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Introduction
There is increasing interest to try to identify uncommon and rare genetic variants that increase the risk of common diseases and that are difficult to identify using traditional genome-wide association studies (GWAS) approaches. 1 Rare variants which are not mapped by GWAS can be identified by using next generation sequencing, that is, exome sequencing in large families with multiple affected individuals. 2 Exome sequencing is now routinely used to identify rare mutations in familial forms of disease in diverse phenotypes. 2
Two recent studies independently performed exome sequencing in large families of Caucasian descent, and identified a mutation in the vacuolar protein sorting 35 (VPS35) gene as a possible cause for an autosomal dominant form of Parkinson disease (PD). 3 4 In addition, several non-synonymous base exchanges were identified, but their involvement in disease pathogenesis remains inconclusive. Furthermore, recently published studies provided conflicting results regarding the role of VPS35 in PD. 5-8 Here, we performed a large multi-centre study to determine the frequency and pathogenicity of VPS35 variants in PD in diverse populations worldwide.
Methods
Consortium
Investigators from the Genetic Epidemiology of Parkinson disease Consortium were invited to participate in this study. A total of 23 sites representing 19 countries from four continents agreed to contribute DNA samples and clinical data for a total of 15 383 individuals (8870 cases and 6513 controls). Control individuals underwent neurological examination and were excluded from the study whenever there was clinical evidence for any extrapyramidal disorder.
Genotyping
We selected seven non-synonymous variants exactly as they were proposed. 3 In addition, we selected tag single nucleotide polymorphisms (SNPs) (HapMap Rel 28 phase II+III, Aug10, National Centre for Biotechnology Information. B36 dbSNP b126; http://www.hapmap.org ) that cover the common genetic variants in the VPS35 gene using an r 2 threshold of 0.8-1.0 to select tag SNPs for VPS35 gene. Using this strategy, we were able to capture 23 SNPs in a 40 kb region, including VPS35 ('chr16:46 693 589-46 723 144 based on hg 19'). Therefore, in total, 10 SNPs located in the VPS35 were genotyped (including seven rare non-synonymous and three common variants). Genotyping was performed by a central genotyping core. Genotyping was performed using a matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry on a MassArray system (Sequenom,...