A systematic screening to identify de novo mutations causing sporadic early-onset Parkinson's disease

Human Molecular Genetics, 2015, Vol. 24, No. 23 6711–6720 doi: 10.1093/hmg/ddv376 Advance Access Publication Date: 11 September 2015 Original Article ORIGINAL ARTICLE A systematic screening to identify de novo mutations causing sporadic early-onset Parkinson’s disease 1 Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, UK, 2Department of Neurology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20246, Germany, 3Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, University College London, London WC1N 3BG, UK, 4Department of Neurology, University Hospital Schleswig Holstein, Campus Kiel 24105, Germany, 5 German Center for Neurodegenerative Diseases, Tübingen, Germany, 6Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen 72076, Germany, 7INSERM U M27, Pitié-Salpê trière Hospital, Brain and Spinal Cord Institute (ICM), Paris 75013, France, 8Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK and 9Laboratory of Neurogenetics, National Institutes on Aging, National Institutes of Health, Bethesda, MD 20892, USA *To whom correspondence should be addressed at: Department of Molecular Neuroscience, Institute of Neurology, University College of London, 8-11 Queen Square, DRC, Box 16, London, WC1N 3AR, UK. Tel: +44 020 3448 3666; Email: Abstract Despite the many advances in our understanding of the genetic basis of Mendelian forms of Parkinson’s disease (PD), a large number of early-onset cases still remain to be explained. Many of these cases, present with a form of disease that is identical to that underlined by genetic causes, but do not have mutations in any of the currently known disease-causing genes. Here, we hypothesized that de novo mutations may account for a proportion of these early-onset, sporadic cases. We performed exome sequencing in full parent–child trios where the proband presents with typical PD to unequivocally identify de novo mutations. This approach allows us to test all genes in the genome in an unbiased manner. We have identified and confirmed 20 coding de novo mutations in 21 trios. We have used publicly available population genetic data to compare variant frequencies and our independent in-house dataset of exome sequencing in PD (with over 1200 cases) to identify additional variants in the same genes. Of the genes identified to carry de novo mutations, PTEN, VAPB and ASNA1 are supported by various sources of data to be involved in PD. We show that these genes are reported to be within a protein–protein interaction network with PD genes and that they contain additional rare, case-specific, mutations in our independent cohort of PD cases. Our results support the involvement of these three genes in PD and suggest that testing for de novo mutations in sporadic disease may aid in the identification of novel disease-causing genes. † The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. A complete list of the IPDGC members is listed in the Supplementary Material. Received: August 4, 2015. Revised and Accepted: September 8, 2015 ‡ © The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 6711 Celia Kun-Rodrigues1,†, Christos Ganos2,3,†, Rita Guerreiro1, Susanne A. Schneider4, Claudia Schulte5,6, Suzanne Lesage7, Lee Darwent1, Peter Holmans8, Andrew Singleton9, International Parkinson’s Disease Genomics Consortium (IPDGC)‡, Kailash Bhatia3 and Jose Bras1, * 6712 | Human Molecular Genetics, 2015, Vol. 24, No. 23 Introduction Results From the systematic analysis of the whole-exome sequencing data, 24 genes showed de novo mutations in the trios. We validated 20 of the 24 variants with Sanger sequencing methods (Table 1) comparing sequences from both parents with the proband (examples for the three genes of interest in Fig. 1). The four variants not validated were false positives from the exome sequencing. We have identified, on average, one de novo coding event per trio, which is in line with what would be expected for the human population (22) (Table 2). Only four of the variants identified have been previously described in population databases: the variants in EPPK1, COL12A1, PEPD and SLC52A1 have Although the detailed aetiology of Parkinson’s disease (PD) remains largely unknown, data suggest the disease may be triggered through different mechanisms: protein inclusions accumulation, diminished mitochondrial activity, proteasomal/ lysosomal dysfunction and impaired dopamine production (1). An increasing number of publications show a strong genetic component for PD. Studies in familial forms of PD have allowed for the identification of disease-causing mutations in several genes, causing either dominant or recessive forms of disease inheritance. Genome-wide association studies (GWAS) have also significantly contributed to a more comprehensive knowledge of the risk loci involved in PD (2). Despite these results, there is still a large number of sporadic, early-onset cases that carry no mutation in the known PD genes. These individuals have, in many cases, a form of disease that is indistinguishable from genetically linked disease. De novo mutations have been commonly studied in neurodevelopmental disorders such as autism (3–5) and schizophrenia (6,7) with only a few examples in neurodegenerative diseases. De novo mutations in the ATP1A3 gene have been found as the cause for rapid-onset dystonia parkinsonism (8), while Rosewich et al. (9) reported de novo mutations in this gene in alternating hemiplegia of childhood. De Carvalho Aguiar and colleagues (10) showed one de novo mutation in TOR1A in a primary torsion dystonia case. Two cases of static encephalopathy of childhood with neurodegeneration in adulthood showed mutations in WDR45 (11). In all these cases, patients start to show symptoms during childhood or adolescence. Recently studies have suggested the involvement of de novo mutations in other neurodegenerative diseases, such as in early-onset Alzheimer’s disease (AD) (12,13) and amyotrophic lateral sclerosis (ALS) (14–17). There is also preliminary evidence supporting the role of de novo mutations in PD: Puschmann and colleagues (18) reported on a presumably de novo A53T mutation in SNCA and nonmendelian multiplications of the gene (19,20) have also been shown. More recently, Hansen and collaborators (21) described two mutations in the SLC6A3 gene (encoding the dopamine transporter, DAT1), one of which was presumed to be de novo (...truncated)