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BMC genomics2013; 14; 487; doi: 10.1186/1471-2164-14-487

Analysis of copy number variants by three detection algorithms and their association with body size in horses.

Abstract: Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. Results: Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. Conclusions: Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
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Publication Date: 2013-07-18 PubMed ID: 23865711PubMed Central: PMC3720552DOI: 10.1186/1471-2164-14-487Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research article analyzes the impact of copy number variants (CNVs) on the body size of horses by leveraging three separate CNV detection programs. Identified CNVs were observed to affect genes related to sensory perception, signal transduction, and cellular components. Some of the detected CNV regions were also significantly connected to human height.

Objective of the Research

  • The study was primarily centered around performing a comparative evaluation of CNVs in horses using three distinct CNV detection applications: CNVPartition, PennCNV, and QuantiSNP. The main goal was to identify the genomic regions associated with the body size of horses.

Research Methodology

  • The analysis was conducted using the Illumina Equine SNP50 Genotyping Beadchip, a technology specifically designed for studying genetic variations in horses. The subject group was composed of 854 horses.
  • The CNV detection was achieved using three different algorithms. The detected CNVs were then compared to enhance the accuracy of the results and increase specificity.

Results of the Research

  • The comparative analysis yielded 50 CNVs impacting 153 different genes. These genes were primarily involved in sensory perception, signal transduction, and cellular components.
  • A Genome-Wide Association Study (GWAS) was performed to associate the detected CNVs with body size in horses.
  • The analysis revealed highly significant deleted regions on ECA1, ECA8, and ECA9 which have a strong correlation with the body size of horses.
  • Interestingly, it was also found that homologous regions to the detected CNVs on ECA1 and ECA9 have been previously correlated with human height, suggesting a potential genetic overlap in determining the size metrics between species.

Conclusions of the Research

  • The comparative analysis of the CNV detection algorithms proved to be effective in augmenting the detection specificity of CNVs. However, this approach also had certain limitations, influenced by the detection tool used.
  • The study concluded that the GWAS analysis effectively highlighted significant CNVs associated with body size in horses. This revelation paves the way for a better genetic understanding of body size in horses and potentially in other mammals, including humans.

Cite This Article

APA
Metzger J, Philipp U, Lopes MS, da Camara Machado A, Felicetti M, Silvestrelli M, Distl O. (2013). Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics, 14, 487. https://doi.org/10.1186/1471-2164-14-487

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 14
Pages: 487

Researcher Affiliations

Metzger, Julia
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany.
Philipp, Ute
    Lopes, Maria Susana
      da Camara Machado, Artur
        Felicetti, Michela
          Silvestrelli, Maurizio
            Distl, Ottmar

              MeSH Terms

              • Algorithms
              • Animals
              • Body Size / genetics
              • DNA Copy Number Variations / genetics
              • Genomics / methods
              • Horses / genetics
              • Horses / growth & development
              • Humans
              • Oligonucleotide Array Sequence Analysis
              • Polymerase Chain Reaction
              • Species Specificity

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