Objective
The goal of this study was to refine our understanding of disease risk attributable to common genetic variation in SNCA, a major locus in Parkinson disease, with potential implications for ...clinical trials targeting α‐synuclein. We aimed to dissect the multiple independent association signals, stratify individuals by SNCA‐specific risk profiles, and explore expression quantitative trait loci.
Methods
We analyzed participant‐level data from 12,503 patients and 12,502 controls, optimizing a risk model and assessing SNCA‐specific risk scores and haplotypes as predictors of individual risk. We also explored hypotheses about functional mechanisms and correlated risk variants to gene expression in human brain and protein levels in cerebrospinal fluid.
Results
We report and replicate a novel, third independent association signal at genome‐wide significance level downstream of SNCA (rs2870004, p = 3.0*10−8, odds ratio OR = 0.88, 95% confidence interval CI = 0.84–0.92). SNCA risk score stratification showed a 2‐fold difference in disease susceptibility between top and bottom quintiles (OR = 1.99, 95% CI = 1.78–2.23). Contrary to previous reports, we provide evidence supporting top variant rs356182 as functional in itself and associated with a specific SNCA 5′ untranslated region transcript isoform in frontal cortex.
Interpretation
The SNCA locus harbors a minimum of 3 independent association signals for Parkinson disease. We demonstrate a fine‐grained stratification of α‐synuclein–related genetic burden in individual patients of potential future clinical relevance. Further efforts to pinpoint the functional mechanisms are warranted, including studies of the likely causal top variant rs356182 and its role in regulating levels of specific SNCA mRNA transcript variants. Ann Neurol 2018;83:117–129
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Genome-wide association studies (GWAS) have identified multiple genetic risk signals for Parkinson's disease (PD), however translation into underlying biological mechanisms remains scarce. Genomic ...functional annotations of neurons provide new resources that may be integrated into analyses of GWAS findings. Altered transcription factor binding plays an important role in human diseases. Insight into transcriptional networks involved in PD risk mechanisms may thus improve our understanding of pathogenesis. We analysed overlap between genome-wide association signals in PD and open chromatin in neurons across multiple brain regions, finding a significant enrichment in the superior temporal cortex. The involvement of transcriptional networks was explored in neurons of the superior temporal cortex based on the location of candidate transcription factor motifs identified by two de novo motif discovery methods. Analyses were performed in parallel, both finding that PD risk variants significantly overlap with open chromatin regions harboring motifs of basic Helix-Loop-Helix (bHLH) transcription factors. Our findings show that cortical neurons are likely mediators of genetic risk for PD. The concentration of PD risk variants at sites of open chromatin targeted by members of the bHLH transcription factor family points to an involvement of these transcriptional networks in PD risk mechanisms.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
•Two coding variants in the glucocerebrosidase (GBA) gene were genotyped in Parkinson’s disease (PD) patients and controls.•We find an association between the low-frequency GBA variant E326K and ...PD.•Two independent association signals within the chromosome 1 SYT11-GBA locus observed in previous GWAS of PD were genotyped.•We find that the GBA variant E326K may fully account for the primary association signal observed at the chromosome 1 SYT11-GBA locus.
Coding variants in the GBA gene have been identified as the numerically most important genetic risk factors for Parkinson's disease (PD). In addition, genome-wide association studies (GWAS) have identified associations with PD in the SYT11-GBA region on chromosome 1q22, but the relationship to GBA coding variants have remained unclear. The aim of this study was to sequence the complete GBA gene in a clinical cohort and to investigate whether coding variants within the GBA gene may be driving reported association signals.
We analyzed high-throughput sequencing data of all coding exons of GBA in 366 patients with PD. The identified low-frequency coding variants were genotyped in three Scandinavian case-controls series (786 patients and 713 controls). Previously reported risk variants from two independent association signals within the SYT11-GBA locus on chromosome 1 were also genotyped in the same samples. We performed association analyses and evaluated linkage disequilibrium (LD) between the variants.
We identified six rare mutations (1.6%) and two low-frequency coding variants in GBA. E326K (rs2230288) was significantly more frequent in PD patients compared to controls (OR 1.65, p=0.03). There was no clear association of T369M (rs75548401) with disease (OR 1.43, p=0.24). Genotyping the two GWAS hits rs35749011 and rs114138760 in the same sample set, we replicated the association between rs35749011 and disease status (OR 1.67, p=0.03), while rs114138760 was found to have similar allele frequencies in patients and controls. Analyses revealed that E326K and rs35749011 are in very high LD (r2 0.95).
Our results confirm that the GBA variant E326K is a susceptibility allele for PD. The results suggest that E326K may fully account for the primary association signal observed at chromosome 1q22 in previous GWAS of PD.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Parkinson's disease (PD) is a disorder with highly variable clinical phenotype. The identification of genetic variants modifying age at onset and other traits is of great interest because it may ...provide insight into disease mechanisms and potential therapeutic targets. A variant in the DNM3 gene (rs2421947) has been reported as a genetic modifier of age at onset in LRRK2-associated PD. To test the possible effect of genetic variation in DNM3 on age at onset in idiopathic PD, we examined rs2421947 in a total of 5918 patients with PD from seven data sets. We also assessed the potential effect of all common variants in the DNM3 locus. There was no significant association between rs2421947 and age at onset in any of the individual studies. Meta-analysis of the seven studies was nonsignificant and the between-study heterogeneity was minimal. No other common variants within the DNM3 locus affected age at onset. In conclusion, we find no evidence of an association between DNM3 variants and age at onset in idiopathic PD.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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