GBA in Parkinson's disease: variant detection and pathogenicity scoring matters

Background: GBA variants are the strongest genetic risk factor for Parkinson's disease (PD). However, the pathogenicity of GBA variants concerning PD is still not fully understood. Additionally, the frequency of GBA variants varies widely across populations. Objectives: To evaluate Oxford Nanopore sequencing as a strategy, to determine the frequency of GBA variants in Norwegian PD patients and controls, and to review the current literature on newly identified variants that add to pathogenicity determination. Methods: We included 462 Norwegian PD patients and 367 healthy controls. We sequenced the full-length GBA gene 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 of GBA variants was performed by Sanger sequencing and the pathogenicity of variants was evaluated. Results: We found 95.8% (115/120) true-positive GBA variant calls, while 4.2% (5/120) variant calls were false-positive, with the NGMLR/Minimap2-BCFtools pipeline performing best. In total, 13 rare GBA variants were detected: two were predicted to be (likely) pathogenic and eleven were of uncertain significance. The odds of carrying one of the two most common GBA variants, 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]). Conclusions: In conclusion, we have demonstrated that Oxford long-read Nanopore sequencing, along with the NGMLR/Minimap2-BCFtools pipeline is an effective tool to investigate GBA variants. Further studies on the pathogenicity of GBA variants are needed to assess their effect on PD.

[1]  Sonja W. Scholz,et al.  Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene , 2022, Communications Biology.

[2]  Z. Gan-Or,et al.  New therapeutic approaches to Parkinson's disease targeting GBA, LRRK2 and Parkin , 2021, Neuropharmacology.

[3]  Jordan M. Eizenga,et al.  Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads , 2021, Nature Methods.

[4]  Heng Li,et al.  New strategies to improve minimap2 alignment accuracy , 2021, Bioinform..

[5]  T. Behl,et al.  Cross-talks among GBA mutations, glucocerebrosidase, and α-synuclein in GBA-associated Parkinson’s disease and their targeted therapeutic approaches: a comprehensive review , 2021, Translational Neurodegeneration.

[6]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[7]  M. Tittgemeyer,et al.  GBA Variants in Parkinson's Disease: Clinical, Metabolomic, and Multimodal Neuroimaging Phenotypes , 2020, Movement disorders : official journal of the Movement Disorder Society.

[8]  T. Clement,et al.  Guidelines for Sanger sequencing and molecular assay monitoring , 2020, Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc.

[9]  Melissa J. Landrum,et al.  ClinVar: improvements to accessing data , 2019, Nucleic Acids Res..

[10]  Bernard Y. Kim,et al.  Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution , 2019, bioRxiv.

[11]  G. Riboldi,et al.  GBA, Gaucher Disease, and Parkinson’s Disease: From Genetic to Clinic to New Therapeutic Approaches , 2019, Cells.

[12]  Christos Proukakis,et al.  Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION , 2019, Molecular genetics & genomic medicine.

[13]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[14]  L. Forsgren,et al.  Association of glucocerebrosidase polymorphisms and mutations with dementia in incident Parkinson's disease , 2018, Alzheimer's & Dementia.

[15]  Alexandros Kouris,et al.  VarSome: the human genomic variant search engine , 2018, bioRxiv.

[16]  Z. Gan-Or,et al.  GBA-Associated Parkinson’s Disease and Other Synucleinopathies , 2018, Current Neurology and Neuroscience Reports.

[17]  Wouter De Coster,et al.  NanoPack: visualizing and processing long-read sequencing data , 2018, bioRxiv.

[18]  B. Thyagarajan,et al.  Review of Clinical Next-Generation Sequencing. , 2017, Archives of pathology & laboratory medicine.

[19]  Michael C. Schatz,et al.  Accurate detection of complex structural variations using single molecule sequencing , 2017, Nature Methods.

[20]  David A. Eccles,et al.  MinION Analysis and Reference Consortium: Phase 1 data release and analysis , 2015, F1000Research.

[21]  Hui Yang,et al.  Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR , 2015, Nature Protocols.

[22]  W. Chung,et al.  Glucocerebrosidase activity in Parkinson's disease with and without GBA mutations. , 2015, Brain : a journal of neurology.

[23]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[24]  N. Hattori,et al.  Clinicogenetic study of GBA mutations in patients with familial Parkinson's disease , 2014, Neurobiology of Aging.

[25]  I. Adzhubei,et al.  Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.

[26]  Ellen Sidransky,et al.  The link between the GBA gene and parkinsonism , 2012, The Lancet Neurology.

[27]  J. Stockman.  Multicenter Analysis of Glucocerebrosidase Mutations in Parkinson's Disease , 2011 .

[28]  A. Singleton,et al.  Glucocerebrosidase mutations in clinical and pathologically proven Parkinson's disease. , 2009, Brain : a journal of neurology.

[29]  Nir Giladi,et al.  Genotype-phenotype correlations between GBA mutations and Parkinson disease risk and onset , 2008, Neurology.

[30]  E. Sidransky,et al.  Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA) , 2008, Human mutation.

[31]  M. Farrer,et al.  Glucocerebrosidase gene mutations and Parkinson disease in the Norwegian population , 2006, Neurology.

[32]  R. Nussbaum,et al.  Parkinsonism among Gaucher disease carriers , 2004, Journal of Medical Genetics.

[33]  J. Aharon-Peretz,et al.  Mutations in the glucocerebrosidase gene and Parkinson's disease in Ashkenazi Jews. , 2004, The New England journal of medicine.

[34]  E. Sidransky,et al.  Glucocerebrosidase mutations in subjects with parkinsonism. , 2004, Molecular genetics and metabolism.

[35]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..