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Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for Tourette Syndrome

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Rare Copy Number Variants in NRXN1 and CNTN6 Increase Risk for Tourette Syndrome bioRxiv preprint doi: https://doi.org/10.1101/062471; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Rare copy number variants in NRXN1 and CNTN6 increase risk for Tourette syndrome Alden Y. Huang1-3, Dongmei Yu4,5, Lea K. Davis6,7, Jae-Hoon Sul1,2, Fotis Tsetsos8, Vasily Ramensky1,2, Ivette Zelaya1-3, Eliana Marisa Ramos1,2, Lisa Osiecki4, Jason A. Chen1-3, Lauren M. McGrath9, Cornelia Illmann4, Paul Sandor10, Cathy L. Barr11, Marco Grados12, Harvey S. Singer12, Markus M. Noethen13,14, Johannes Hebebrand15, Robert A. King16, Yves Dion17, Guy Rouleau18, Cathy L. Budman19, Christel Depienne20,21, Yulia Worbe21, Andreas Hartmann21, Kirsten R. Muller-Vahl22, Manfred Stuhrmann23, Harald Aschauer24,25, Mara Stamenkovic24, Monika Schloegelhofer25, Anastasios Konstantinidis24,26, Gholson J. Lyon27, William M. McMahon28, Csaba Barta29, Zsanett Tarnok30, Peter Nagy30, James R. Batterson31, Renata Rizzo32, Danielle C. Cath33, Tomasz Wolanczyk34, Cheston Berlin35, Irene A. Malaty36, Michael S. Okun36, Douglas W. Woods37,38, Elliott Rees39, Carlos N. Pato40, Michele T. Pato40, James A Knowles41, Danielle Posthuma42, David L. Pauls4, Nancy J. Cox6,7, Benjamin M. Neale4,5,43, Nelson B. Freimer1,2, Peristera Paschou8,47, Carol A. Mathews44,47, Jeremiah M. Scharf4,5,45,46,47, & Giovanni Coppola1,2,47, on behalf of the Tourette Syndrome Association International Consortium for Genomics (TSAICG) and the Gilles de la Tourette Syndrome GWAS Replication Initiative (GGRI) Correspondence should be addressed to J.M.S. ([email protected]) or G.C. ([email protected]). 1Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA 2Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, California, USA 3Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, USA 4Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetics Research, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA 5Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA 6Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA 7Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA bioRxiv preprint doi: https://doi.org/10.1101/062471; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 8Department of Molecular Biology and Genetics, Democritus University of Thrace, Greece 9Department of Psychology, University of Denver, Denver, Colorado, USA 10Toronto Western Hospital, University Health Network and Youthdale Treatment Centres, Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada 11Krembil Research Institute, Toronto Western Hospital, University Health Network, Department of Psychiatry, University of Toronto, Toronto, Canada 12Johns Hopkins University School of Medicine, Baltimore, Maryland, USA 13Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany 14Institute of Human Genetics, University of Bonn, Bonn, Germany 15Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen 16Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA 17University of Montréal, Montreal, Canada 18Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada 19Hofstra Northwell School of Medicine, Hempstead, New York, USA 20Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, 67400 Illkirch, France 21Brain and Spine Institute, UPMC/INSERM UMR_S1127, Paris, France 22Clinic of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Germany 23Institute of Human Genetics, Medical School, Hannover, Germany 24Medical University Vienna, Department of Psychiatry and Psychotherapy, Vienna, Austria 25Biopsychosocial Corporation, Vienna, Austria 26Center for Mental Health Muldenstrasse, BBRZMed, Linz, Austria 27Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA 28Department of Psychiatry, University of Utah, Utah, USA 29Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary bioRxiv preprint doi: https://doi.org/10.1101/062471; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 30Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary 31Children’s Mercy Kansas City, Kansas City, Kansas, USA 32Dipartimento di Medicina Clinica e Sperimentale, Università di Catania, Catania, Italy 33Utrecht University, Department of Clinical Psychology and Altrecht Academic Anxiety Center, Utrecht, the Netherlands 34Department of Child Psychiatry, Medical University of Warsaw, Poland 35Penn State University College of Medicine, Hershey, Pennsylvania, USA 36Department of Neurology and Center for Movement Disorders and Neurorestoration, University of Florida, Gainesville, Florida, USA 37Marquette University, Milwaukee, Wisconsin, USA 38University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA 39Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, Wales, United Kingdom 40SUNY Downstate Medical Center, Brooklyn, New York, USA 41Department of Psychiatry & Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California, USA 42Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, the Netherlands 43Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA 44Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, Florida, USA 45Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA 46Department of Neurology, Massachusetts General Hospital, Boston, MA, USA 47These authors jointly directed this work. bioRxiv preprint doi: https://doi.org/10.1101/062471; this version posted July 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Tourette syndrome (TS) is highly heritable, although identification of its underlying genetic cause(s) has remained elusive. We examined a European ancestry sample composed of 2,435 TS cases and 4,100 controls for copy-number variants (CNVs) using SNP microarrays and identified two genome-wide significant loci that confer a substantial increase in risk for TS (NRXN1, OR=20.3, 95%CI [2.6-156.2], p=6.0 × 10-6; CNTN6, OR=10.1, 95% CI [2.3-45.4], p=3.7 × 10-5). Approximately 1% of TS cases carried one of these CNVs, indicating that rare structural variation contributes significantly to the genetic architecture of TS. Tourette syndrome (TS) is a complex developmental neuropsychiatric disorder of childhood onset characterized by multiple motor and vocal tics, with an estimated population prevalence of 0.3-0.9%1. Twin and family-based studies of TS have repeatedly demonstrated that it is highly heritable (e.g., h2 of 0.77 in a recent analysis of the Swedish National Patient Register2), while analysis of genome-wide SNP data suggests that TS risk is highly polygenic and distributed across both common and rare variation3. To date, the TS samples with available genome-wide genotyping have been inadequately sized for common variant association studies of a complex trait. To further characterize the genetic influences on TS, we assessed the impact of rare CNVs on disease risk, as it has been shown repeatedly that such variants contribute to susceptibility for other heritable neurodevelopmental disorders, including intellectual disability (ID), autism spectrum disorder (ASD) and schizophrenia (SCZ)4. We genotyped TS cases and ancestry-matched controls on the same genome-wide SNP array platform (Illumina OmniExpress, Supplementary Table 1a). Following standard quality control (QC) steps (Supplementary Table 1b, Supplementary Figure 1, and Supplementary Text), including genotype-based determination of ancestry (Supplementary Figure 2), we analyzed CNVs in a SNP dataset of 6,535 unrelated European ancestry samples, including 2,435 individuals diagnosed with TS (by DSM-IV-TR criteria) and 4,100 healthy controls. To improve specificity, we generated CNV calls with two widely-used Hidden Markov Model (HMM)-based segmentation algorithms, PennCNV5 and QuantiSNP6 and retained the intersection of CNVs detected by both methods. We also conducted an additional QC step to test
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