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Zampieri S, Cattarossi S, Pavan E, Barbato A, Fiumara A, Peruzzo P, Scarpa M, Ciana G, Dardis A. Accurate Molecular Diagnosis of Gaucher Disease Using Clinical Exome Sequencing as a First-Tier Test. Int J Mol Sci 2021; 22:ijms22115538. [PMID: 34073924 PMCID: PMC8197298 DOI: 10.3390/ijms22115538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Gaucher disease (GD) is an autosomal recessive lysosomal disorder due to beta-glucosidase gene (GBA) mutations. The molecular diagnosis of GD is complicated by the presence of recombinant alleles originating from a highly homologous pseudogene. Clinical exome sequencing (CES) is a rapid genetic approach for identifying disease-causing mutations. However, copy number variation and recombination events are poorly detected, and further investigations are required to avoid mis-genotyping. The aim of this work was to set-up an integrated strategy for GD patients genotyping using CES as a first-line test. Eight patients diagnosed with GD were analyzed by CES. Five patients were fully genotyped, while three were revealed to be homozygous for mutations that were not confirmed in the parents. Therefore, MLPA (multiplex ligation-dependent probe amplification) and specific long-range PCR were performed, and two recombinant alleles, one of them novel, and one large deletion were identified. Furthermore, an MLPA assay performed in one family resulted in the identification of an additional novel mutation (p.M124V) in a relative, in trans with the known p.N409S mutation. In conclusion, even though CES has become extensively used in clinical practice, our study emphasizes the importance of a comprehensive molecular strategy to provide proper GBA genotyping and genetic counseling.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Eleonora Pavan
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Antonio Barbato
- Department of Clinical Medicine and Surgery, Federico II University Hospital, 80131 Naples, Italy
| | - Agata Fiumara
- Pediatric Unit, Regional Referral Center for Inherited Metabolic Disease, University of Catania, 95123 Catania, Italy
| | - Paolo Peruzzo
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Maurizio Scarpa
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Giovanni Ciana
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, University Hospital of Udine, 33100 Udine, Italy
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Zampieri S, Cattarossi S, Bembi B, Dardis A. GBA Analysis in Next-Generation Era: Pitfalls, Challenges, and Possible Solutions. J Mol Diagn 2017; 19:733-741. [PMID: 28727984 DOI: 10.1016/j.jmoldx.2017.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
Mutations in the gene encoding the lysosomal enzyme acid β-glucosidase (GBA) are responsible for Gaucher disease and represent the main genetic risk factor for developing Parkinson disease. In past years, next-generation sequencing (NGS) technology has been applied for the molecular analysis of the GBA gene, both as a single gene or as part of gene panels. However, the presence of complex gene-pseudogene rearrangements, resulting from the presence of a highly homologous pseudogene (GBAP1) located downstream of the GBA gene, makes NGS analysis of GBA challenging. Therefore, adequate strategies should be adopted to avoid misdetection of GBA recombinant mutations. Here, we validated a strategy for the identification of GBA mutations using parallel massive sequencing and provide an overview of the major drawbacks encountered during GBA analysis by NGS. We implemented a NGS workflow, using a set of 38 patients with Gaucher disease carrying different GBA alleles identified previously by Sanger sequencing. As expected, the presence of the pseudogene significantly affected data output. However, the combination of specific procedures for the library preparation and data analysis resulted in maximal repeatability and reproducibility, and a robust performance with 97% sensitivity and 100% specificity. In conclusion, the pipeline described here represents a useful approach to deal with GBA sequencing using NGS technology.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Bruno Bembi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy.
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Sechi A, Salvadego D, Da Ponte A, Bertin N, Dardis A, Cattarossi S, Devigili G, Reccardini F, Bembi B, Grassi B. Investigation on acute effects of enzyme replacement therapy and influence of clinical severity on physiological variables related to exercise tolerance in patients with late onset Pompe disease. Neuromuscul Disord 2017; 27:542-549. [PMID: 28433478 DOI: 10.1016/j.nmd.2017.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/10/2017] [Accepted: 03/05/2017] [Indexed: 11/19/2022]
Abstract
Exercise intolerance is one of the clinical hallmarks of late-onset Pompe disease (LOPD). We studied the acute effects of ERT on the physiological variables associated with exercise tolerance in patients chronically ERT treated. Moreover, we assessed the influence of clinical severity on the investigated variables. The day before (B) and the day after (A) ERT injection, 11 LOPD patients performed on a cycle-ergometer an exercise tolerance test to voluntary exhaustion; VO2, HR, RPE, and GAA activity were determined in B and A. The disease severity was characterized by Walton scale, 6MWT, and pulmonary function tests. No significant differences in the variables related to exercise tolerance were found in A vs B, despite a significant increase in GAA activity in peripheral lymphocytes. No differences in VO2 peak were observed between patients with only skeletal muscle impairment and patients with both skeletal and respiratory muscle impairment. Distance walked at 6MWT was significantly higher than VO2 peak expressed as percentage of normal values. In conclusion, in LOPD patients the exercise tolerance test is not acutely affected by ERT administration; the peripheral muscle component seems more prominent in determining the VO2 peak decrease than the respiratory component; VO2 peak might be more sensitive than 6MWT in estimating exercise tolerance in LOPD.
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Affiliation(s)
- Annalisa Sechi
- Regional Coordinator Center for Rare Diseases, Academic Hospital of Udine, Udine, Italy.
| | - Desy Salvadego
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Alessandro Da Ponte
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Nicole Bertin
- Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Center for Rare Diseases, Academic Hospital of Udine, Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Center for Rare Diseases, Academic Hospital of Udine, Udine, Italy
| | | | | | - Bruno Bembi
- Regional Coordinator Center for Rare Diseases, Academic Hospital of Udine, Udine, Italy
| | - Bruno Grassi
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
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Zampieri S, Cattarossi S, Oller Ramirez AM, Rosano C, Lourenco CM, Passon N, Moroni I, Uziel G, Pettinari A, Stanzial F, de Kremer RD, Azar NB, Hazan F, Filocamo M, Bembi B, Dardis A. Sequence and copy number analyses of HEXB gene in patients affected by Sandhoff disease: functional characterization of 9 novel sequence variants. PLoS One 2012; 7:e41516. [PMID: 22848519 PMCID: PMC3407239 DOI: 10.1371/journal.pone.0041516] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/21/2012] [Indexed: 11/18/2022] Open
Abstract
Sandhoff disease (SD) is a lysosomal disorder caused by mutations in the HEXB gene. To date, 43 mutations of HEXB have been described, including 3 large deletions. Here, we have characterized 14 unrelated SD patients and developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay to investigate the presence of large HEXB deletions. Overall, we identified 16 alleles, 9 of which were novel, including 4 sequence variation leading to aminoacid changes [c.626C>T (p.T209I), c.634C>A (p.H212N), c.926G>T (p.C309F), c.1451G>A (p.G484E)] 3 intronic mutations (c.1082+5G>A, c.1242+1G>A, c.1169+5G>A), 1 nonsense mutation c.146C>A (p.S49X) and 1 small in-frame deletion c.1260_1265delAGTTGA (p.V421_E422del). Using the new MLPA assay, 2 previously described deletions were identified. In vitro expression studies showed that proteins bearing aminoacid changes p.T209I and p.G484E presented a very low or absent activity, while proteins bearing the p.H212N and p.C309F changes retained a significant residual activity. The detrimental effect of the 3 novel intronic mutations on the HEXB mRNA processing was demonstrated using a minigene assay. Unprecedentedly, minigene studies revealed the presence of a novel alternative spliced HEXB mRNA variant also present in normal cells. In conclusion, we provided new insights into the molecular basis of SD and validated an MLPA assay for detecting large HEXB deletions.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Center for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Center for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
| | - Ana Maria Oller Ramirez
- Centro de Estudio de las Metabolopatias Congénitas, CEMECO, University of Córdoba, Córdoba, Argentine
| | - Camillo Rosano
- Patologia Molecolare Integrata – A.O.U. IRCSS San Martino – IST, Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Charles Marques Lourenco
- Medical Genetics Service, Clinics Hospital of Ribeirao Preto, University of Sao Paulo, Sao Paulo, Brazil
| | - Nadia Passon
- Dipartimento di Scienze Mediche e Biologiche, Università di Udine, Udine, Italy
| | - Isabella Moroni
- Department of Child Neurology, Fondazione Istituto Neurologico Besta, Milan, Italy
| | - Graziella Uziel
- Department of Child Neurology, Fondazione Istituto Neurologico Besta, Milan, Italy
| | - Antonella Pettinari
- Laboratorio di Genetica Medica, Clinica Pediatrica, Ospedali Riuniti Ancona, Ancona, Italy
| | - Franco Stanzial
- Servizio di Consulenza Genetica, Centro Provinciale di Coordinamento della Rete delle Malattie Rare, Azienda Sanitaria dell’Alto-Adige, Bolzano, Italy
| | - Raquel Dodelson de Kremer
- Centro de Estudio de las Metabolopatias Congénitas, CEMECO, University of Córdoba, Córdoba, Argentine
| | - Nydia Beatriz Azar
- Centro de Estudio de las Metabolopatias Congénitas, CEMECO, University of Córdoba, Córdoba, Argentine
| | - Filiz Hazan
- Medical Faculty, Genetic Department, Izmir, Turkey
| | - Mirella Filocamo
- U.O.S.D. Laboratorio Diagnosi Pre-Postnatale Malattie Metaboliche, Istituto G. Gaslini, Genova, Italy
| | - Bruno Bembi
- Regional Coordinator Center for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Center for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
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