TY - JOUR T1 - A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population JF - bioRxiv DO - 10.1101/036897 SP - 036897 AU - Jayne Y. Hehir-Kwa AU - Tobias Marschall AU - Wigard P. Kloosterman AU - Laurent C. Francioli AU - Jasmijn A. Baaijens AU - Louis J. Dijkstra AU - Abdel Abdellaoui AU - Vyacheslav Koval AU - Djie Tjwan Thung AU - René Wardenaar AU - Ivo Renkens AU - Bradley P. Coe AU - Patrick Deelen AU - Joep de Ligt AU - Eric-Wubbo Lameijer AU - Freerk van Dijk AU - Fereydoun Hormozdiari AU - The Genome of the Netherlands Consortium AU - André G. Uitterlinden AU - Evan E. Eichler AU - Paul de Bakker AU - Morris A. Swertz AU - Cisca Wijmenga AU - Gert-Jan B. van Ommen AU - P. Eline Slagboom AU - Dorret I. Boomsma AU - Alexander Schöenhuth AU - Kai ye AU - Victor Guryev Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/07/02/036897.abstract N2 - Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation.Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals. Our findings are essential for genome-wide association studies. ER -