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Dardis A, Michelakakis H, Rozenfeld P, Fumic K, Wagner J, Pavan E, Fuller M, Revel-Vilk S, Hughes D, Cox T, Aerts J. Patient centered guidelines for the laboratory diagnosis of Gaucher disease type 1. Orphanet J Rare Dis 2022; 17:442. [PMID: 36544230 PMCID: PMC9768924 DOI: 10.1186/s13023-022-02573-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022] Open
Abstract
Gaucher disease (GD) is an autosomal recessive lysosomal storage disorder due to the deficient activity of the acid beta-glucosidase (GCase) enzyme, resulting in the progressive lysosomal accumulation of glucosylceramide (GlcCer) and its deacylated derivate, glucosylsphingosine (GlcSph). GCase is encoded by the GBA1 gene, located on chromosome 1q21 16 kb upstream from a highly homologous pseudogene. To date, more than 400 GBA1 pathogenic variants have been reported, many of them derived from recombination events between the gene and the pseudogene. In the last years, the increased access to new technologies has led to an exponential growth in the number of diagnostic laboratories offering GD testing. However, both biochemical and genetic diagnosis of GD are challenging and to date no specific evidence-based guidelines for the laboratory diagnosis of GD have been published. The objective of the guidelines presented here is to provide evidence-based recommendations for the technical implementation and interpretation of biochemical and genetic testing for the diagnosis of GD to ensure a timely and accurate diagnosis for patients with GD worldwide. The guidelines have been developed by members of the Diagnostic Working group of the International Working Group of Gaucher Disease (IWGGD), a non-profit network established to promote clinical and basic research into GD for the ultimate purpose of improving the lives of patients with this disease. One of the goals of the IWGGD is to support equitable access to diagnosis of GD and to standardize procedures to ensure an accurate diagnosis. Therefore, a guideline development group consisting of biochemists and geneticists working in the field of GD diagnosis was established and a list of topics to be discussed was selected. In these guidelines, twenty recommendations are provided based on information gathered through a systematic review of the literature and two different diagnostic algorithms are presented, considering the geographical differences in the access to diagnostic services. Besides, several gaps in the current diagnostic workflow were identified and actions to fulfill them were taken within the IWGGD. We believe that the implementation of recommendations provided in these guidelines will promote an equitable, timely and accurate diagnosis for patients with GD worldwide.
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Affiliation(s)
- A. Dardis
- grid.411492.bRegional Coordinator Centre for Rare Disease, University Hospital of Udine, P.Le Santa Maria Della Misericordia 15, 33100 Udine, Italy
| | - H. Michelakakis
- grid.414709.f0000 0004 0383 4326Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - P. Rozenfeld
- grid.9499.d0000 0001 2097 3940Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Estudios Inmunológicos Y Fisiopatológicos (IIFP), UNLP, CONICET, Asociado CIC PBA, La Plata, Argentina
| | - K. Fumic
- grid.412688.10000 0004 0397 9648Department for Laboratory Diagnostics, University Hospital Centre Zagreb and School of Medicine, Zagreb, Croatia
| | - J. Wagner
- grid.412680.90000 0001 1015 399XDepartment of Medical Biology and Genetics, Faculty of Medicine, J.J. Strossmayer University, Osijek, Croatia ,International Gaucher Alliance, Dursley, UK
| | - E. Pavan
- grid.411492.bRegional Coordinator Centre for Rare Disease, University Hospital of Udine, P.Le Santa Maria Della Misericordia 15, 33100 Udine, Italy
| | - M. Fuller
- grid.1010.00000 0004 1936 7304Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital and Adelaide Medical School, University of Adelaide, Adelaide, SA 5005 Australia
| | - S. Revel-Vilk
- grid.415593.f0000 0004 0470 7791Gaucher Unit, Shaare Zedek Medical Center, Jerusalem, Israel ,grid.9619.70000 0004 1937 0538Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - D. Hughes
- grid.437485.90000 0001 0439 3380Lysosomal Storage Disorders Unit, Royal Free London NHS Foundation Trust and University College London, London, UK
| | - T. Cox
- grid.5335.00000000121885934Department of Medicine, University of Cambridge, Cambridge, UK
| | - J. Aerts
- grid.5132.50000 0001 2312 1970Department of Medical Biochemistry, Leiden Institute of Chemistry, Leiden, The Netherlands
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Leija‐Salazar M, Sedlazeck FJ, Toffoli M, Mullin S, Mokretar K, Athanasopoulou M, Donald A, Sharma R, Hughes D, Schapira AH, Proukakis C. Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION. Mol Genet Genomic Med 2019; 7:e564. [PMID: 30637984 PMCID: PMC6418358 DOI: 10.1002/mgg3.564] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/23/2018] [Accepted: 12/13/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Mutations in GBA cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aimed to design and validate a method for sequencing GBA using long reads. METHODS We sequenced GBA on the Oxford Nanopore MinION as an 8.9 kb amplicon from 102 individuals, including patients with Parkinson's and Gaucher diseases. We used NanoOK for quality metrics, NGMLR to align data (after comparing with GraphMap), Nanopolish and Sniffles to call variants, and WhatsHap for phasing. RESULTS We detected all known missense mutations in these samples, including the common p.N409S (N370S) and p.L483P (L444P) in multiple samples, and nine rarer ones, as well as a splicing and a truncating mutation, and intronic SNPs. We demonstrated the ability to phase mutations, confirm compound heterozygosity, and assign haplotypes. We also detected two known risk variants in some Parkinson's patients. Rare false positives were easily identified and filtered, with the Nanopolish quality score adjusted for the number of reads a very robust discriminator. In two individuals carrying a recombinant allele, we were able to detect and fully define it in one carrier, where it included a 55-base pair deletion, but not in another one, suggesting a limitation of the PCR enrichment method. Missense mutations were detected at the correct zygosity, except for the case where the RecNciI one was missed. CONCLUSION The Oxford Nanopore MinION can detect missense mutations and an exonic deletion in this difficult gene, with the added advantages of phasing and intronic analysis. It can be used as an efficient research tool, but additional work is required to exclude all recombinants.
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Affiliation(s)
- Melissa Leija‐Salazar
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | | | - Marco Toffoli
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Stephen Mullin
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
- Institute of Translational and Stratified MedicinePlymouth University Peninsula School of MedicinePlymouthUK
| | - Katya Mokretar
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Maria Athanasopoulou
- Department of Molecular Neuroscience, Institute of NeurologyUniversity College LondonLondonUK
| | - Aimee Donald
- Department of PaediatricsRoyal Manchester Children’s HospitalManchesterUK
| | - Reena Sharma
- The Mark Holland Metabolic Unit, Salford Royal Foundation NHS TrustSalfordUK
| | - Derralynn Hughes
- Institute of Immunity and TransplantationLysosomal Storage Disorders Unit, Royal Free HospitalLondonUK
| | - Anthony H.V. Schapira
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Institute of NeurologyUniversity College LondonLondonUK
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Duran R, Mencacci NE, Angeli AV, Shoai M, Deas E, Houlden H, Mehta A, Hughes D, Cox TM, Deegan P, Schapira AH, Lees AJ, Limousin P, Jarman PR, Bhatia KP, Wood NW, Hardy J, Foltynie T. The glucocerobrosidase E326K variant predisposes to Parkinson's disease, but does not cause Gaucher's disease. Mov Disord 2013; 28:232-236. [PMID: 23225227 PMCID: PMC4208290 DOI: 10.1002/mds.25248] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/30/2012] [Accepted: 08/20/2012] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Heterozygous loss-of-function mutations in the acid beta-glucocerebrosidase (GBA1) gene, responsible for the recessive lysosomal storage disorder, Gaucher's disease (GD), are the strongest known risk factor for Parkinson's disease (PD). Our aim was to assess the contribution of GBA1 mutations in a series of early-onset PD. METHODS One hundred and eighty-five PD patients (with an onset age of ≤50) and 283 age-matched controls were screened for GBA1 mutations by Sanger sequencing. RESULTS We show that the frequency of GBA1 mutations is much higher in this patient series than in typical late-onset patient cohorts. Furthermore, our results reveal that the most prevalent PD-associated GBA1 mutation is E326K, a variant that does not, when homozygous, cause GD. CONCLUSIONS Our results confirm recent reports that the mutation, E326K, predisposes to PD and suggest that, in addition to reduced GBA1 activity, other molecular mechanisms may contribute to the development of the disease.
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Affiliation(s)
- Raquel Duran
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Niccolo E. Mencacci
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
,Department of Neurology and Laboratory of Neuroscience, “Dino Ferrari” Center, Universitá degli Studi di Milano, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Aikaterini V. Angeli
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, London, UK
| | - Maryam Shoai
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Emma Deas
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Atul Mehta
- Lysosomal Storage Disorders Unit, Department of Haematology, UCL Medical School, Royal Free Hospital, London, UK
| | - Derralynn Hughes
- Lysosomal Storage Disorders Unit, Department of Haematology, UCL Medical School, Royal Free Hospital, London, UK
| | - Timothy M. Cox
- Lysosomal Diseases Unit, Addenbrookes Hospital, and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Patrick Deegan
- Lysosomal Diseases Unit, Addenbrookes Hospital, and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anthony H. Schapira
- Department of Clinical Neurosciences, Institute of Neurology, UCL Medical School, Royal Free Hospital, London, UK
| | - Andrew J. Lees
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Patricia Limousin
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, London, UK
| | - Paul R. Jarman
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, London, UK
| | - Kailash P. Bhatia
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, London, UK
| | - Nicholas W. Wood
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - John Hardy
- Reta Lila Weston Laboratories and Departments of Molecular Neuroscience, UCL Institute of Neurology, London, UK
,Correspondence to: Prof. John Hardy, Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK;
| | - Tom Foltynie
- Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of Neurology, London, UK
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