Functional annotation of rare structural variation in the human brain
Lide Han, Xuefang Zhao, Mary Lauren Benton, Thanneer M. Perumal, Ryan L. Collins, Gabriel E. Hoffman, Jessica Johnson, Laura Sloofman, Harold Z. Wang, Matthew R. Stone, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alexander W. Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso‐Gil, Kiran Girdhar, Attila Gulyás-Kovács, Raquel E. Gur, Chang-Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura M. Huckins, Rivky Jacobov, Yan Jiang, Jessica Johnson, Bibi Kassim, Yungil Kim, Lambertus Klei, Robin S. S. Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Lingyun Song, Eli Stahl, Patrick Sullivan, Roberto Visintainer, Jiebiao Wang, Ying‐Chih Wang, Jennifer Wiseman, Eva Xia, Wen Zhang, Elizabeth Zharovsky, Kristen Brennand, Harrison Brand, Solveig K. Sieberts, Stefano Marenco, Mette A. Peters, Barbara K. Lipska, Panos Roussos, John A. Capra, Michael E. Talkowski, Douglas M. Ruderfer
Abstract
Structural variants (SVs) contribute to many disorders, yet, functionally annotating them remains a major challenge. Here, we integrate SVs with RNA-sequencing from human post-mortem brains to quantify their dosage and regulatory effects. We show that genic and regulatory SVs exist at significantly lower frequencies than intergenic SVs. Functional impact of copy number variants (CNVs) stems from both the proportion of genic and regulatory content altered and loss-of-function intolerance of the gene. We train a linear model to predict expression effects of rare CNVs and use it to annotate regulatory disruption of CNVs from 14,891 independent genome-sequenced individuals. Pathogenic deletions implicated in neurodevelopmental disorders show significantly more extreme regulatory disruption scores and if rank ordered would be prioritized higher than using frequency or length alone. This work shows the deleteriousness of regulatory SVs, particularly those altering CTCF sites and provides a simple approach for functionally annotating the regulatory consequences of CNVs.