The LRRK2 p.Gly2019Ser pathogenic variant has reduced penetrance and presents a wide range of age at onset (AAO) in patients with Parkinson’s disease (PD). We aim to elucidate differences in the cumulative incidence of LRRK2 p.Gly2019Ser-related PD (LRRK2-PD) between ancestries and countries. We included N=922 unrelated LRRK2 p.Gly2019Ser variant carriers (affected: N=762, unaffected: N=160) from the Global Parkinson’s Genetics Program (GP2) in addition to cohorts recruited from the Israeli Ashkenazi Jewish and Tunisian Arab-Berber population. The p.Gly2019Ser variant was present in five ancestries: Ashkenazi Jewish (N=534), North African (N=223), European (N=132), Middle Eastern (N=19) and Latino and Indigenous people of the Americas (N=14). In addition to ancestry derived from the genetic data, we assessed the country of origin in our analysis. The Cox proportional-hazards model and Kaplan-Meier analysis were applied to examine differences in cumulative incidence. All analyses were adjusted for biological sex, and the outcome variable was AAO, including affected and unaffected variant carriers with right censoring for affection status, and all analysis were exploratory. The median AAO of LRRK2-PD was five years younger in the North African (HR=1.48, 95% CI: 1.18-1.86, p=7.0×10−4) compared to the European ancestry group. In contrast, the median AAO was five years older in the Ashkenazi Jewish (HR=0.61, 95% CI: 0.50-0.75, p=4.0×10−6) compared to the European ancestry group. Additionally, patients from Israel (HR=1.59, 95% CI: 1.30-1.39, p=4.0×10−6) and Tunisia (HR=2.57, 95% CI: 2.16-3.06, p<2.0×10−16) had a median 5-year and 10-year younger AAO compared to patients from the USA, respectively. Lastly, when focusing only on individuals with an Ashkenazi Jewish background, patients from Israel still had a younger AAO than those from the USA (HR=1.82, 95% CI: 1.48-2.24, p=1.5×10−8). Analogously, assessing only patients from the USA, the Ashkenazi Jewish ancestry group still had an older AAO than the European ancestry group (HR=0.51, 95% CI: 0.39-0.67, p=1.3×10−6).

Genome-wide association studies (GWAS) have been successful in identifying over 100 loci associated with Parkinson’s disease (PD) susceptibility. However, the majority of these studies have focused on European cohorts with few including diverse ancestries. Using genotyped and imputed data from 691 South African PD cases and 826 controls, we conducted a conventional GWAS, two local ancestry GWAS (LA-GWAS) approaches (one using local ancestry as a covariate and the other separating the dosage per ancestry), and an association analysis to identify regions of homozygosity associated with PD status. Furthermore, we replicated these findings using another admixed population, a Latin American cohort (LARGE-PD). The ancestry inference suggested that the South African cohort is admixed from five populations, including African (AFR), European (EUR), Malaysian (MAL), Nama (NAMA), and South Asian (SAS), though with varying accuracy levels. The conventional GWAS successfully identified one locus (rs17098735-T) with genome-wide significance (p-value: 1.23×10-8; beta= 2.286; SE= 0.401). Within the local ancestry window of the top GWAS hit, among individuals carrying the variant, 86.7% had AFR ancestry, 11% NAMA ancestry, and 2.2% MAL ancestry, with no EUR or SAS ancestry observed, highlighting a potential ancestry-specific genetic risk factor. Three lead loci were replicated in the LARGE-PD cohort. LA-GWAS using the Cochran-Armitage trend test identified 35 lead SNPs above suggestive significance after multiple test correction. Tractor-based approaches identified three lead loci when analyzing all five ancestry components jointly, as well as three additional lead loci in the AFR-only component, highlighting ancestry-specific loci that may contribute to genetic risk in diverse populations. For the LA-GWAS, one independent locus was replicated in LARGE-PD. Our findings suggest ancestry specificity in PD risk and underscores the importance of including diverse populations in genetics research. The study contributes towards a global understanding of the genetic etiology underlying PD.

The genetic architecture of Parkinson’s disease (PD) varies considerably across ancestries, yet most genetic studies have focused on individuals of European descent, limiting our insights into the genetic architecture of PD at a global scale. We conducted a large-scale, multi-ancestry investigation of causal and risk variants in PD-related genes. Using genetic datasets from the Global Parkinson’s Genetics Program, we analyzed sequencing and genotyping data from 69,881 individuals, including 41,139 affected and 28,742 unaffected, from eleven different ancestries, including ∼30% of individuals from non-European ancestries. Our findings revealed shared and ancestry-specific patterns in the prevalence and spectrum of PD-associated variants. Overall, ∼2% of affected individuals carried a causative variant, with substantial variations across ancestries ranging from 10% in Middle Eastern and Ashkenazi Jewish ancestries. Including disease-associated GBA1 and LRRK2 risk variants raised the yield to ∼12.5%, largely driven by GBA1, except in East Asians, where LRRK2 risk variants dominated. GBA1 variants were most frequent globally, albeit with substantial differences in frequencies and variant spectra. While GBA1 variants were identified across all ancestries, frequencies ranged from 3·4% in Middle Eastern to 51·7% in African ancestry. Similarly, LRRK2 variants showed ancestry-specific enrichment, with G2019S most frequently seen in Middle Eastern and Ashkenazi Jewish, and risk variants predominating in East Asians. However, clinical trials targeting proteins encoded by these genes are primarily based in Europe and North America.

The Latin American Research Consortium on the Genetics of Parkinson’s Disease (LARGE-PD) is a multicenter collaboration aimed at understanding the genetic architecture of Parkinson’s disease (PD) in this underrepresented population using data from 15 countries across the Americas and the Caribbean. In this study, we conducted the largest genome-wide association studies (GWAS) for PD susceptibility in Latin Americans. We analyzed genotype data from LARGE-PD Phase 1 (n = 1,498) and Phase 2 (n = 4,401) using multiple GWAS approaches: SAIGE, which incorporates a genetic relationship matrix in the model; ATT, which includes global ancestry on the model; TRACTOR, which splits allele dosages by ancestry to detect ancestry-specific risk loci; and admixture mapping. We also assessed linkage disequilibrium (LD) patterns and performed Meta-Regression of Multi-AncEstry Genetic Association (MR-MEGA), integrating data from both LARGE-PD phases and two South Asian GWAS. We identified PD-associated loci on chromosomes 1 and 4. Our results replicated previous findings, including the well-established SNCA variant rs356182-A (OR = 1.517, p = 1.62×10−16). Notably, we identified a locus in ITPKB (rs117185933-A, OR = 1.75, p = 3.8×10−12), which had the highest CADD Phred score (17.92, top ∼3% most deleterious) among all candidate variants, suggesting strong functional relevance. Functional annotation predicted that this variant may create a premature start codon in the 5′ UTR of ITPKB. Although rs117185933-A is in high LD (r2 > 0.8) with a variant previously reported by Kishore et al., our LD analysis and MR-MEGA results indicate that this signal is correlated with ancestry heterogeneity and likely represents an independent PD risk locus and a novel putative causal variant. This variant is most frequent in Peruvians from the 1000 Genomes Project (MAF = 0.20) and more common in admixed American populations in gnomAD (MAF = 0.0835), but nearly absent in non-Finnish Europeans (MAF = 0.0002).

Dystonia and Parkinson’s disease (PD) show clinical and genetic overlap, but the relevance of dystonia gene variants in PD remains unclear. To assess the frequency of dystonia-linked pathogenic variants in PD, we screened sequencing data from 15,738 individuals (7,851 PD, 4,287 atypical parkinsonism, and 3,600 unaffected) from GP2 and AMP-PD for variants in genes linked to isolated dystonia, dystonia-parkinsonism, and myoclonus-dystonia. Pathogenic variants were only identified in PD patients. Forty-five PD individuals (0.57%) carried 26 distinct (likely) pathogenic variants in nine dystonia-linked genes, most frequently in GCH1, followed by VPS16. Though rare, pathogenic variants in dystonia-linked genes are present in clinically and pathologically diagnosed PD. Our results reinforce GCH1 as a PD-relevant gene with clinical implications, while variants identified in other genes are rare and of sometimes uncertain relation to the PD phenotype.

Variants in PGLYRP2, particularly rs892145-T, have been suggested as Parkinson’s disease (PD) risk factors. We analyzed data from 31,334 PD patients and 17,772 controls across diverse ancestries. A significant sex-dependent effect of rs892145-T was observed in African (AFR) ancestry males (OR=0.73, 95%CI: 0.57-0.94, p=0.014). Gene-based analyses identified another variant, rs7251871-A, as significantly associated with PD in AFR males (OR=1.34, 95%CI:1.13-1.59, p=6.65E-04, Bonferroni p=0.0432). No associations were observed in other ancestries. Further studies are needed to understand PGLYRP2’s role in PD.