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Shekhawat DS, Didel S, Dixit SG, Singh P, Singh K. Carrier Screening and Diagnosis for Spinal Muscular Atrophy Using Droplet Digital PCR Versus MLPA: Analytical Validation and Early Test Outcome. Genet Test Mol Biomarkers 2024; 28:207-212. [PMID: 38533877 DOI: 10.1089/gtmb.2023.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background: Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular life-threatening disorder. Owing to high carrier frequency, population-wide SMA screening to quantify the copy number of SMN gene is recommended by American College of Medical Genetics and Genomics. An accurate, reliable, short runaround time and cost-effective method may be helpful in mass population screening for SMA. Methods: Multiplex ligation-dependent probe amplification (MLPA) is a gold standard to estimate the copy number variation (CNV) for SMN1 and SMN2 genes. In this study, we validated droplet digital polymerase chain reaction (ddPCR) for the determination of CNV for both SMN1 and SMN2 exon 7 for a diagnostic purpose. In total, 66 clinical samples were tested using ddPCR, and results were compared with the MLPA as a reference test. Results: For all samples, CNV for SMN1 and SMN2 exon 7 was consentaneous between ddPCR and MLPA test results (κ = 1.000, p < 0.0001). In addition, ddPCR also showed a significant acceptable degree of test repeatability, coefficient of variation < 4%. Conclusion: ddPCR is expected to be utilitarian for CNV detection for carrier screening and diagnosis of SMA. ddPCR test results for CNV detection for SMN1/SMN2 exon 7 are concordant with the gold standard. ddPCR is a more cost-effective and time-saving diagnostic test for SMA than MLPA. Furthermore, it can be used for population-wide carrier screening for SMA.
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Affiliation(s)
- Dolat Singh Shekhawat
- Department of Pediatrics, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- Department of Medical Genetics, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- NIDAN Kendra, Genetic Laboratory, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
| | - Siyaram Didel
- Department of Pediatrics, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
| | - Shilpi Gupta Dixit
- NIDAN Kendra, Genetic Laboratory, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- Department of Anatomy, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
| | - Pratibha Singh
- NIDAN Kendra, Genetic Laboratory, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- Department of Obstetrics & Gynaecology, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
| | - Kuldeep Singh
- Department of Pediatrics, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- Department of Medical Genetics, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
- NIDAN Kendra, Genetic Laboratory, All India Institute of Medical Science Jodhpur, Jodhpur, Rajasthan, India
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Abd El Mutaleb ANH, Ibrahim FAR, Megahed FAK, Atta A, Ali BA, Omar TEI, Rashad MM. NAIP Gene Deletion and SMN2 Copy Number as Molecular Tools in Predicting the Severity of Spinal Muscular Atrophy. Biochem Genet 2024:10.1007/s10528-023-10657-6. [PMID: 38388850 DOI: 10.1007/s10528-023-10657-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/29/2023] [Indexed: 02/24/2024]
Abstract
Spinal muscular atrophy (SMA) is one of the most prevalent autosomal recessive illnesses with type I being the most severe type. Genomic alterations including survival motor neuron (SMN) copy number as well as deletions in SMN and Neuronal Apoptosis Inhibitory Protein (NAIP) are greatly implicated in the emergence of SMA. However, the association of such alterations with the severity of the disease is yet to be investigated. This study was directed to elucidate the molecular assessment of NAIP and SMN genomic alterations as a useful tool in predicting the severity of SMA among patients. This study included 65 SMA pediatric patients (30 type I and 35 type II) and 65 healthy controls. RFLP-PCR was employed to determine the genetic polymorphisms of the SMN1, SMN2, and NAIP genes. In addition, qRT-PCR was used to identify the expression of the SMN1 and SMN2 genes, and serum levels of creatine kinase were measured using a colorimetric method. DNA sequencing was performed on some samples to detect any single nucleotide polymorphisms in SMN1, SMN2, and NAIP genes. All SMA patients had a homozygous deficiency of SMN1 exon 7. The homozygous deficiency of SMN1 exons 7 and 8, with the deletion of NAIP exon 5 was found among the majority of Type I patients. In contrast, patients with the less severe condition (type II) had SMN1 exons 7 and 8 deleted but did not have any deletions in NAIP, additionally; 65.7% of patients had multiple copies of SMN2. Analysis of NAIP deletion alongside assessing SMN2 copy number might enhance the effectiveness of the diagnosis that can predict severity among Spinal Muscular Atrophy patients.
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Affiliation(s)
| | - Fawziya A R Ibrahim
- Department of Applied Medical Chemistry, Medical Research Institute, University of Alexandria, Alexandria, Egypt.
| | - Fayed A K Megahed
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Ahmed Atta
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Bahy A Ali
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Tarek E I Omar
- Department of Pediatric Neurology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | - Mona M Rashad
- Department of Applied Medical Chemistry, Medical Research Institute, University of Alexandria, Alexandria, Egypt
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3
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Abiusi E, Costa-Roger M, Bertini ES, Tiziano FD, Tizzano EF, Abiusi E, Baranello G, Bertini E, Boemer F, Burghes A, Codina-Solà M, Costa-Roger M, Dangouloff T, Groen E, Gos M, Jędrzejowska M, Kirschner J, Lemmink HH, Müller-Felber W, Ouillade MC, Quijano-Roy S, Rucinski K, Saugier-Veber P, Tiziano FD, Tizzano EF, Wirth B. 270th ENMC International Workshop: Consensus for SMN2 genetic analysis in SMA patients 10-12 March, 2023, Hoofddorp, the Netherlands. Neuromuscul Disord 2024; 34:114-122. [PMID: 38183850 DOI: 10.1016/j.nmd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
The 270th ENMC workshop aimed to develop a common procedure to optimize the reliability of SMN2 gene copy number determination and to reinforce collaborative networks between molecular scientists and clinicians. The workshop involved neuromuscular and clinical experts and representatives of patient advocacy groups and industry. SMN2 copy number is currently one of the main determinants for therapeutic decision in SMA patients: participants discussed the issues that laboratories may encounter in this molecular test and the cruciality of the accurate determination, due the implications as prognostic factor in symptomatic patients and in individuals identified through newborn screening programmes. At the end of the workshop, the attendees defined a set of recommendations divided into four topics: SMA molecular prognosis assessment, newborn screening for SMA, SMN2 copies and treatments, and modifiers and biomarkers. Moreover, the group draw up a series of recommendations for the companies manufacturing laboratory kits, that will help to minimize the risk of errors, regardless of the laboratories' expertise.
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Affiliation(s)
- Emanuela Abiusi
- Section of Genomic Medicine, Department of Public Health and Life Sciences, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Mar Costa-Roger
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Enrico Silvio Bertini
- Research Unit of Neuromuscular Disease, Bambino Gesu’ Children's Hospital, IRCCS, Roma, Italy
| | - Francesco Danilo Tiziano
- Section of Genomic Medicine, Department of Public Health and Life Sciences, Università Cattolica del Sacro Cuore, Roma, Italy
- Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Eduardo F Tizzano
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Emanuela Abiusi
- Section of Genomic Medicine, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, Roma, Italy
| | - Giovanni Baranello
- The Dubowitz Neuromuscular Centre, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre & Great Ormond Street Hospital NHS Foundation Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Enrico Bertini
- Italy, Research Unit of Neuromuscular Disease, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy
| | - François Boemer
- Biochemical Genetics Lab, Department of Human Genetics, University Hospital, University of Liège, 4000 Liège, Belgium
| | - Arthur Burghes
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Marta Codina-Solà
- Neuromuscular Reference Center, Department of Paediatrics, University Hospital Liege & University of Liege, Belgium
| | - Mar Costa-Roger
- Department of Neurology & Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tamara Dangouloff
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewout Groen
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Monika Gos
- Department of Neuropediatrics and Muscle Disorders, Medical Center University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maria Jędrzejowska
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Janbernd Kirschner
- Centre for Neuromuscular Disorders, Center for Translational Neuro and Behavioral Sciences, Department of Pediatric Neurology, University Duisburg-Essen, 45147 Essen, Germany
| | - Henny H Lemmink
- AFM Téléthon, Évry, France; SMA Europe; European Alliance for Newborn Screening in Spinal Muscular Atrophy
| | - Wolfgang Müller-Felber
- Pediatric Neuromuscular Unit (NEIDF Reference Center at FILNEMUS & Euro-NMD), Child Neurology Department, Raymond Poincaré Hospital (UVSQ), APHP Université Paris Saclay, Garches France
| | - Marie-Christine Ouillade
- Fundacja SMA, Warsaw, Poland; SMA Europe; European Alliance for Newborn Screening in Spinal Muscular Atrophy
| | - Susana Quijano-Roy
- Univ Rouen Normandie, Inserm U1245, Normandie Univ and CHU Rouen, Department of Genetics and Nord/Est/Ile de France Neuromuscular Reference Center, F-76000 Rouen, France
| | - Kacper Rucinski
- Institute of Medical Genomics, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, and Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Pascale Saugier-Veber
- Institute of Human Genetics, University Hospital of Cologne, Center for Molecular Medicine, University of Cologne and Center for Rare Diseases Cologne, University Hopsital of Cologne, Cologne, Germany
| | - Francesco Danilo Tiziano
- Institute of Medical Genomics, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, and Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Eduardo Fidel Tizzano
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, Center for Molecular Medicine, University of Cologne and Center for Rare Diseases Cologne, University Hopsital of Cologne, Cologne, Germany
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4
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Zhou Y, Jiang Y. Current Advances in Genetic Testing for Spinal Muscular Atrophy. Curr Genomics 2023; 24:273-286. [PMID: 38235355 PMCID: PMC10790334 DOI: 10.2174/0113892029273388231023072050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/19/2024] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate technique for genetic testing have become priorities for optimizing the clinical pathway for SMA. In this review, we summarize the latest technological innovations in genetic testing for SMA, including MassArray®, digital PCR (dPCR), next-generation sequencing (NGS), and third-generation sequencing (TGS). Implementation recommendations for rationally choosing different technical strategies in the tertiary prevention of SMA are also explored.
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Affiliation(s)
- Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
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5
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Čupāne TL, Dīriks M, Tauriņa G, Korņejeva L, Gailīte L, Mālniece I, Auzenbaha M. The First Registered Type 0 Spinal Muscular Atrophy Patient in Latvia: Call for Change in Prenatal Diagnostic Procedures. Case Rep Med 2023; 2023:3480298. [PMID: 37303748 PMCID: PMC10250090 DOI: 10.1155/2023/3480298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023] Open
Abstract
This case report presents the first registered patient in Latvia with type 0 spinal muscular atrophy (SMA). During the first-trimester ultrasonography of the unborn patient, an increased thickness of the nuchal fold was detected. The mother reported decreased foetal movements during the pregnancy. After the boy was born, his general condition was extremely severe. The clinical signs indicated a suspected neuromuscular disorder. A precise diagnosis, type 0 SMA, was determined 7 days after birth through a newborn pilot-screening for SMA, which was conducted for all newborns whose parents consented to participate. The condition of the infant deteriorated. He had severe respiratory distress followed by multiple events leading to his death. Currently, there are only a few published case reports detailing an increased nuchal translucency (NT) measurement in association with a diagnosis of SMA in the foetus. However, an increased NT measurement is a clinically relevant sign as it can be related to genetic syndromes, foetal malformations, disruptions, and dysplasias. Since there is no cure for infants with type 0 SMA at present, it is crucial to be able to detect this disease prenatally in order to provide the best possible care for the patient and parents. This includes the provision of palliative care for the patient, among other measures. This case report highlights the prenatal signs and symptoms in relation to type 0 SMA.
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Affiliation(s)
- Tīna Luīze Čupāne
- University of Latvia, Faculty of Medicine, Riga, Latvia
- European Reference Network EURO-NMD, Paris, France
| | - Mikus Dīriks
- European Reference Network EURO-NMD, Paris, France
- Children's Clinical University Hospital (CCUH), Department of Neurology and Neurosurgery, Riga, Latvia
| | - Gita Tauriņa
- Children's Clinical University Hospital (CCUH), Medical Genetics and Prenatal Diagnostic Clinic, Riga, Latvia
| | | | - Linda Gailīte
- Riga Stradins University, Scientific Laboratory of Molecular Genetics, Riga, Latvia
| | - Ieva Mālniece
- Children's Clinical University Hospital (CCUH), Medical Genetics and Prenatal Diagnostic Clinic, Riga, Latvia
| | - Madara Auzenbaha
- Children's Clinical University Hospital (CCUH), Medical Genetics and Prenatal Diagnostic Clinic, Riga, Latvia
- Riga Stradins University, Scientific Laboratory of Molecular Genetics, Riga, Latvia
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6
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Huang Z, Yang Q, Ye J, Huang J, Lin J, Chen J, Liang Z, Cao Z. Screening and prenatal diagnosis of survival motor neuron gene deletion in pregnant women in Zhaoqing city, Guangdong Province. BMC Med Genomics 2023; 16:39. [PMID: 36859245 PMCID: PMC9976494 DOI: 10.1186/s12920-023-01468-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVE A total of 5,200 pregnant women in Zhaoqing city, Guangdong Province, were screened to identify spinal muscular atrophy (SMA) mutation carriers to guide the prevention of SMA and prevent the birth of children with SMA. METHODS Exons 7 and 8 (E7 and E8) of the survival motor neuron (SMN) 1 gene were detected in women using real-time fluorescence quantitative polymerase chain reaction. SMN1 and SMN2 copy numbers in those who were initially identified as carriers were verified via targeted region capture and next-generation sequencing. When both partners were identified as carriers, prenatal diagnosis of the fetus was performed. RESULTS Among the screened women, 75 SMA carriers (71 cases had both E7 and E8 heterozygous deletions and 4 cases only had an E7 heterozygous deletion) were identified, with a carrier frequency of 1.44% (95% confidence interval: 1.31-1.65%). Three couples where both spouses were identified as SMA carriers, and their three fetuses were subjected to prenatal genetic analysis. Of the three, one had homozygous deletions of E7 and E8 and the other two had heterozygous deletions of E7 and E8. After a detailed prenatal consultation, the former couple decided to terminate the pregnancy. CONCLUSION Through screening and prenatal diagnosis of pregnant women in Zhaoqing city, Guangdong Province, the incidence of SMA can be reduced, prevention of birth defects can be improved, incidence of birth defects can be effectively minimized.
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Affiliation(s)
- Zhiwei Huang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China. .,Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China. .,Clinical Laboratory, The Second People's Hospital of Zhaoqing, No. 2, Jiansheer Street, 526000, Zhaoqing City, Guangdong province, The People's Republic of China.
| | - Qingchan Yang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jianxiang Ye
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jianxing Huang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jin Lin
- Obstetrical Department, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jing Chen
- Prenatal Diagnosis Center, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Zizhao Liang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Zijie Cao
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
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Ng KWP, Chin HL, Chin AXY, Goh DLM. Using gene panels in the diagnosis of neuromuscular disorders: A mini-review. Front Neurol 2022; 13:997551. [PMID: 36313509 PMCID: PMC9602396 DOI: 10.3389/fneur.2022.997551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023] Open
Abstract
The diagnosis of inherited neuromuscular disorders is challenging due to their genetic and phenotypic variability. Traditionally, neurophysiology and histopathology were primarily used in the initial diagnostic approach to these conditions. Sanger sequencing for molecular diagnosis was less frequently utilized as its application was a time-consuming and cost-intensive process. The advent and accessibility of next-generation sequencing (NGS) has revolutionized the evaluation process of genetically heterogenous neuromuscular disorders. Current NGS diagnostic testing approaches include gene panels, whole exome sequencing (WES), and whole genome sequencing (WGS). Gene panels are often the most widely used, being more accessible due to availability and affordability. In this mini-review, we describe the benefits and risks of clinical genetic testing. We also discuss the utility, benefits, challenges, and limitations of using gene panels in the evaluation of neuromuscular disorders.
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Affiliation(s)
- Kay W. P. Ng
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Hui-Lin Chin
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda X. Y. Chin
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Denise Li-Meng Goh
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene. Sci Rep 2022; 12:223. [PMID: 34997153 PMCID: PMC8741787 DOI: 10.1038/s41598-021-04325-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common and severe genetic diseases. SMA carrier screening is an effective way to identify couples at risk of having affected children. Next-generation sequencing (NGS)-based expanded carrier screening could detect SMN1 gene copy number without extra experiment and with high cost performance. However, its performance has not been fully evaluated. Here we conducted a systematic comparative study to evaluate the performance of three common methods. 478 samples were analyzed with multiplex ligation probe amplification (MLPA), real-time quantitative polymerase chain reaction (qPCR) and NGS, simultaneously. Taking MLPA-based results as the reference, for 0 copy, 1 copy and ≥ 2 copy SMN1 analysis with NGS, the sensitivity, specificity and precision were all 100%. Using qPCR method, the sensitivity was 100%, 97.52% and 94.30%, respectively; 98.63%, 95.48% and 100% for specificity; and 72.72%, 88.72% and 100% for precision. NGS repeatability was higher than that of qPCR. Moreover, among three methods, NGS had the lowest retest rate. Thus, NGS is a relatively more reliable method for SMN1 gene copy number detection. In expanded carrier screening, compared with the combination of multiple methods, NGS method could reduce the test cost and simplify the screening process.
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Butchbach MER. Genomic Variability in the Survival Motor Neuron Genes ( SMN1 and SMN2): Implications for Spinal Muscular Atrophy Phenotype and Therapeutics Development. Int J Mol Sci 2021; 22:ijms22157896. [PMID: 34360669 PMCID: PMC8348669 DOI: 10.3390/ijms22157896] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of infant death worldwide that is characterized by loss of spinal motor neurons leading to muscle weakness and atrophy. SMA results from the loss of survival motor neuron 1 (SMN1) gene but retention of its paralog SMN2. The copy numbers of SMN1 and SMN2 are variable within the human population with SMN2 copy number inversely correlating with SMA severity. Current therapeutic options for SMA focus on increasing SMN2 expression and alternative splicing so as to increase the amount of SMN protein. Recent work has demonstrated that not all SMN2, or SMN1, genes are equivalent and there is a high degree of genomic heterogeneity with respect to the SMN genes. Because SMA is now an actionable disease with SMN2 being the primary target, it is imperative to have a comprehensive understanding of this genomic heterogeneity with respect to hybrid SMN1–SMN2 genes generated by gene conversion events as well as partial deletions of the SMN genes. This review will describe this genetic heterogeneity in SMA and its impact on disease phenotype as well as therapeutic efficacy.
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Affiliation(s)
- Matthew E. R. Butchbach
- Center for Applied Clinical Genomics, Nemours Children’s Health Delaware, Wilmington, DE 19803, USA;
- Center for Pediatric Research, Nemours Children’s Health Delaware, Wilmington, DE 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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10
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Bowen BM, Truty R, Aradhya S, Bristow SL, Johnson BA, Morales A, Tan CA, Westbrook MJ, Winder TL, Chavez JC. SMA Identified: Clinical and Molecular Findings From a Sponsored Testing Program for Spinal Muscular Atrophy in More Than 2,000 Individuals. Front Neurol 2021; 12:663911. [PMID: 34025568 PMCID: PMC8134668 DOI: 10.3389/fneur.2021.663911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Spinal muscular atrophy (SMA) linked to chromosome 5q is an inherited progressive neuromuscular disorder with a narrow therapeutic window for optimal treatment. Although genetic testing provides a definitive molecular diagnosis that can facilitate access to effective treatments, limited awareness and other barriers may prohibit widespread testing. In this study, the clinical and molecular findings of SMA Identified—a no-charge sponsored next-generation sequencing (NGS)-based genetic testing program for SMA diagnosis—are reported. Methods: Between March 2018 and March 2020, unrelated individuals who had a confirmed or suspected SMA diagnosis or had a family history of SMA were eligible. All individuals underwent diagnostic genetic testing for SMA at clinician discretion. In total, 2,459 individuals were tested and included in this analysis. An NGS-based approach interrogated sequence and copy number of SMN1 and SMN2. Variants were confirmed by multiplex ligation-dependent probe amplification sequencing. Individuals were categorized according to genetic test results: diagnostic (two pathogenic SMN1 variants), nearly diagnostic (SMN1 exon-7 deletion with a variant of uncertain significance [VUS] in SMN1 or SMN2), indeterminate VUS (one VUS in SMN1 or SMN2), carrier (heterozygous SMN1 deletion only), or negative (no pathogenic variants or VUS in SMN1 or SMN2). Diagnostic yield was calculated. Genetic test results were analyzed based on clinician-reported clinical features and genetic modifiers (SMN2 copy number and SMN2 c.859G>C). Results: In total, 2,459 unrelated individuals (mean age 24.3 ± 23.0 years) underwent diagnostic testing. The diagnostic yield for diagnostic plus nearly diagnostic results was 31.3% (n = 771/2,459). Age of onset and clinical presentation varied considerably for individuals and was dependent on SMN2 copy number. Homozygous deletions represented the most common genetic etiology (96.2%), with sequence variants also observed in probands with clinical diagnoses of SMA. Conclusions: Using a high-yield panel test in a no-charge sponsored program early in the diagnostic odyssey may open the door for medical interventions in a substantial number of individuals with SMA. These findings have potential implications for clinical management of probands and their families.
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Keinath MC, Prior DE, Prior TW. Spinal Muscular Atrophy: Mutations, Testing, and Clinical Relevance. APPLICATION OF CLINICAL GENETICS 2021; 14:11-25. [PMID: 33531827 PMCID: PMC7846873 DOI: 10.2147/tacg.s239603] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Spinal muscular atrophy (SMA) is a heritable neuromuscular disorder that causes degeneration of the alpha motor neurons from anterior horn cells in the spinal cord, which causes severe progressive hypotonia and muscular weakness. With a carrier frequency of 1 in 40–50 and an estimated incidence of 1 in 10,000 live births, SMA is the second most common autosomal recessive disorder. Affected individuals with SMA have a homozygous loss of function of the survival motor neuron gene SMN1 on 5q13 but keep the modifying SMN2 gene. The most common mutation causing SMA is a homozygous deletion of the SMN1 exon 7, which can be readily detected and used as a sensitive diagnostic test. Because SMN2 produces a reduced number of full-length transcripts, the number of SMN2 copies can modify the clinical phenotype and as such, becomes an essential predictive factor. Population-based SMA carrier screening identifies carrier couples that may pass on this genetic disorder to their offspring and allows the carriers to make informed reproductive choices or prepare for immediate treatment for an affected child. Three treatments have recently been approved by the Food and Drug Administration (FDA). Nusinersen increases the expression levels of the SMN protein using an antisense oligonucleotide to alter splicing of the SMN2 transcript. Onasemnogene abeparvovec is a gene therapy that utilizes an adeno-associated virus serotype 9 vector to increase low functional SMN protein levels. Risdiplam is a small molecule that alters SMN2 splicing in order to increase functional SMN protein. Newborn screening for SMA has been shown to be successful in allowing infants to be treated before the loss of motor neurons and has resulted in improved clinical outcomes. Several of the recommendations and guidelines in the review are based on studies performed in the United States.
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Affiliation(s)
- Melissa C Keinath
- Pathology, University Hospitals Center for Human Genetics, Cleveland, OH, USA
| | - Devin E Prior
- Neurology, Mount Auburn Hospital, Cambridge, MA, USA
| | - Thomas W Prior
- Pathology, University Hospitals Center for Human Genetics, Cleveland, OH, USA
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Allamand V. [Incorporating spinal muscular atrophy analysis by next-generation sequencing into a comprehensive multigene panel for neuromuscular disorders]. Med Sci (Paris) 2021; 36 Hors série n° 2:51-52. [PMID: 33427636 DOI: 10.1051/medsci/2020209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Valérie Allamand
- Centre de Recherche en Myologie, Sorbonne Université, Inserm UMRS 974, Institut de Myologie, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
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