Genomic Structural Variants pp 311-328

Part of the Methods in Molecular Biology book series (MIMB, volume 838)

Targeted Screening and Validation of Copy Number Variations

  • Shana Ceulemans
  • Karlijn van der Ven
  • Jurgen Del-Favero
Protocol

Abstract

The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.

Key words

Copy number variation CNV analysis CNV validation Targeted screening 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Shana Ceulemans
    • 1
    • 2
  • Karlijn van der Ven
    • 1
    • 2
  • Jurgen Del-Favero
    • 3
  1. 1.Applied Molecular Genomics Unit VIB Department of Molecular GeneticsFlandersBelgium
  2. 2.University of Antwerp (UA)AntwerpenBelgium
  3. 3.Applied Molecular Genomics Unit VIB Department of Molecular Genetics, University of Antwerp (UA)AntwerpenBelgium

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