@article{van Bree01042022,
author = {van Bree, Elisabeth J. and Guimarães, Rita L.F.P. and Lundberg, Mischa and Blujdea, 
Elena R. and Rosenkrantz, Jimi L. and White, Fred T.G. and Poppinga, Josse and Ferrer-Raventós, 
Paula and Schneider, Anne-Fleur E. and Clayton, Isabella and Haussler, David and Reinders, Marcel J.T. and Holstege, Henne and Ewing, Adam D. and Moses, Colette and Jacobs, Frank M.J.}, 
title = {A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci},
volume = {32}, 
number = {4}, 
pages = {656-670}, 
year = {2022}, 
doi = {10.1101/gr.275515.121}, 
abstract ={Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease–associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease–associated risk loci and in the BCKDK Parkinson's disease–associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.}, 
URL = {http://genome.cshlp.org/content/32/4/656.abstract}, 
eprint = {http://genome.cshlp.org/content/32/4/656.full.pdf+html}, 
journal = {Genome Research} 
}