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Copy Number Variation

  • Aurélien Macé
  • Zoltán Kutalik
  • Armand ValsesiaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1793)

Abstract

Differences between genomes can be due to single nucleotide variants (SNPs), translocations, inversions and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 250 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease or phenotypic traits.

While the link between SNPs and disease susceptibility has been well studied, to date there are still very few published CNV genome-wide association studies; probably owing to the fact that CNV analysis remains a slightly more complex task than SNP analysis (both in term of bioinformatics workflow and uncertainty in the CNV calling leading to high false positive rates and unknown false negative rates). This chapter aims at explaining computational methods for the analysis of CNVs, ranging from study design, data processing and quality control, up to genome-wide association study with clinical traits.

Key words

Copy number variation DNA Duplication Deletion Structural variation Genome-wide association studies Human genetics Human disease 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Aurélien Macé
    • 1
    • 2
    • 3
  • Zoltán Kutalik
    • 1
    • 3
  • Armand Valsesia
    • 4
    Email author
  1. 1.Institute of Social and Preventive MedicineUniversity Hospital of LausanneLausanneSwitzerland
  2. 2.Department of Computational BiologyUniversity of LausanneLausanneSwitzerland
  3. 3.Swiss Institute of BioinformaticsLausanneSwitzerland
  4. 4.Nestlé Institute of Health SciencesLausanneSwitzerland

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