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Title: Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients
Author: Spataro, Nino
Roca Umbert, Ana
Cervera Carles, Laura
Vallés Valero, Mònica
Anglada Busquets, Roger
Pagonabarraga, Javier
Pascual Sedano, Berta María  
Campolongo Perillo, Antonia
Kulisevsky Bojarski, Jaume  
Casals López, Ferran
Clarimon Echavarria, Jordi
Bosch Fusté, Elena
Keywords: Parkinson's disease
next generation sequencing
structural variants
XHMM software
Issue Date: Jan-2017
Publisher: Movement Disorders
Citation: Spataro, N., Roca-Umbert, A., Cervera-Carles, L., Vallès, M., Anglada, R., Pagonabarraga, J., Pascual Sedano, B.M., Campolongo, A., Kulisevsky, J., Casals, F., Clarimon, J. & Bosch, E. (2017). "Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients". Movement Disorders, 32(1), pp. 165-169. ISSN 0885-3185. doi: 10.1002/mds.26845
Abstract: The analysis of coverage depth in next-generation sequencing data allows the detection of gene dose alterations. We explore the frequency of such structural events in a Spanish cohort of sporadic PD cases. Gene dose alterations were detected with the eXome-Hidden Markov Model (XHMM) software from depth of coverage in resequencing data available for 38 Mendelian and other risk PD loci in 394 individuals (249 cases and 145 controls) and subsequently validated by quantitative PCR. We identified 10 PD patients with exon dosage alterations in PARK2, GBA-GBAP1, and DJ1. Additional functional variants, including 2 novel nonsense mutations (p.Arg1552Ter in LRRK2 and p.Trp90Ter in PINK1), were confirmed by Sanger sequencing. This combined approach disclosed the genetic cause of 12 PD cases. Gene dose alterations related to PD can be correctly identified from targeting resequencing data. This approach substantially improves the detection rate of cases with causal genetic alterations.
Language: English
ISSN: 0885-3185MIAR
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