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Peterlin B, Gualandi F, Maver A, Servidei S, van der Maarel SM, Lamy F, Mejat A, Evangelista T, Ferlini A. Genetic testing offer for inherited neuromuscular diseases within the EURO-NMD reference network: A European survey study. PLoS One 2020; 15:e0239329. [PMID: 32946487 PMCID: PMC7500674 DOI: 10.1371/journal.pone.0239329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/03/2020] [Indexed: 11/19/2022] Open
Abstract
The genetic diagnostics of inherited neuromuscular diseases (NMDs) is challenging due to their clinical and genetic heterogeneity. We launched an online survey within the EURO-NMD European Reference Network (ERN) to collect information about the availability/distribution of genetic testing across 61 ERN health care providers (HCPs). A 17 items questionnaire was designed to address methods used, the number of genetic tests available, the clinical pathway to access genetic testing, the use of next-generation sequencing (NGS) and participation to quality assessment schemes (QAs). A remarkable number of HCPs (49%) offers ≥ 500 genetic tests per year, 43,6% offers 100–500 genetic tests per year, and 7,2% ≤ 100 per year. NGS is used by 94% of centres, Sanger sequencing by 84%, MLPA by 66% and Southern blotting by 36%. The majority of centres (60%) offer NGS for all patients that fulfil criteria for NMD of genetic origin. Pipelines for NGS vary amongst centres, even within the same national system. Referral of patients to genetic laboratories by specialists was frequently reported (58%), and 65% of centres participates in genetic testing QAs. We specifically evaluated how many centres cover SMA, DMD, Pompe, LGMDs, and TTR genes/diseases genetic diagnosis, since these rare diseases benefit from personalised therapies. We used the Orphanet EUGT numbers, provided by 82% of HCPs. SMA, DMD, LGMD, TTR and GAA genes are covered by EUGTs although with different numbers and modalities. The number of genetic tests for NMDs offered across HCPs National Health systems is quite high, including routine techniques and NGS. The number and type of tests offered and the clinical practices differ among centres. We provided evidence that survey tools might be useful to learn about the state-of-the-art of ERN health-related activities and to foster harmonisation and standardisation of the complex care for the rare disease patients in the EU.
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Affiliation(s)
- Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Serenella Servidei
- Neurophysiopathology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | | | - Teresinha Evangelista
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, Sorbonne Université, Paris, France
- * E-mail: (AF); (TE)
| | - Alessandra Ferlini
- Unit of Medical Genetics, University Hospital Ferrara, Ferrara, Italy
- * E-mail: (AF); (TE)
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Cerino M, Gorokhova S, Laforet P, Ben Yaou R, Salort-Campana E, Pouget J, Attarian S, Eymard B, Deleuze JF, Boland A, Behin A, Stojkovic T, Bonne G, Levy N, Bartoli M, Krahn M. Genetic Characterization of a French Cohort of GNE-mutation negative inclusion body myopathy patients with exome sequencing. Muscle Nerve 2017; 56:993-997. [PMID: 28256728 DOI: 10.1002/mus.25638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2017] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Hereditary inclusion body myopathy (hIBM) refers to a group of clinically and genetically heterogeneous diseases. The overlapping histochemical features of hIBM with other genetic disorders lead to low diagnostic rates with targeted single-gene sequencing. This is true for the most prevalent form of hIBM, GNEpathy. Therefore, we used whole-exome sequencing (WES) to determine whether a cohort of clinically suspected GNEpathy patients undiagnosed by targeted GNE analysis could be genetically characterized. METHODS Twenty patients with hIBM but undiagnosed by targeted GNE sequencing were analyzed by WES before data filtering on 306 genes associated with neuromuscular disorders. RESULTS Seven patients out of 20 were found to have disease-causing mutations in genes associated with hIBM or genes allowing for hIBM in the differential diagnosis or associated with unexpected diagnosis. DISCUSSION Next-generation sequencing is an efficient strategy in the context of hIBM, resulting in a molecular diagnosis for 35% of the patients initially undiagnosed by targeted GNE analysis. Muscle Nerve 56: 993-997, 2017.
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Affiliation(s)
- Mathieu Cerino
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital Timone Enfants, Département de Génétique Médicale, Marseille, France
| | - Svetlana Gorokhova
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Pascal Laforet
- APHP, G.H. Pitié Salpêtrière, Centre de Référence Maladies Neuromusculaires Paris-Est, Institut de Myologie, Paris, France
| | - Rabah Ben Yaou
- APHP, G.H. Pitié Salpêtrière, Centre de Référence Maladies Neuromusculaires Paris-Est, Institut de Myologie, Paris, France.,Sorbonne Universités, UPMC University of Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Emmanuelle Salort-Campana
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital La Timone, Centre de Référence des Maladies Neuromusculaires et de la SLA, Marseille, France
| | - Jean Pouget
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital La Timone, Centre de Référence des Maladies Neuromusculaires et de la SLA, Marseille, France
| | - Shahram Attarian
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital La Timone, Centre de Référence des Maladies Neuromusculaires et de la SLA, Marseille, France
| | - Bruno Eymard
- APHP, G.H. Pitié Salpêtrière, Centre de Référence Maladies Neuromusculaires Paris-Est, Institut de Myologie, Paris, France
| | | | - Anne Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Anthony Behin
- APHP, G.H. Pitié Salpêtrière, Centre de Référence Maladies Neuromusculaires Paris-Est, Institut de Myologie, Paris, France
| | - Tanya Stojkovic
- APHP, G.H. Pitié Salpêtrière, Centre de Référence Maladies Neuromusculaires Paris-Est, Institut de Myologie, Paris, France
| | - Gisele Bonne
- Sorbonne Universités, UPMC University of Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Institut de Myologie, G.H. Pitié Salpêtrière, Paris, France
| | - Nicolas Levy
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital Timone Enfants, Département de Génétique Médicale, Marseille, France
| | - Marc Bartoli
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital Timone Enfants, Département de Génétique Médicale, Marseille, France
| | - Martin Krahn
- Aix Marseille University, GMGF, INSERM AMU UMR_S910, Faculté de Médecine de Marseille, 4e étage Aile Verte, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.,APHM, Hôpital Timone Enfants, Département de Génétique Médicale, Marseille, France
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Magariello A, Russo C, Citrigno L, Züchner S, Patitucci A, Mazzei R, Conforti FL, Ferlazzo E, Aguglia U, Muglia M. Exome sequencing reveals two FA2H mutations in a family with a complicated form of Hereditary Spastic Paraplegia and psychiatric impairments. J Neurol Sci 2016; 372:347-349. [PMID: 28017243 DOI: 10.1016/j.jns.2016.11.069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/09/2016] [Accepted: 11/28/2016] [Indexed: 01/15/2023]
Affiliation(s)
- A Magariello
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - C Russo
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy
| | - L Citrigno
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - S Züchner
- Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - A Patitucci
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - R Mazzei
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - F L Conforti
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy
| | - E Ferlazzo
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy
| | - U Aguglia
- Regional Epilepsy Centre, Bianchi-Melacrino-Morelli Hospital, Reggio Calabria, Italy; Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - M Muglia
- Institute of Neurological Sciences, National Research Council, Mangone, CS, Italy.
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4
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LACOSTE CAROLINE, DESVIGNES JEANPIERRE, SALGADO DAVID, PECHEUX CHRISTOPHE, VILLARD LAURENT, BARTOLI MARC, BEROUD CHRISTOPHE, LEVY NICOLAS, BADENS CATHERINE, KRAHN MARTIN. Coverage analysis of lists of genes involved in heterogeneous genetic diseases following benchtop exome sequencing using the ion proton. J Genet 2016; 95:203-8. [DOI: 10.1007/s12041-016-0619-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Cherukuri PF, Maduro V, Fuentes-Fajardo KV, Lam K, Adams DR, Tifft CJ, Mullikin JC, Gahl WA, Boerkoel CF. Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data. BMC Genomics 2015; 16:998. [PMID: 26602380 PMCID: PMC4659195 DOI: 10.1186/s12864-015-2107-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/16/2015] [Indexed: 12/18/2022] Open
Abstract
Background Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES coverage of nucleotides in targeted regions are recognized, it is not well understood how repetition of WES improves the interpretation of sequencing results in a clinical diagnostic setting. Method To address this, we compared independently generated exome-capture of six individuals from three-generations sequenced in triplicate. This generated between 48x-86x mean target depth of high-quality mapped bases (>Q20) for each technical replicate library. Cumulatively, we achieved 179 - 208x average target coverage for each individual in the pedigree. Using this experimental design, we evaluated stochastics in WES interpretation, genotyping sensitivity, and accuracy to detect de novo variants. Results In this study, we show that repetition of WES improved the interpretation of the capture target regions after aggregating the data (93.5 - 93.9 %). Compared to 81.2 - 89.6 % (50.2-55.4 Mb of 61.7 M) coverage of targeted bases at ≥20x in the individual technical replicates, the aggregated data covered 93.5 - 93.9 % of targeted bases (57.7 – 58.0 of 61.7 M) at ≥20x threshold, suggesting a 4.3 – 12.7 % improvement in coverage. Each individual’s aggregate dataset recovered 3.4 – 6.4 million bases within variable targeted regions. We uncovered technical variability (2-5 %) inherent to WES technique. We also show improved interpretation in assessing clinically important regions that lack interpretation under current conditions, affecting 12–16 of the 56 genes recommended for secondary analysis by American College of Medical Genetics (ACMG). We demonstrate that comparing technical replicate WES datasets and their derived aggregate data can effectively address overall WES genotyping discrepancies. Conclusion We describe a method to evaluate the reproducibility and stochastics in exome library preparation, and delineate the advantages of aggregating the data derived from technical replicates. The implications of this study are directly applicable to improved experimental design and provide an opportunity to rapidly, efficiently, and accurately arrive at reliable candidate nucleotide variants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2107-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Praveen F Cherukuri
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA.
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Karin V Fuentes-Fajardo
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Kevin Lam
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | | | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
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6
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Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
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Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
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7
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Gorokhova S, Biancalana V, Lévy N, Laporte J, Bartoli M, Krahn M. Clinical massively parallel sequencing for the diagnosis of myopathies. Rev Neurol (Paris) 2015; 171:558-71. [PMID: 26022190 DOI: 10.1016/j.neurol.2015.02.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/28/2015] [Accepted: 02/04/2015] [Indexed: 02/07/2023]
Abstract
Massively parallel sequencing, otherwise known as high-throughput or next-generation sequencing, is rapidly gaining wide use in clinical practice due to possibility of simultaneous exploration of multiple genomic regions. More than 300 genes have been implicated in neuromuscular disorders, meaning that many genes need to be considered in a differential diagnosis for a patient affected with myopathy. By providing sequencing information for numerous genes at the same time, massively parallel sequencing greatly accelerates the diagnostic processes of myopathies compared to the classical "gene-after-gene" approach by Sanger sequencing. In this review, we describe multiple advantages of this powerful sequencing method for applications in myopathy diagnosis. We also outline recent studies that used this approach to discover new myopathy-causing genes and to diagnose cohorts of patients with muscular disorders. Finally, we highlight the key aspects and limitations of massively parallel sequencing that a neurologist considering this test needs to know in order to interpret the results of the test and to deal with other issues concerning the test.
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Affiliation(s)
- S Gorokhova
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France
| | - V Biancalana
- Laboratoire Diagnostic Génétique, Nouvel Hôpital Civil, 1, place de l'Hôpital, BP 426, 67091 Strasbourg cedex, France; Department of Translational Medicine and Neurogenetics, I.G.B.M.C., INSERM U964, CNRS UMR7104, Strasbourg University, 1, rue Laurent-Fries, 67404 Illkirch, France
| | - N Lévy
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France
| | - J Laporte
- Department of Translational Medicine and Neurogenetics, I.G.B.M.C., INSERM U964, CNRS UMR7104, Strasbourg University, 1, rue Laurent-Fries, 67404 Illkirch, France
| | - M Bartoli
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France
| | - M Krahn
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France.
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8
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Shin HY, Jang H, Han JH, Park HJ, Lee JH, Kim SW, Kim SM, Park YE, Kim DS, Bang D, Lee MG, Lee JH, Choi YC. Targeted next-generation sequencing for the genetic diagnosis of dysferlinopathy. Neuromuscul Disord 2015; 25:502-10. [PMID: 25868377 DOI: 10.1016/j.nmd.2015.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/16/2015] [Accepted: 03/11/2015] [Indexed: 12/25/2022]
Abstract
Dysferlinopathy comprises a group of autosomal recessive muscular dystrophies caused by mutations in the DYSF gene. Due to the large size of the gene and its lack of mutational hot spots, analysis of the DYSF gene is time-consuming and laborious using conventional sequencing methods. By next-generation sequencing (NGS), DYSF gene analysis has previously been validated through its incorporation in multi-gene panels or exome analyses. However, individual validation of NGS approaches for DYSF gene has not been performed. Here, we established and validated a hybridization capture-based target-enrichment followed by next-generation sequencing to detect mutations in patients with dysferlinopathy. With this approach, mean depth of coverage was approximately 450 fold and almost all (99.3%) of the targeted region had sequence coverage greater than 20 fold. When this approach was tested on samples from patients with known DYSF mutations, all known mutations were correctly retrieved. Using this method on 32 consecutive patient samples with dysferlinopathy, at least two pathogenic variants were detected in 28 (87.5%) samples and at least one pathogenic variant was identified in all samples. Our results suggested that the NGS-based screening method could facilitate efficient and accurate genetic diagnosis of dysferlinopathy.
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Affiliation(s)
- Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Joo Hyung Han
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Jun Park
- Department of Neurology, Mokdong Hospital, Ewha Womans University College of Medicine, Seoul, Republic of Korea
| | - Jung Hwan Lee
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - So Won Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea; Department of Clinical Pharmacology, Inje University, Busan Paik Hospital, Busan, Republic of Korea
| | - Seung Min Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Young-Eun Park
- Department of Neurology, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Dae-Seong Kim
- Department of Neurology, Pusan National University School of Medicine, Busan, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Pharmacogenomic Research Center for Membrane Transporters, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, Republic of Korea.
| | - Young-Chul Choi
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Manase D, D'Alessandro LCA, Manickaraj AK, Al Turki S, Hurles ME, Mital S. High throughput exome coverage of clinically relevant cardiac genes. BMC Med Genomics 2014; 7:67. [PMID: 25496018 PMCID: PMC4272796 DOI: 10.1186/s12920-014-0067-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 11/26/2014] [Indexed: 01/27/2023] Open
Abstract
Background Given the growing use of whole-exome sequencing (WES) for clinical diagnostics of complex human disorders, we evaluated coverage of clinically relevant cardiac genes on WES and factors influencing uniformity and depth of coverage of exonic regions. Methods Two hundred and thirteen human DNA samples were exome sequenced via Illumina HiSeq using different versions of the Agilent SureSelect capture kit. 50 cardiac genes were further analyzed including 31 genes from the American College of Medical Genetics (ACMG) list for reporting of incidental findings and 19 genes associated with congenital heart disease for which clinical testing is available. Gene coordinates were obtained from two databases, CCDS and Known Gene and compared. Read depth for each region was extracted from the exomes and used to assess capture variability between kits for individual genes, and for overall coverage. GC content, gene size, and inter-sample variability were also tested as potential contributors to variability in gene coverage. Results All versions of capture kits (designed based on Consensus coding sequence) included only 55% of known genomic regions for the cardiac genes. Although newer versions of each Agilent kit showed improvement in capture of CCDS regions to 99%, only 64% of Known Gene regions were captured even with newer capture kits. There was considerable variability in coverage of the cardiac genes. 10 of the 50 genes including 6 on the ACMG list had less than the optimal coverage of 30X. Within each gene, only 32 of the 50 genes had the majority of their bases covered at an interquartile range ≥30X. Heterogeneity in gene coverage was modestly associated with gene size and significantly associated with GC content. Conclusions Despite improvement in overall coverage across the exome with newer capture kit versions and higher sequencing depths, only 50% of known genomic regions of clinical cardiac genes are targeted and individual gene coverage is non-uniform. This may contribute to a bias with greater attribution of disease causation to mutations in well-represented and well-covered genes. Improvements in WES technology are needed before widespread clinical application. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0067-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dorin Manase
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Lisa C A D'Alessandro
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | - Ashok Kumar Manickaraj
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
| | | | | | - Seema Mital
- Division of Cardiology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada. .,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
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10
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Bartoli M, Desvignes JP, Nicolas L, Martin K. Exome sequencing as a second-tier diagnostic approach for clinically suspected dysferlinopathy patients. Muscle Nerve 2014; 50:1007-10. [PMID: 25046369 DOI: 10.1002/mus.24344] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2014] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Autosomal recessive muscular dystrophies are heterogeneous genetic disorders, with 39 genes currently implicated. Genetic diagnosis using targeted single-gene analysis by Sanger sequencing yields negative results in 10-20% of samples, warranting clinical re-evaluation and time-consuming testing of additional genes. This applies to dysferlinopathies caused by mutations in the gene encoding dysferlin (DYSF), which presents mainly as limb-girdle muscular dystrophy (LGMD) or distal myopathy. METHODS We evaluated exome sequencing associated with data filtering for selected genes as a second-tier approach for genetic diagnosis in a cohort of 37 patients with an initial negative result on targeted DYSF analysis. RESULTS Exome sequencing allowed for establishing (16%) or suggesting (8%) the molecular diagnosis by implicating other known LGMD or distal myopathy genes or by revealing DYSF mutations previously missed using mutation-screening techniques with incomplete detection yields. CONCLUSIONS Exome sequencing associated with data filtering constitutes an efficient second-tier analysis for genes implicated in LGMD or distal myopathies.
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Affiliation(s)
- Marc Bartoli
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, 13385, Marseille, France; APHM, Département de Génétique Médicale, Hôpital Timone Enfants, Marseille, 13385, France
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11
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Dias C, Rupps R, Millar B, Choi K, Marra M, Demos M, Kratz LE, Boerkoel CF. Desmosterolosis: an illustration of diagnostic ambiguity of cholesterol synthesis disorders. Orphanet J Rare Dis 2014; 9:94. [PMID: 24961299 PMCID: PMC4076431 DOI: 10.1186/1750-1172-9-94] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Desmosterolosis is an autosomal recessive disorder of cholesterol biosynthesis caused by biallelic mutations of DHCR24 (homozygous or compound heterozygous), which encodes 3-β-hydroxysterol Δ-24-reductase. We report two sisters homozygous for the 571G>A (E191K) DHCR24 mutation. Comparison of the propositae to other reported individuals shows that psychomotor developmental delay, failure to thrive, dysgenesis of the corpus callosum, cerebral white matter atrophy and spasticity likely constitute the minimal desmosterolosis phenotype. The nonspecific features of desmosterolosis make it difficult to suspect clinically and therefore screening for it should be entertained early in the diagnostic evaluation.
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Affiliation(s)
| | | | | | | | | | | | | | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, 4500 Oak St,, Vancouver, British Columbia, V6H 3N1, Canada.
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12
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Schuster J, Khan TN, Tariq M, Shaiq PA, Mäbert K, Baig SM, Klar J. Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy. BMC MEDICAL GENETICS 2014; 15:71. [PMID: 24961962 PMCID: PMC4076434 DOI: 10.1186/1471-2350-15-71] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/10/2014] [Indexed: 11/10/2022]
Abstract
Background Exome sequencing has become more and more affordable and the technique has emerged as an important diagnostic tool for monogenic disorders at early stages of investigations, in particular when clinical information is limited or unspecific as well as in cases of genetic heterogeneity. Methods We identified a consanguineous Pakistani family segregating an autosomal recessive phenotype characterized by muscular hypertrophy, mild mental retardation and skeletal abnormalities. The available clinical information was incomplete and we applied whole exome sequencing in an affected family member for the identification of candidate gene variants. Results Exome sequencing identified a previously unreported homozygous mutation in the acceptor splice site of intron 5 in the BSCL2 gene (c.574-2A > G). Expression analysis revealed that the mutation was associated with skipping of exon 6. BSCL2 mutations are associated with Berardinelli-Seip congenital lipodystrophy and a clinical re-evaluation of affected individuals confirmed the diagnosis. Conclusions Exome sequencing is a powerful technique for the identification of candidate gene variants in Mendelian traits. We applied this technique on a single individual affected by a likely autosomal recessive disorder without access to complete clinical details. A homozygous and truncating mutation was identified in the BSCL2 gene suggesting congenital generalized lipodystrophy. Incomplete phenotypic delineations are frequent limiting factors in search for a diagnosis and may lead to inappropriate care and follow-up. Our study exemplifies exome sequencing as a powerful diagnostic tool in Mendelian disorders that may complement missing clinical information and accelerate clinical diagnosis.
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Affiliation(s)
| | | | | | | | | | | | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala, Sweden.
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13
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Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SMJ, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JGR, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 2013; 42:D865-72. [PMID: 24217909 PMCID: PMC3965069 DOI: 10.1093/nar/gkt1059] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
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Affiliation(s)
- Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Dias C, McDonald A, Sincan M, Rupps R, Markello T, Salvarinova R, Santos RF, Menghrajani K, Ahaghotu C, Sutherland DP, Fortuno ES, Kollmann TR, Demos M, Friedman JM, Speert DP, Gahl WA, Boerkoel CF. Recurrent subacute post-viral onset of ataxia associated with a PRF1 mutation. Eur J Hum Genet 2013; 21:1232-9. [PMID: 23443029 PMCID: PMC3798831 DOI: 10.1038/ejhg.2013.20] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 11/19/2012] [Accepted: 01/23/2013] [Indexed: 12/14/2022] Open
Abstract
Inflammation is an important contributor to pediatric and adult neurodegeneration. Understanding the genetic determinants of neuroinflammation provides valuable insight into disease mechanism. We characterize a disorder of recurrent immune-mediated neurodegeneration. We report two sisters who presented with neurodegeneration triggered by infections. The proband, a previously healthy girl, presented at 22.5 months with ataxia and dysarthria following mild gastroenteritis. MRI at onset showed a symmetric signal abnormality of the cerebellar and peritrigonal white matter. Following a progressive course of partial remissions and relapses, she died at 5 years of age. Her older sister had a similar course following varicella infection, she died within 13 months. Both sisters had unremarkable routine laboratory testing, with exception of a transient mild cytopenia in the proband 19 months after presentation. Exome sequencing identified a biallelic perforin1 mutation (PRF1; p.R225W) previously associated with familial hemophagocytic lymphohistiocytosis (FHL). In contrast to FHL, these girls did not have hematopathology or cytokine overproduction. However, 3 years after disease onset, the proband had markedly deficient interleukin-1 beta (IL-1β) production. These observations extend the spectrum of disease associated with perforin mutations to immune-mediated neurodegeneration triggered by infection and possibly due to primary immunodeficiency.
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Affiliation(s)
- Cristina Dias
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Genetics and Health Cluster, Child and Family Research Institute, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Allison McDonald
- Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Murat Sincan
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Genetics and Health Cluster, Child and Family Research Institute, BC Children's Hospital, Vancouver, British Columbia, Canada
- Rare Disease Foundation, Vancouver, British Columbia, Canada
| | - Thomas Markello
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Ramona Salvarinova
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rui F Santos
- Department of Radiology, BC Children's Hospital & University of British Columbia, Vancouver, British Columbia, Canada
| | - Kamal Menghrajani
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Chidi Ahaghotu
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Darren P Sutherland
- Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edgardo S Fortuno
- Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tobias R Kollmann
- Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Genetics and Health Cluster, Child and Family Research Institute, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - David P Speert
- Centre for Understanding and Preventing Infection in Children, Child and Family Research Institute, Vancouver, British Columbia, Canada
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William A Gahl
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Genetics and Health Cluster, Child and Family Research Institute, BC Children's Hospital, Vancouver, British Columbia, Canada
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
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Rupps R, Hukin J, Balicki M, Mercimek-Mahmutoglu S, Rolfs A, Dias C. Novel Mutations in FA2H-Associated Neurodegeneration: An Underrecognized Condition? J Child Neurol 2013; 28:1500-1504. [PMID: 22965561 DOI: 10.1177/0883073812458538] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Hereditary spastic paraplegias and related genetically heterogeneous disorders may be difficult to distinguish clinically. The FA2H gene has been associated with autosomal recessive neurodegenerative phenotypes encompassing spastic paraplegia with or without dystonia, and demyelinating leukodystrophy. To date, few individuals with mutations in the FA2H gene have been described. We report a 5-year-old girl of mixed Filipino and Vietnamese origin who presented with progressive lower limb spasticity and periventricular leukomalacia. The clinical diagnosis of FA2H-associated neurodegeneration was confirmed on the basis of 2 novel mutations in compound heterozygosity in the FA2H gene (p.S70L/p.P323L). This family highlights that FA2H-associated disorders may be underrecognized in children with neurodegeneration of many different ethnicities. Magnetic resonance imaging features play an important role as diagnostic clues in this and other hereditary spastic paraplegias. The consideration of this diagnosis is essential in providing families with important information on prognosis, as well as accurate genetic counseling.
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Affiliation(s)
- Rosemarie Rupps
- 1Department of Medical Genetics, University of British Columbia, Canada
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Exome sequencing reveals HINT1 mutations as a cause of distal hereditary motor neuropathy. Eur J Hum Genet 2013; 22:847-50. [PMID: 24105373 DOI: 10.1038/ejhg.2013.231] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 12/13/2022] Open
Abstract
Distal hereditary motor neuropathies (dHMNs) are a heterogenous group of genetic disorders with length-dependent degeneration of motor axons. Obtaining a genetic diagnosis in patients with dHMN remains challenging. We performed exome sequencing in a diagnostic setting in 12 patients with a clinical diagnosis of dHMN. Potential disease-causing variants in genes associated with dHMN and other forms of inherited neuropathies/motor neuron diseases were validated using Sequenom. The coverage in the genes studied was >95% with an average coverage of >50 times. In none of the patients a mutations was found in genes previously reported to be associated with dHMN. However, in 2/12 patients a recessive mutation in histidine triad nucleotide binding protein 1 (HINT1, recently discovered as a cause of axonal neuropathy with neuromyotonia) was identified. Our results demonstrate the diagnostic value of exome sequencing for patients with inherited neuropathies. The phenotypic spectrum of recessive mutations in HINT1 includes dHMN. HINT1 should be added to the list of genes to check for in dHMN.
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Alavi A, Nafissi S, Shamshiri H, Nejad MM, Elahi E. Identification of mutation in NPC2 by exome sequencing results in diagnosis of Niemann-Pick disease type C. Mol Genet Metab 2013; 110:139-44. [PMID: 23791309 DOI: 10.1016/j.ymgme.2013.05.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 01/19/2023]
Abstract
We report identification of a homozygous mutation in NPC2 in two Iranian siblings with a neurologic dysfunction whose disease had not been diagnosed prior to our genetic analysis. The mutation was identified by exome sequencing. The finding resulted in diagnosis of Niemann-Pick disease type C (NPC) in the siblings, and initiation of treatment with Miglustat. The clinical features of the patients are presented. It has been suggested that NPC is under diagnosed, particularly when presentations are not very severe, as was the situation in the cases studied here. NPC is a fatal autosomal recessive disorder clinically characterized by hepatosplenomegaly and progressive neurological deterioration. At the cellular level, it causes aberrant cholesterol trafficking and accumulation of unesterified cholesterol in lysosomes. Mutations in NPC1 and NPC2 are cause of disease in respectively, 95% and 5% of NPC patients. The p.Pro120Ser causing mutation in NPC2 observed in the Iranian patients was earlier observed in the only other NPC2 patient reported from the Middle East. The study demonstrates that in addition to greatly facilitating gene discovery, exome sequencing has notable potentials for diagnosis, particularly for diagnosis of atypical cases.
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Affiliation(s)
- Afagh Alavi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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18
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Davis EE, Savage JH, Willer JR, Jiang YH, Angrist M, Androutsopoulos A, Katsanis N. Whole exome sequencing and functional studies identify an intronic mutation in TRAPPC2 that causes SEDT. Clin Genet 2013; 85:359-64. [PMID: 23656395 DOI: 10.1111/cge.12189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Revised: 05/06/2013] [Accepted: 05/06/2013] [Indexed: 12/11/2022]
Abstract
Skeletal dysplasias are challenging to diagnose because of their phenotypic variability, genetic heterogeneity, and diverse inheritance patterns. We conducted whole exome sequencing of a Turkish male with a suspected X-linked skeletal dysplasia of unknown etiology as well as his unaffected mother and maternal uncle. Bioinformatic filtering of variants implicated in skeletal system development revealed a novel hemizygous mutation, c.341-(11_9)delAAT, in an intron of TRAPPC2, the causative locus of spondyloepiphyseal dysplasia tarda (SEDT). We show that this deletion leads to the loss of wild-type TRAPPC2 and the generation of two functionally impaired mRNAs in patient cells. These consequences are predicted to disrupt function of SEDLIN/TRAPPC2. The clinical and research data were returned, with appropriate caveats, to the patient and informed his disease status and reproductive choices. Our findings expand the allelic repertoire of SEDT and show how prior filtering of the morbid human genome informed by inheritance pattern and phenotype, when combined with appropriate functional tests in patient-derived cells, can expedite discovery, overcome issues of missing data and help interpret variants of unknown significance. Finally, this example shows how the return of a clinically confirmed mutational finding, supported by research allele pathogenicity data, can assist individuals with inherited disorders with life choices.
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Impacts of massively parallel sequencing for genetic diagnosis of neuromuscular disorders. Acta Neuropathol 2013; 125:173-85. [PMID: 23224362 DOI: 10.1007/s00401-012-1072-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 12/11/2022]
Abstract
Neuromuscular disorders (NMD) such as neuropathy or myopathy are rare and often severe inherited disorders, affecting muscle and/or nerves with neonatal, childhood or adulthood onset, with considerable burden for the patients, their families and public health systems. Genetic and clinical heterogeneity, unspecific clinical features, unidentified genes and the implication of large and/or several genes requiring complementary methods are the main drawbacks in routine molecular diagnosis, leading to increased turnaround time and delay in the molecular validation of the diagnosis. The application of massively parallel sequencing, also called next generation sequencing, as a routine diagnostic strategy could lead to a rapid screening and fast identification of mutations in rare genetic disorders like NMD. This review aims to summarize and to discuss recent advances in the genetic diagnosis of neuromuscular disorders, and more generally monogenic diseases, fostered by massively parallel sequencing. We remind the challenges and benefit of obtaining an accurate genetic diagnosis, introduce the massively parallel sequencing technology and its novel applications in diagnosis of patients, prenatal diagnosis and carrier detection, and discuss the limitations and necessary improvements. Massively parallel sequencing synergizes with clinical and pathological investigations into an integrated diagnosis approach. Clinicians and pathologists are crucial in patient selection and interpretation of data, and persons trained in data management and analysis need to be integrated to the diagnosis pipeline. Massively parallel sequencing for mutation identification is expected to greatly improve diagnosis, genetic counseling and patient management.
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Cho SY, Ki CS, Park HD, Kim SJ, Sohn YB, Maeng SH, Jung YJ, Jin DK. Genetic investigation of patients with undetectable peaks of growth hormone after two provocation tests. Clin Endocrinol (Oxf) 2013; 78:317-20. [PMID: 22844977 DOI: 10.1111/j.1365-2265.2012.04514.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Abstract
Over the past year huge advances have been made in our ability to determine the genetic aetiology of many neurological diseases through the utilisation of next generation sequencing platforms. This technology is, on a daily basis, providing new breakthroughs in neurological disease. The aim of this article is to clearly describe the technological platforms, methods of data analysis, established breakthroughs, and potential future clinical and research applications of this innovative and exciting technique which has relevance to all those working within clinical neuroscience.
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Affiliation(s)
- M J Keogh
- Mitochondrial Research Group, Newcastle University, UK
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McDonald KK, Stajich J, Blach C, Ashley-Koch AE, Hauser MA. Exome analysis of two limb-girdle muscular dystrophy families: mutations identified and challenges encountered. PLoS One 2012; 7:e48864. [PMID: 23155419 PMCID: PMC3498247 DOI: 10.1371/journal.pone.0048864] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 10/04/2012] [Indexed: 12/17/2022] Open
Abstract
The molecular diagnosis of muscle disorders is challenging: genetic heterogeneity (>100 causal genes for skeletal and cardiac muscle disease) precludes exhaustive clinical testing, prioritizing sequencing of specific genes is difficult due to the similarity of clinical presentation, and the number of variants returned through exome sequencing can make the identification of the disease-causing variant difficult. We have filtered variants found through exome sequencing by prioritizing variants in genes known to be involved in muscle disease while examining the quality and depth of coverage of those genes. We ascertained two families with autosomal dominant limb-girdle muscular dystrophy of unknown etiology. To identify the causal mutations in these families, we performed exome sequencing on five affected individuals using the Agilent SureSelect Human All Exon 50 Mb kit and the Illumina HiSeq 2000 (2×100 bp). We identified causative mutations in desmin (IVS3+3A>G) and filamin C (p.W2710X), and augmented the phenotype data for individuals with muscular dystrophy due to these mutations. We also discuss challenges encountered due to depth of coverage variability at specific sites and the annotation of a functionally proven splice site variant as an intronic variant.
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Affiliation(s)
- Kristin K. McDonald
- Center for Human Genetics, Duke University, Durham, North Carolina, United States
| | - Jeffrey Stajich
- Center for Human Genetics, Duke University, Durham, North Carolina, United States
| | - Colette Blach
- Center for Human Genetics, Duke University, Durham, North Carolina, United States
| | - Allison E. Ashley-Koch
- Center for Human Genetics, Duke University, Durham, North Carolina, United States
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A. Hauser
- Center for Human Genetics, Duke University, Durham, North Carolina, United States
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
- * E-mail:
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Majewski J, Rosenblatt DS. Exome and whole-genome sequencing for gene discovery: The future is now! Hum Mutat 2012; 33:591-2. [DOI: 10.1002/humu.22055] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Thompson R, Drew CJG, Thomas RH. Next generation sequencing in the clinical domain: clinical advantages, practical, and ethical challenges. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 89:27-63. [PMID: 23046881 DOI: 10.1016/b978-0-12-394287-6.00002-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There has been an academic "gold rush" with researchers mining the deep seams of whole-exome and whole-genome sequencing since 2008. Although undoubtedly a major advance initially for identifying new disease-associated genes for rare monogenetic disorders--more recently, common and complex conditions have been successfully studied using these techniques. With great power comes great responsibility, however, and we must not forget that next generation sequencing produces unique ethical conundrums and validation challenges. We review the progression of published papers using whole-exome sequencing from a clinical and technical viewpoint before then reflecting on the key arguments that need to be fully understood before these tools can become a routine part of clinical practice and we ask what may be the role for the biomedical scientists?
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Affiliation(s)
- Rose Thompson
- Welsh Centre for Learning Disabilities, Cardiff University, Cardiff, UK
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