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Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era

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Pseudogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1167))

Abstract

In this chapter, we focus on issues related to the application of next-generation sequencing (NGS) strategies for the analysis of genes with pseudogenes in a clinical setting. Hereby, target enrichment and mapping strategies are crucial factors to avoid “contaminating” pseudogene sequences, which are characterized by higher mutation rates than their functional parental genes. For the target enrichment strategies, we describe advantages and disadvantages of PCR- and capture-based enrichment methodologies. For the mapping strategies, we discuss crucial parameters that need to be considered to accurately distinguish sequences of functional genes from pseudogenic sequences. Finally, we discuss some concrete examples of genes with known pseudogenes and associated with Mendelian disorders that were analyzed by NGS on various platforms and starting from different library preparations.

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Authors and Affiliations

  1. Center for Medical Genetics, Ghent University Hospital, Gent, Belgium

    Kathleen B. M. Claes Ph.D.

  2. Center for Medical Genetics, Ghent University Hospital, Medical Research Building, De Pintelaan 185, 9000, Gent, Belgium

    Kim De Leeneer

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  1. Kathleen B. M. Claes Ph.D.
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  2. Kim De Leeneer
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Correspondence to Kathleen B. M. Claes Ph.D. .

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  1. Istituto Toscano Tumori, Pisa, Italy

    Laura Poliseno

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Claes, K.B.M., De Leeneer, K. (2014). Dealing with Pseudogenes in Molecular Diagnostics in the Next-Generation Sequencing Era. In: Poliseno, L. (eds) Pseudogenes. Methods in Molecular Biology, vol 1167. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0835-6_21

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  • DOI: https://doi.org/10.1007/978-1-4939-0835-6_21

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  • Publisher Name: Humana Press, New York, NY

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