Objective: Assess the entire set of variants in the glucocerebrosidase (GBA) gene by long-read sequencing in the Luxembourg Parkinson’s study (LuxPARK) and characterize genotype-phenotype correlations of Parkinson’s disease (PD) patients carrying different types of GBA mutations (severe, mild, and low-risk mutations).

Background: Heterozygous mutations in the GBA gene are an important risk factor for PD. Because of the pseudogene GBAP1 that shares 96% sequence homology with the coding region of the GBA, accurate variant calling in the GBA gene by array-based or short-read sequencing methods remains a major challenge in understanding the genetic landscape of GBA-related PD.

Method: We use a new sequencing technology targeting the full GBA gene, called real-time single-molecule sequencing, developed by Pacific BioScience (PacBio). PacBio HiFi reads offer long read length, high accuracy and solve the issues arising from the presence of the pseudogene. We sequenced 792 cases and 805 healthy controls enrolled in LuxPARK. All identified variants were validated by Sanger sequencing.

Results: 10.8% of PD cases carried GBA mutations, compared with 4.5% of controls (P-values = 0.0001, odds ratio [OR] 2.5, 95% CI 1.6 to 3.9). We compared the rate of true positives detection, for the same samples genotyped by the NeuroChip array and the GBA-targeted PacBio sequencing method. We observed that more samples with GBA variants were detected by GBA-targeted PacBio sequencing. The Sanger validation confirmed that 100% of variants detected by GBA-targeted PacBio are true positives in comparison with NeuroChip which only has a sensitivity of 51.5%. The low-risk mutation, p.E365K, was the most common mutation among Luxembourgish PD patients. In addition, six novel variants and one previously described variant of unknown significance were identified. Further, we found a higher prevalence of psychosis, REM sleep behavior disorder, depression, and apathy among patients with GBA variants.

Conclusion: For the first time, we showed the utility of GBA-targeted PacBio sequencing as a high specificity method to identify known and novel GBA variants. These findings offer important access for stratified therapies in the future. Furthermore, our study describes the full landscape of GBA-related PD in the current Luxembourg population showing the high prevalence of GBA variants as the major genetic risk in PD.

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MDS Abstracts - https://www.mdsabstracts.org/abstract/identification-and-clinical-characterization-of-gba-variants-in-the-luxembourg-parkinsons-study/