Genetics of Movement Disorders In the Next-Generation Sequencing Era Simone Olgiati The work described in this thesis was performed at the Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands. The studies presented in this thesis were financially supported by: Erasmus MC, The Netherlands; Stichting ParkinsonFonds, The Netherlands; BGI-Shenzen, China; The Netherlands Organization for Scientific Research (NWO, VIDI Grant, project n. 91786395). The production costs of this thesis were entirely supported by: ISBN: 978-94-6299-316-7 Cover: Simone Olgiati Layout: Simone Olgiati Printing: Ridderprint BV, Ridderkerk, The Netherlands Copyright © S. Olgiati, 2016 All rights reserved. No part of this book may be reproduced, stored in a retrieval system or transmitted in any form or by any means, without prior permission of the author. The copyright of the published papers remains with the publisher 2 Genetics of Movement Disorders in the Next-Generation Sequencing Era Genetica van bewegingsstoornissen in het next-generation sequencing tijdperk Thesis to obtain the degree of Doctor from the Erasmus University Rotterdam by command of the rector magnificus Prof.dr. H.A.P. Pols and in accordance with the decision of the Doctorate Board. The public defense shall be held on Tuesday 12 April 2016 at 13:30 hrs by Simone Olgiati born in Busto Arsizio, Italy Doctoral Committee Promotors: Prof.dr. V. Bonifati Prof.dr. R.M.W. Hofstra Other members: Prof.dr. R. Krüger Prof.dr. C.C.W. Klaver Prof.dr. J.C. van Swieten 4 Table of contents List of abbreviations 6 Part I – Introduction and scope of the thesis Chapter 1.1 Introduction 11 Scope of the thesis 31 Part II – Parkinson’s disease Chapter 2.1 DNAJC6 mutations associated with early-onset Parkinson’s disease 41 Chapter 2.2 Early-onset parkinsonism caused by alpha-synuclein gene triplication: 67 clinical and genetic findings in a novel family Chapter 2.3 An exome study of Parkinson’s disease in Sardinia, a Mediterranean 79 genetic isolate Part III – Atypical parkinsonism Chapter 3.1 Mutation in the SYNJ1 gene associated with autosomal recessive, 105 early-onset parkinsonism Chapter 3.2 PARK20 caused by SYNJ1 homozygous Arg258Gln mutation in 127 a new Italian family Chapter 3.3 A new Turkish family with homozygous FBXO7 truncating mutation 141 and juvenile atypical parkinsonism Part IV – Other movement disorders Chapter 4.1 Paroxysmal exercise-induced dystonia within the phenotypic 155 spectrum of ECHS1 deficiency Chapter 4.2 A recurrent mutation in the C19orf12 gene causes MPAN in Turkey 177 Part V – General discussion Chapter 5.1 General discussion 191 Appendix Summary, Samenvatting, Riassunto 204 Curriculum vitae 210 List of publications 211 PhD portfolio 213 Acknowledgments 215 5 List of abbreviations ACMG American College of Medical Genetics and Genomics AD Autosomal dominant AR Autosomal recessive BAC Bacterial artificial chromosome BFMRS Burke-Fahn-Marsden dystonia rating scale bp Base pairs BPAN Beta-propeller protein-associated neurodegeneration CCV Clathrin-coated vesicle Chr Chromosome CME Clathrin-mediated endocytosis CNV Copy number variant Comp Het Compound heterozygous CoPAN CoA synthase protein-associated neurodegeneration DBS Deep brain stimulation DNA Deoxyribonucleic acid dNTP Deoxynucleotide triphosphate ERM Ezrin/radixin/moesin EVS NHLBI Exome Variant Server ExAC Exome Aggregation Consortium FAB Frontal assessment battery FISH Fluorescence in situ hybridization FLAIR Fluid-attenuated inversion recovery GC Guanine-cytosine GoNL Genome of The Netherlands GRCh Genome Reference Consortium human build GWAS Genome-wide association studies Het Heterozygous Hom Homozygous ICC Immunocytochemistry Indels Insertions and deletions KO Knock-out LD Linkage disequilibrium LOD Logarithm of odds MAF Minor allele frequency MLPA Multiplex ligation-dependent probe amplification MMSE Mini-mental state examination MPAN Mitochondrial-membrane protein associated neurodegeneration MP-RAGE Magnetization prepared rapid acquisition gradient-echo MRI Magnetic resonance imaging NBIA Neurodegeneration with brain iron accumulation 6 NGS Next-generation sequencing OR Odds ratio PBS Phosphate-buffered saline PCR Polymerase chain reaction PD Parkinson’s disease PED Paroxysmal exercise-induced dyskinesia PET Positron emission tomography PKD Paroxysmal kinesigenic dyskinesia PxDs Paroxysmal dyskinesias qPCR Real-time quantitative PCR RFU Relative fluorescence unit RNA Ribonucleic acid RR Relative risk SNP Single nucleotide polymorphism SNV Single nucleotide variant SPECT Single photon emission computed tomography STR Short tandem repeat UPDRS Unified Parkinson’s disease rating scale UTR Untranslated region VUS Variant of unknown significance WES Whole-exome sequencing WGS Whole-genome sequencing XD X-linked dominant XR X-linked recessive 7 PART I Introduction and Scope of the Thesis 10 1.1 Introduction and Scope of the Thesis Adapted from: “Genetics of Movement Disorders in the Next-Generation Sequencing Era” S. Olgiati,1 M. Quadri,1 and V. Bonifati.1,# Published in Movement Disorders 2016, doi: 10.1002/mds.26521 # Corresponding author. 1) Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands. Concerning the previously-published material: © 2016 International Parkinson and Movement Disorder Society Reprinted with permission of John Wiley & Sons, Inc. 11 Chapter 1.1 Movement Disorders Movement disorders are defined as neurologic syndromes in which there is either an excess of movements or a paucity of voluntary and automatic movements, unrelated to weakness or spasticity [1]. This group of disorders comprises neurological conditions that are clinically, pathologically, and genetically heterogeneous, but they all present with defective control, planning, or execution of movements. The frequency of these syndromes in the general population is very diverse but, overall, movement disorders are common neurological problems, with the most common conditions being restless legs, essential tremor, and Parkinson’s disease [2-4]. The majority of the movement disorders are associated with dysfunctions of the basal ganglia, a group of gray matter nuclei with a primary function in the control of movements, but having also cognitive, behavioral, and emotional functions. Exceptions to this general concept are disorders of movement due to pathologies of the cerebellum (ataxia, asynergia, and dysmetria). The role of basal ganglia and cerebellum is to orches- trate the adequate control of movements, based on internal and external stimuli. Tradi- tionally, only disorders of the basal ganglia and/or cerebellum with clear consciousness are listed as movement disorders. However, disorders of movement can also arise from pathologies of cerebral cortex, brainstem, and spinal cord (several forms of myoclonus and tremor) [5,6]. Movement disorders can be classified into syndromes with too little movements or syndromes with an excess of movements. The first group, the syndromes with too little movements, are commonly referred to as hypokinesias (decrease amplitude of movements), but the terms bradykinesia (slowness of movements) and akinesia (loss of movements) have also been used to describe this category. The most frequent hypokinetic syndromes are the parkinsonisms. The second group, the syndromes with an excess of movements, are referred to as hyperkinesias (excessive movements), but the term dyskinesia (abnormal movements) has been used interchangeably [6]. Many different neurological conditions are listed in this category, including tremor, dystonia, chorea, myoclonus, and tics. Genetics of Movement Disorders in the Next-Generation Sequencing Era During the past few years, the advent of innovative and extremely powerful methods for sequencing nucleic acids (DNA and RNA) has produced a major boost in our under- standing of the role of genes and genetic variability in biology and pathology, and is offering novel research and clinical opportunities for all fields of medicine, including 12 Introduction and Scope of the Thesis the movement disorders. These new methods, collectively called Next-Generation Sequencing (NGS) technologies, provide a way to rapidly generate an unprecedented amount of DNA or RNA sequences at very low costs. As a consequence, new research 1.1 and diagnostic approaches have been made available for the exploration of the genetic bases of diseases. As a result of these novel approaches, the pace of discovery of novel disease-causing or disease-predisposing genes is accelerating (Table 1). Furthermore, the phenotypic spectra associated with previously-known disease-genes are expanding. For instance, ATP1A3 mutations, initially recognized as the cause of rapid-onset dystonia parkinsonism (DYT12), have been more recently identified also as the cause of alter- nating hemiplegia of childhood, [7-9] and the phenotype of PRRT2 mutations, initially considered to consist of paroxysmal kinesigenic dyskinesias, has been later expanded to also include migraine and epileptic syndromes [10-12]. Last, the NGS technologies provide novel tools for rapid, cheap, and comprehensive genetic testing in the clinical setting. There are great expectations about the opportunities offered by these novel technologies. However, their use in both research and clinical settings comes with certain challenges and limitations that should also be taken into account. Here, we provide an update on the current DNA sequencing technologies, focusing on their possible applications for gene-finding in both research and