GBAin Parkinson’s disease: variant detection and pathogenicity scoring matters

Abstract

AbstractBackgroundGBAvariants are the strongest genetic risk factor for Parkinson’s disease (PD). However, the pathogenicity ofGBAvariants concerning PD is still not fully understood. Additionally, the frequency ofGBAvariants varies widely across populations.ObjectivesTo evaluate Oxford Nanopore sequencing as a strategy, to determine the frequency ofGBAvariants in Norwegian PD patients and controls, and to review the current literature on newly identified variants that add to pathogenicity determination.MethodsWe included 462 Norwegian PD patients and 367 healthy controls. We sequenced the full-lengthGBAgene on the Oxford Nanopore GridION as an 8.9 kb amplicon. Six analysis pipelines were compared using two aligners (NGMLR, Minimap2) and three variant callers (BCFtools, Clair3, Pepper-Margin-Deepvariant). Confirmation ofGBAvariants was performed by Sanger sequencing and the pathogenicity of variants was evaluated.ResultsWe found 95.8% (115/120) true-positiveGBAvariant calls, while 4.2% (5/120) variant calls were false-positive, with the NGMLR/Minimap2-BCFtools pipeline performing best. In total, 13 rareGBAvariants were detected: two were predicted to be (likely) pathogenic and eleven were of uncertain significance. The odds of carrying one of the two most commonGBAvariants, p.L483P or p.N409S, in PD patients were estimated to be 4.11 times the odds of carrying one of these variants in controls (OR=4.11 [1.39, 12.12]).ConclusionsIn conclusion, we have demonstrated that Oxford long-read Nanopore sequencing, along with the NGMLR/Minimap2-BCFtools pipeline is an effective tool to investigateGBAvariants. Further studies on the pathogenicity ofGBAvariants are needed to assess their effect on PD.