Parkinson's Disease Genome-wide Association Research Articles

Parkinson's disease GWAS-linked Park16 variant is associated with a lower risk of cognitive impairment: a 4-year observational study.

Genome wide association study (GWAS)-linked variant (Park16 rs6679073) modulates the risk of Parkinson's disease (PD). We postulate that there may be differences in clinical characteristics between Park16 rs6679073 carriers and non-carriers. In a prospective study, we investigate the clinical characteristics between Park16 rs6679073 A allele carriers and non-carriers over 4 years. A total of 204 PD patients, comprising 158 Park16 rs6679073 A allele carriers and 46 non carriers were recruited. All patients underwent motor, non-motor symptoms and cognitive assessments yearly over 4 years. Park16 rs6679073 carriers were less likely to have mild cognitive impairment (MCI) compared to non-carriers at both baseline (48.1% vs 67.4%, p=0.027) and 4-year follow-up (29.3% vs 58.6%, p=0.007). PD Park16 rs6679073 carriers had significantly lower frequency of MCI in a 4-year follow-up study, suggesting that the variant may have potential neuroprotective effect on cognitive functions.

Characterizing the Genetic Architecture of Parkinson's Disease in Latinos.

This work was undertaken in order to identify Parkinson's disease (PD) risk variants in a Latino cohort, to describe the overlap in the genetic architecture of PD in Latinos compared to European-ancestry subjects, and to increase the diversity in PD genome-wide association (GWAS) data. We genotyped and imputed 1,497 PD cases and controls recruited from nine clinical sites across South America. We performed a GWAS using logistic mixed models; variants with a p-value <1 × 10-5 were tested in a replication cohort of 1,234 self-reported Latino PD cases and 439,522 Latino controls from 23andMe, Inc. We also performed an admixture mapping analysis where local ancestry blocks were tested for association with PD status. One locus, SNCA, achieved genome-wide significance (p-value <5 × 10-8 ); rs356182 achieved genome-wide significance in both the discovery and the replication cohorts (discovery, G allele: 1.58 OR, 95% CI 1.35-1.86, p-value 2.48 × 10-8 ; 23andMe, G allele: 1.26 OR, 95% CI 1.16-1.37, p-value 4.55 × 10-8 ). In our admixture mapping analysis, a locus on chromosome 14, containing the gene STXBP6, achieved significance in a joint test of ancestries and in the Native American single-ancestry test (p-value <5 × 10-5 ). A second locus on chromosome 6, containing the gene RPS6KA2, achieved significance in the African single-ancestry test (p-value <5 × 10-5 ). This study demonstrated the importance of the SNCA locus for the etiology of PD in Latinos. By leveraging the demographic history of our cohort via admixture mapping, we identified two potential PD risk loci that merit further study. ANN NEUROL 2021;90:353-365.

Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.

We conducted a meta analysis of Parkinson’s disease genome-wide association studies using a common set of 7,893,274 variants across 13,708 cases and 95,282 controls. Twenty-six loci were identified as genome-wide significant; these and six additional previously reported loci were then tested in an independent set of 5,353 cases and 5,551 controls. Of the 32 tested SNPs, 24 replicated, including 6 novel loci. Conditional analyses within loci show four loci including GBA, GAK/DGKQ, SNCA, and HLA contain a secondary independent risk variant. In total we identified and replicated 28 independent risk variants for Parkinson disease across 24 loci. While the effect of each individual locus is small, a risk profile analysis revealed a substantial cummulative risk in a comparison highest versus lowest quintiles of genetic risk (OR=3.31, 95% CI: 2.55, 4.30; p-value = 2×10−16). We also show 6 risk loci associated with proximal gene expression or DNA methylation.

Alzheimer's disease and Parkinson's disease genome-wide association study top hits and risk of Parkinson's disease in Korean population

Alzheimer's disease (AD) and Parkinson's disease (PD) have overlapping clinical and pathological features, suggesting a common pathway for these 2 neurodegenerative disorders. Here we investigated the association of both AD and PD GWAS top hits with PD susceptibility. We selected 25 single nucleotide polymorphisms (SNPs) in 9 genes (ABCA7, APOE, BST1, CLU, CR1, LRRK2, PARK16, PICALM, and SNCA) that were genotyped in 1036 PD case patients and 1208 controls. Case patients and controls were all ethnic Koreans. Logistic regression analysis was performed to calculate age- and sex-adjusted odds ratios. None of the AD-susceptibility loci (ABCA7, APOE, CLU, CR1, and PICALM) showed statistically significant association with PD susceptibility. In contrast, we replicated associations of SNCA, LRRK2, BST1, and PARK16 with PD susceptibility in Koreans. Of those, the SNCA SNP rs11931074 showed the most significant association with PD susceptibility (adjusted odds ratio = 1.48; 95% confidence interval = 1.31–1.67; p = 2.20E-10). In a logistic regression analysis with SNPs coded under an additive model, there was no significant genetic interaction between the LRRK2 and the PARK16 locus gene RAB7L1 in PD risk. Our results confirm the associations of SNCA, LRRK2, BST1, and PARK16 with PD susceptibility and fail to show significant associations of AD genome-wide association study (GWAS) top hits with PD susceptibility in a Korean population.

Is Parkinson disease associated with lysosomal integral membrane protein type-2?: Challenges in interpreting association data

Several genetic risk factors have been identified for Parkinson disease (PD), including mutations in glucocerebrosidase (GBA1). Recently, two single nucleotide polymorphisms (SNPs) described as SCARB2 SNPs were reported to be associated with PD. SCARB2 is an attractive candidate gene for PD as it encodes for lysosomal integral membrane protein type 2 (LIMP-2), a protein involved in transporting glucocerebrosidase from the ER to the lysosome. The first SNP, rs6812193, located 64kb upstream of SCARB2, was identified in a Parkinson disease Genome Wide Association study of Americans with European ancestry (p=7.6×10−10, OR=0.84), but was not replicated in a study in the Han Chinese. The second SNP, rs6825004, located within intron 2 of SCARB2 was reported in an association study of Parkinson disease in Greece (p=0.02, OR=0.68). We explored whether the two SNPs impact SCARB2 expression or LIMP-2 protein levels, testing fifteen control samples. First, the genotypes for each subject were determined for both SNPs using a Taqman assay. Then, RNA and protein were extracted from the corresponding cell pellets. Neither the relative RNA expression by real-time PCR, nor LIMP-2 levels on Western blots correlated with SNP genotype. Thus, these two reported SNPs may not be related to SCARB2 and demonstrate the challenges in interpreting some association studies. While LIMP-2 could still play a role in PD pathogenesis, this study does not provide evidence that the SNPs identified are in fact related to LIMP-2.

Genome-wide association study heterogeneous cohort homogenization via subject weight knock-down.

Population structure can be a source of both false-positive and false-negative findings in a genome-wide association study. This article proposes an approach that helps to reduce the false-positives. It consists of homogenizing the diseased/healthy phenotype ratio across the cohort, by decreasing the statistical weight of selected individuals. After homogenization, the cohort is statistically handled as if originating from a single well-mixed population. The method was applied to homogenize a Parkinson's disease genome-wide association study cohort.

Meta‐analysis of Parkinson's Disease: Identification of a novel locus, RIT2

Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR]=1.37; p=9.3×10(-21)), MAPT (rs242559; C: OR=0.78; p=1.5×10(-10)), GAK/DGKQ (rs11248051; T: OR=1.35; p=8.2×10(-9)/rs11248060; T: OR=1.35; p=2.0×10(-9)), and the human leukocyte antigen (HLA) region (rs3129882; A: OR=0.83; p=1.2×10(-8)), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR=1.71; p=5×10(-8) Combined Sample) (N370; OR=3.08; p=7×10(-5) Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p=5×10(-5) Discovery Sample; p=1.52×10(-7) Replication sample; p=2×10(-10) Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.

Evidence for a common pathway linking neurodegenerative diseases

In the largest Parkinson's disease genome-wide association studies to date, common variants in three familiar genes—SNCA, MAPT and LRRK2—and two new loci are found to increase disease susceptibility. The studies suggest genetic heterogeneity for Parkinson's disease risk in different human populations and lend support to the idea of a common pathway for Parkinson's and Alzheimer's diseases.