Genomics
Animal Genetics
Molecular Biology

Background:

Phenotypic diversity is driven by genetic variation.
Copy number variation (CNV) is increasingly recognized as a key factor in phenotypic variability and disease susceptibility.
Understanding CNVs in chickens is crucial for trait improvement and disease management.

Purpose of the Study:

To conduct a genome-wide scan for copy number variations (CNVs) in diverse chicken breeds.
To characterize the identified CNVs and their genomic distribution.
To investigate the potential role of CNVs in chicken traits, particularly immune responses.

Main Methods:

Genome-wide CNV scan using high-density Affymetrix 600K SNP arrays in 96 chickens across 12 breeds.
Identification and characterization of autosomal CNV regions (CNVRs).
Validation of novel CNVRs using qPCR assays.

Main Results:

Identified 231 autosomal CNVRs covering 5.41 Mb (0.59% of the autosomal genome).
CNVRs varied in size, with deletions showing lower GC content and enrichment in gene deserts.
102 CNVRs contained 128 chicken genes, predominantly involved in immune responses; 153 CNVRs were novel.
qPCR validated 72.73% of 11 tested novel CNVRs.

Conclusions:

High-density SNP arrays are effective for efficient and accurate CNV detection in chickens.
CNVs, particularly deletions, represent a significant source of genetic variation in the chicken genome.
These findings enhance the understanding of chicken genetic architecture and aid in identifying CNVs linked to important traits.