O E E Graham1, T L Pitcher2, Y Liau3, A L Miller3, J C Dalrymple-Alford4, T J Anderson5, M A Kennedy3. 1. Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand. Electronic address: graos994@student.otago.ac.nz. 2. Department of Medicine, University of Otago, Christchurch, New Zealand; New Zealand Brain Research Institute, Christchurch, New Zealand. 3. Gene Structure and Function Laboratory, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand. 4. New Zealand Brain Research Institute, Christchurch, New Zealand; School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand. 5. Department of Medicine, University of Otago, Christchurch, New Zealand; New Zealand Brain Research Institute, Christchurch, New Zealand; Neurology Department, Christchurch Hospital, Christchurch, New Zealand.
Abstract
INTRODUCTION: Bi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinson's disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD. METHOD: We examined amplicons encompassing the coding region of GBA (8.9 kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation. RESULTS: We detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408 M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C > T or p.(L335 = ), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants. CONCLUSION: This work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.
INTRODUCTION: Bi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinson's disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD. METHOD: We examined amplicons encompassing the coding region of GBA (8.9 kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation. RESULTS: We detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408 M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C > T or p.(L335 = ), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants. CONCLUSION: This work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.
Authors: William Schierding; Sophie Farrow; Tayaza Fadason; Oscar E E Graham; Toni L Pitcher; Sara Qubisi; Alan J Davidson; Jo K Perry; Tim J Anderson; Martin A Kennedy; Antony Cooper; Justin M O'Sullivan Journal: Mov Disord Date: 2020-06-18 Impact factor: 10.338
Authors: Jonas M den Heijer; Valerie C Cullen; Marialuisa Quadri; Arnoud Schmitz; Dana C Hilt; Peter Lansbury; Henk W Berendse; Wilma D J van de Berg; Rob M A de Bie; Jeffrey M Boertien; Agnita J W Boon; M Fiorella Contarino; Jacobus J van Hilten; Jorrit I Hoff; Tom van Mierlo; Alex G Munts; Anne A van der Plas; Mirthe M Ponsen; Frank Baas; Danielle Majoor-Krakauer; Vincenzo Bonifati; Teus van Laar; Geert J Groeneveld Journal: Mov Disord Date: 2020-07-02 Impact factor: 10.338