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Detection of Genetic Rearrangements in the Regulators of Complement Activation RCA Cluster by High-Throughput Sequencing and MLPA

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The Complement System

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2227))

Abstract

The regulators of complement activation (RCA) gene cluster in 1q31-1q32 includes most of the genes encoding complement regulatory proteins. Genetic variability in the RCA gene cluster frequently involve copy number variations (CNVs), a type of chromosome structural variation causing alterations in the number of copies of specific regions of DNA. CNVs in the RCA gene cluster often relate with gene rearrangements that result in the generation of novel genes, carrying internal duplications or deletions, and hybrid genes, resulting from the fusion or exchange of genetic material between two different genes. These gene rearrangements are strongly associated with a number of rare and common diseases characterized by complement dysregulation. Identification of CNVs in the RCA gene cluster is critical in the molecular diagnostic of these diseases. It can be done by bioinformatics analysis of DNA sequence data generated by massive parallel sequencing techniques (NGS, next generation sequencing) but often requires special techniques like multiplex ligation-dependent probe amplification (MLPA). This is because the currently used massive parallel DNA sequencing approaches do not easily identify all the structural variations in the RCA gene cluster. We will describe here how to use the MLPA assays and two computational tools to analyze NGS data, NextGENe and ONCOCNV, to detect CNVs and gene rearrangements in the RCA gene cluster.

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Acknowledgments

SRdeC is supported by the Spanish “Ministerio de Economía y Competitividad-FEDER” (SAF2015-66287R, PID2019-104912RB-I00, RTC-2016-4635-1 and the Autonomous Region of Madrid (S2017/BMD-3673). Secugen has received a soft loan from the Spanish “Ministerio de Economía y Competitividad” Retos Program RTC-2016-4635-1 cofinanced by FEDER funds.

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Authors and Affiliations

  1. Centro de Investigaciones Biológicas and Ciber de Enfermedades Raras, Madrid, Spain

    Jesús García-Fernández & Santiago Rodríguez de Córdoba

  2. Secugen S.L., Madrid, Spain

    Susana Vilches-Arroyo, Leticia Olavarrieta & Julián Pérez-Pérez

Authors
  1. Jesús García-Fernández
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  2. Susana Vilches-Arroyo
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  3. Leticia Olavarrieta
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  4. Julián Pérez-Pérez
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  5. Santiago Rodríguez de Córdoba
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Corresponding author

Correspondence to Santiago Rodríguez de Córdoba .

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Editors and Affiliations

  1. Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Paris, France

    Lubka T. Roumenina

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García-Fernández, J., Vilches-Arroyo, S., Olavarrieta, L., Pérez-Pérez, J., Rodríguez de Córdoba, S. (2021). Detection of Genetic Rearrangements in the Regulators of Complement Activation RCA Cluster by High-Throughput Sequencing and MLPA. In: Roumenina, L.T. (eds) The Complement System. Methods in Molecular Biology, vol 2227. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1016-9_16

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  • DOI: https://doi.org/10.1007/978-1-0716-1016-9_16

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  • Publisher Name: Humana, New York, NY

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