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Analysis of the retrotransposon SINE-VNTR-Alu (SVA) polymorphisms in the genetics and pathophysiology of complex diseases

Kõks, S., Singleton, L.M., Quinn, J.P., Bubb, V.J. and Pfaff, A.L.ORCID: 0000-0002-2231-9800 (2022) Analysis of the retrotransposon SINE-VNTR-Alu (SVA) polymorphisms in the genetics and pathophysiology of complex diseases. In: Proukakis, C., (ed.) Genomic Structural Variants in Nervous System Disorders. Humana Press, pp. 63-77.

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Transposable elements (TEs) form a large proportion of many eukaryotic genomes and we are beginning to develop an understanding of their function. TEs are a large and diverse family of elements forming part of the repetitive genome or genomic dark matter that has not been addressed in detail in the majority of genetic studies. These repetitive and large elements are impossible to call from SNP-based genotyping data, and this is the main factor limiting research in this field thus far. However, the increasing availability of whole genome sequencing data provides the necessary data structure and quality needed for correct calling of TEs. Here we focus on the calling of variation of the composite element SINE-VNTR-Alu (SVA) which is the youngest TE family present in the human genome. Utilizing high-coverage whole genome sequencing data, we address the presence/absence and size variation of these elements. These data can be combined with whole transcriptome data to provide potential functional importance of SVAs in the regulation of the transcriptome and the pathophysiology of diseases. We recently applied this technology to analyze the effect of SVAs on the longitudinal course of Parkinson’s disease in the Parkinson’s Progression Markers Initiative cohort. This chapter briefly describes the background of transposable elements with the emphasis on SVAs and the available methods to study SVAs in genetic analysis of complex diseases.

Item Type: Book Chapter
Murdoch Affiliation(s): Centre for Molecular Medicine and Innovative Therapeutics
Publisher: Humana Press
Copyright: © 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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