Back to Search Start Over

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

Authors :
Claes KBM
Rosseel T
De Leeneer K
Source :
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2324, pp. 363-381.
Publication Year :
2021

Abstract

Presence of pseudogenes is a dreadful issue in next generation sequencing (NGS), because their contamination can interfere with the detection of variants in the genuine gene and generate false positive and false negative variants.In this chapter we focus on issues related to the application of NGS strategies for analysis of genes with pseudogenes in a clinical setting. The degree to which a pseudogene impacts the ability to accurately detect and map variants in its parent gene depends on the degree of similarity (homology) with the parent gene itself. Hereby, target enrichment and mapping strategies are crucial factors to avoid "contaminating" pseudogene sequences. For target enrichment, we describe advantages and disadvantages of PCR- and capture-based strategies. For 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 examples of genes associated with Mendelian disorders, for which interesting NGS approaches are described to avoid interference with pseudogene sequences.

Details

Language :
English
ISSN :
1940-6029
Volume :
2324
Database :
MEDLINE
Journal :
Methods in molecular biology (Clifton, N.J.)
Publication Type :
Academic Journal
Accession number :
34165726
Full Text :
https://doi.org/10.1007/978-1-0716-1503-4_22