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Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinsons disease cohort

Publication

Date: 28th August 2019 | Source: BioRxiv

Authors: Oscar E E Graham, Toni L Pitcher, Yusmiati Liau, Allison Miller, John C Dalrymple-Alford, Tim J Anderson, Martin A Kennedy.

Mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. GBA mutation carriers have an elevated risk of Parkinson's disease (PD) compared with non-carriers and can experience an earlier age of onset and more aggressive disease. GBA analysis is technically challenging due to a related pseudogene and complex structural variations (SVs) that can occur at this locus. We have applied a recently developed nanopore sequencing method to analyze GBA variants in a New Zealand longitudinal cohort of PD, which includes extensive clinical assessment. We examined amplicons encompassing the coding region of GBA (8.9kb) from 229 PD cases using the GridION nanopore-sequencing platform. This revealed 23 mutations in 21 PD cases, which were confirmed via Sanger sequencing. We detected a strong PD risk allele p.N409S (rs76763715) in one case. Modest risk mutations included p.E365K (rs2230288) in 12 cases, and p.T408M (rs75548401) in seven cases, one of whom had p.E365K on the other allele. We also detected the possible risk alleles R78C (rs146774384) in one case, D179H (rs147138516) in one case, which occurred on the same haplotype as an E365K, and one novel pL335= (C>T) mutation that is predicted to impact splicing of GBA transcripts. This work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA mutations, and to assign precise haplotypes. Additionally, through clinical assessment, we provide support for the role of GBA mutations on disease aggression. This work may contribute our understanding of the effects of these mutations on disease presentation or progression, and to the development of more targeted treatments.

Read the full text Detection of GBA mutations Workflow: Detection of GBA mutations using the MinION

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