1
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Wang N, Jiao K, He J, Zhu B, Cheng N, Sun J, Chen L, Chen W, Gong L, Qiao K, Xi J, Wu Q, Zhao C, Zhu W. Diagnosis of Challenging Spinal Muscular Atrophy Cases with Long-Read Sequencing. J Mol Diagn 2024; 26:364-373. [PMID: 38490302 DOI: 10.1016/j.jmoldx.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder primarily caused by the deletion or mutation of the survival motor neuron 1 (SMN1) gene. This study assesses the diagnostic potential of long-read sequencing (LRS) in three patients with SMA. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of multiplex ligation-dependent probe amplification, LRS, and PCR across the breakpoint. The third patient, born to a consanguineous family, bore four copies of hybrid SMN genes. LRS determined the genomic structures, indicating two distinct hybrids of SMN2 exon 7 and SMN1 exon 8. However, a discrepancy was found between the SMN1/SMN2 ratio interpretations by LRS (0:2) and multiplex ligation-dependent probe amplification (0:4), which suggested a limitation of LRS in SMA diagnosis. In conclusion, this newly adapted long PCR-based third-generation sequencing introduces an additional avenue for SMA diagnosis.
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Affiliation(s)
- Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Chen
- Department of Neurology, Nantong First People's Hospital, Nantong, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Lingyun Gong
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qihan Wu
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, National Health Commission Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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2
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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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Yalcintepe S, Karal Y, Demir S, Atli EI, Atli E, Eker D, Mail C, Zhuri D, Guler HS, Gurkan H. The Frequency of SMN1, SMN2 Copy Numbers in 246 Turkish Cases Analyzed with MLPA Method. Glob Med Genet 2023; 10:117-122. [PMID: 37332684 PMCID: PMC10275673 DOI: 10.1055/s-0043-1770055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
This study aimed to define the copy numbers of SMN1 and SMN2 genes and the diagnosis rate and carrier frequency of spinal muscular atrophy (SMA) in the Thrace region of Turkey. In this study, the frequency of deletions in exons 7 and 8 in the SMN1 gene and SMN2 copy numbers were investigated. A total of 133 cases with the preliminary diagnosis of SMA and 113 cases with the suspicion of being an SMA carrier from independent families were analyzed by multiplex ligation-dependent probe amplification method for SMN1 and SMN2 gene copy numbers. SMN1 homozygous deletions were detected in 34 patients (25.5%) of 133 cases with the suspicion of SMA. Cases diagnosed with SMA type I was 41.17% (14/34), 29.4% (10/34) with type II, 26.4% (9/34) with type III, and 2.94% (1/34) with type IV. The SMA carrier rate was 46.01% in 113 cases. In 34 SMA cases, SMN2 copy numbers were: two copies - 28 cases (82.3%), three copies - 6 cases (17.6%). SMN2 homozygous deletions were detected in 15% (17/113) of carrier analysis cases. The consanguinity rate of the parents was 23.5% in SMA diagnosed cases. In this study, we had a 25.5% of SMA diagnosis rate and 46% SMA carrier frequency. The current study also showed the relatively low consanguinity rate of the Thrace region, with 23.5% according to the east of Turkey.
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Affiliation(s)
- Sinem Yalcintepe
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Yasemin Karal
- Department of Pediatric Neurology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Emine Ikbal Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Engin Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Damla Eker
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Cisem Mail
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Drenushe Zhuri
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hazal Sezginer Guler
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
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5
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Chen X, Harting J, Farrow E, Thiffault I, Kasperaviciute D, Hoischen A, Gilissen C, Pastinen T, Eberle MA. Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing. Am J Hum Genet 2023; 110:240-250. [PMID: 36669496 PMCID: PMC9943720 DOI: 10.1016/j.ajhg.2023.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/21/2023] Open
Abstract
Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7%-3.0%). Extending beyond simple copy-number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.
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Affiliation(s)
| | | | - Emily Farrow
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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6
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Sypniewski M, Kresa D, Dobosz P, Topolski P, Kotuła L, Sztromwasser P, Mroczek M. Population WGS-based spinal muscular atrophy carrier screening in a cohort of 1076 healthy Polish individuals. J Appl Genet 2023; 64:135-139. [PMID: 36417168 DOI: 10.1007/s13353-022-00737-5] [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: 08/24/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Spinal muscular atrophy is a severe neuromuscular disorder with an autosomal recessive inheritance pattern. The disease-causing gene is SMN1, and its paralogue, SMN2, is a disease course modifier. Both genes SMN1 and SMN2 show over 99.9% sequence identity and a high rate of crossing over in the genomic region. Due to this reason, SMN1/SMN2 is usually excluded from the whole-genome sequencing (WGS) analysis and investigated with traditional methods, such as MLPA and qPCR. Recently, novel bioinformatic algorithms dedicated to analyzing this particular genomic region have been developed. Here, we analyze the SMN1/SMN2 genomic region with a dedicated program, SMNCopyNumberCaller. We report a similar prevalence of SMN1 gene deletion carrier status (1 per 41 people) to published data from the Polish population (1 per 35 people). Additionally, SMNCopyNumberCaller can identify SMN2 CNVs and SMN2Δ7-8 present in 153 healthy Polish individuals. Two other programs for the CNV analysis in standard genomic regions were not able to provide reliable results. Using WGS-based tools for SMN1/2 genomic region analysis is not only an efficient method in terms of time but will also enable more complex analysis such screening for markers related with a silent carrier status and identification of further genetic modifiers. Although still an experimental method, soon WGS-based SMN1/SMN2 carrier identification may become a standard method for patients screened with WGS for other purposes.
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Affiliation(s)
- Mateusz Sypniewski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Dominika Kresa
- Faculty of Bioscience Engineering, KU Leuven, Louvain, Belgium
| | - Paula Dobosz
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Piotr Topolski
- Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507, Warsaw, Poland
| | - Lidia Kotuła
- Zakład Genetyki Klinicznej, Uniwersytet Medyczny w Lublinie, Lublin, Poland
| | | | - Magdalena Mroczek
- Center for Cardiovascular Genetics & Gene Diagnostics, Foundation for People With Rare Diseases, 8952, Schlieren-Zurich, Switzerland.
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7
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Hassan HA, Fahmy NA, El-Bagoury NM, Eissa NR, Sharaf-Eldin WE, Issa MY, Zaki MS, Essawi ML. MLPA analysis for molecular diagnosis of spinal muscular atrophy and correlation of 5q13.2 genes with disease phenotype in Egyptian patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00373-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease representing the most prevalent monogenic cause of infant mortality. It results from the loss of SMN1 gene, but retention of its paralog SMN2 whose copy number can modulate the disease severity and guide the therapeutic regimen.
Methods
For SMA molecular analysis, 236 unrelated Egyptian patients were enrolled at our institution. The Multiplex ligation-dependent probe amplification analysis (MLPA) was applied to investigate the main genetic defect in the enrolled patients (SMN1 loss) and to determine a possible genotype–phenotype correlation between the copy number of other genes in the SMN locus (5q13.2) and disease severity in Egyptian patients with SMA. A small cohort of healthy subjects (n = 57) was also included to investigate the possible differences in the distributions of SMN2 and NAIP genes between patients and healthy individuals.
Results
Disease diagnosis was confirmed in only 148 patients (62.7%) highlighting the clinical overlapping of the disease and emphasizing the importance of molecular diagnosis. In patients with homozygous SMN1 loss, the disease was mediated by gene deletion and conversion in 135 (91.2%) and 13 (8.8%) patients, respectively. In the study cohort, SMN2 and NAIP copy numbers were inversely correlated with disease severity. However, no significant association was detected between GTF2H2A and SERF1B copy numbers and patient phenotype. Significant differences were demonstrated in the copy numbers of SMN2 and NAIP between SMA patients and healthy subjects.
Conclusion
Molecular analysis of SMA is essential for disease diagnosis. Consistent with previous studies on other populations, there is a close relationship between SMN2 and NAIP copy numbers and clinical phenotype. Additionally, potential differences in these two genes distributions are existing between patients and healthy subjects. National program for carrier screening should be established as a preventive disease strategy. On the other hand, neonatal testing would provide accurate estimation for disease incidence.
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8
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Jin W, Yang Z, Tang X, Wang X, Huang Y, Hui C, Yao J, Luan J, Tang S, Wu S, Jin S, Ding C. Simultaneous quantification of SMN1 and SMN2 copy numbers by MALDI-TOF mass spectrometry for spinal muscular atrophy genetic testing. Clin Chim Acta 2022; 532:45-52. [DOI: 10.1016/j.cca.2022.05.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/22/2022] [Indexed: 11/25/2022]
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9
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Prodanov T, Bansal V. Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing. Nat Commun 2022; 13:3221. [PMID: 35680869 PMCID: PMC9184528 DOI: 10.1038/s41467-022-30930-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
The human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than 150 duplicated genes that overlap LCRs have been implicated in monogenic and complex human diseases. We describe a computational tool, Parascopy, for estimating the aggregate and paralog-specific copy number of duplicated genes using whole-genome sequencing (WGS). Parascopy is an efficient method that jointly analyzes reads mapped to different repeat copies without the need for global realignment. It leverages multiple samples to mitigate sequencing bias and to identify reliable paralogous sequence variants (PSVs) that differentiate repeat copies. Analysis of WGS data for 2504 individuals from diverse populations showed that Parascopy is robust to sequencing bias, has higher accuracy compared to existing methods and enables prioritization of pathogenic copy number changes in duplicated genes.
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Affiliation(s)
- Timofey Prodanov
- Bioinformatics and Systems Biology Graduate Program, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Vikas Bansal
- Department of Pediatrics, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA.
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10
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Tan C, Yan Y, Guo N, Wang F, Wang S, Zhu L, Wang Y, Ma Y, Guo Y. Single-Tube Multiplex Digital Polymerase Chain Reaction Assay for Molecular Diagnosis and Prediction of Severity of Spinal Muscular Atrophy. Anal Chem 2022; 94:3517-3525. [PMID: 35137581 DOI: 10.1021/acs.analchem.1c04403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease characterized by the degeneration of motor neurons and progressive muscle atrophy. Accurate detection of SMN1 and SMN2 copy numbers is essential for SMA diagnosis, carrier screening, disease severity prediction, therapy, and prognosis. However, a method for SMN1 and SMN2 copy number determination that is simultaneously accurate, simple, rapid, multitargeted, and applicable to various samples has not previously been reported. Here, we developed a single-tube multiplex digital polymerase chain reaction (dPCR) assay for simultaneous determination of the copy numbers of SMN1 exons 7 and 8 and SMN2 exons 7 and 8. A total of 317 clinical samples, including peripheral blood, amniotic fluid, chorionic villus, buccal swabs, and dried blood spots, were collected to evaluate the performance of this dPCR-based assay. The test results were accurate for all the clinical samples. Our assay is accurate, rapid, easy to handle, and applicable to many types of samples and uses a small amount of DNA; it is a powerful tool for SMA molecular diagnosis, large-scale screening, and disease severity assessment.
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Affiliation(s)
- Chianru Tan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Na Guo
- TargetingOne Corporation, Beijing 100190, China
| | - Fang Wang
- TargetingOne Corporation, Beijing 100190, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | | | - Yipeng Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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The Importance of Digging into the Genetics of SMN Genes in the Therapeutic Scenario of Spinal Muscular Atrophy. Int J Mol Sci 2021; 22:ijms22169029. [PMID: 34445733 PMCID: PMC8396600 DOI: 10.3390/ijms22169029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
After 26 years of discovery of the determinant survival motor neuron 1 and the modifier survival motor neuron 2 genes (SMN1 and SMN2, respectively), three SMN-dependent specific therapies are already approved by FDA and EMA and, as a consequence, worldwide SMA patients are currently under clinical investigation and treatment. Bi-allelic pathogenic variants (mostly deletions) in SMN1 should be detected in SMA patients to confirm the disease. Determination of SMN2 copy number has been historically employed to correlate with the phenotype, predict disease evolution, stratify patients for clinical trials and to define those eligible for treatment. In view that discordant genotype-phenotype correlations are present in SMA, besides technical issues with detection of SMN2 copy number, we have hypothesized that copy number determination is only the tip of the iceberg and that more deepen studies of variants, sequencing and structures of the SMN2 genes are necessary for a better understanding of the disease as well as to investigate possible influences in treatment responses. Here, we highlight the importance of a comprehensive approach of SMN1 and SMN2 genetics with the perspective to apply for better prediction of SMA in positive neonatal screening cases and early diagnosis to start treatments.
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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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Bos JW, Groen EJN, Wadman RI, Curial CAD, Molleman NN, Zegers M, van Vught PWJ, Snetselaar R, Vijzelaar R, van der Pol WL, van den Berg LH. SMN1 Duplications Are Associated With Progressive Muscular Atrophy, but Not With Multifocal Motor Neuropathy and Primary Lateral Sclerosis. NEUROLOGY-GENETICS 2021; 7:e598. [PMID: 34169148 PMCID: PMC8220964 DOI: 10.1212/nxg.0000000000000598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/02/2021] [Indexed: 11/30/2022]
Abstract
Objective To assess the association between copy number (CN) variation in the survival motor neuron (SMN) locus and multifocal motor neuropathy (MMN), progressive muscular atrophy (PMA), and primary lateral sclerosis (PLS) susceptibility and to determine the association of SMN1 and SMN2 CN with MMN, PMA, and PLS disease course. Methods In this monocenter study, we used multiplex ligation-dependent probe amplification to determine SMN1 and SMN2 CN in Dutch patients with MMN, PMA, and PLS and controls. We stratified clinical parameters for SMN1 and SMN2 CN. We analyzed SMN1 and SMN2 exons 1–6, intron 6, and exon 8 CN to study the genetic architecture of SMN1 duplications. Results SMN1 and SMN2 CN were determined in 132 patients with MMN, 150 patients with PMA, 104 patients with PLS, and 956 control subjects. MMN and PLS were not associated with CN variation in SMN1 or SMN2. By contrast, patients with PMA more often than controls carried SMN1 duplications (≥3 SMN1 copies, 12.0% vs 5.0%, odds ratio 2.69 (1.43–4.91), p 0.0020). SMN1 and SMN2 CN status was not associated with MMN, PLS, or PMA disease course. In case of SMN1 exon 7 duplications, exons 1–6, exon 8, and introns 6 and 7 were also duplicated, suggesting full SMN1 duplications. Conclusions SMN1 duplications are associated with PMA, but not with PLS and MMN. SMN1 duplications in PMA are balanced duplications. The results of this study highlight the primary effect of altered SMN CN on lower motor neurons.
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Affiliation(s)
- Jeroen W Bos
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Ewout J N Groen
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Renske I Wadman
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Chantall A D Curial
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Naomi N Molleman
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Marinka Zegers
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Paul W J van Vught
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Reinier Snetselaar
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Raymon Vijzelaar
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - W Ludo van der Pol
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery (J.W.B., E.J.N.G., R.I.W., C.A.D.C., W.L.v.d.P., L.H.v.d.B.), UMC Utrecht Brain Center, Utrecht University, Utrecht, the Netherlands; and MRC Holland (N.N.M., M.Z., P.W.J.v.V., R.S., R.V.), Amsterdam, the Netherlands
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Blasco-Pérez L, Paramonov I, Leno J, Bernal S, Alias L, Fuentes-Prior P, Cuscó I, Tizzano EF. Beyond copy number: A new, rapid, and versatile method for sequencing the entire SMN2 gene in SMA patients. Hum Mutat 2021; 42:787-795. [PMID: 33739559 PMCID: PMC8252042 DOI: 10.1002/humu.24200] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/13/2021] [Accepted: 03/11/2021] [Indexed: 01/16/2023]
Abstract
Spinal muscular atrophy (SMA) is caused by bi‐allelic loss or pathogenic variants in the SMN1 gene. SMN2, the highly homologous copy of SMN1, is considered the major phenotypic modifier of the disease. Determination of SMN2 copy number is essential to establish robust genotype–phenotype correlations and predict disease evolution, to stratify patients for clinical trials, as well as to define those eligible for treatment. Discordant genotype–phenotype correlations are not uncommon in SMA, some of which are due to intragenic SMN2 variants that may influence the amount of complete SMN transcripts and, therefore, of full‐length SMN protein. Detection of these variants is crucial to predict SMA phenotypes in the present scenario of therapeutic advances and with the perspective of SMA neonatal screening and early diagnosis to start treatments. Here, we present a novel, affordable, and versatile method for complete sequencing of the SMN2 gene based on long‐range polymerase chain reaction and next‐generation sequencing. The method was validated by analyzing samples from 53 SMA patients who lack SMN1, allowing to characterize paralogous, rare variants, and single‐nucleotide polymorphisms of SMN2 as well as SMN2–SMN1 hybrid genes. The method identifies partial deletions and can be adapted to determine rare pathogenic variants in patients with at least one SMN1 copy.
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Affiliation(s)
- Laura Blasco-Pérez
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Ida Paramonov
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Jordi Leno
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Barcelona, Spain
| | - Sara Bernal
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
| | - Laura Alias
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
| | - Pablo Fuentes-Prior
- Molecular Bases of Disease, Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Ivon Cuscó
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)
| | - Eduardo F Tizzano
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Barcelona, Spain
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Niba ETE, Nishio H, Wijaya YOS, Lai PS, Tozawa T, Chiyonobu T, Yamadera M, Okamoto K, Awano H, Takeshima Y, Saito T, Shinohara M. Clinical phenotypes of spinal muscular atrophy patients with hybrid SMN gene. Brain Dev 2021; 43:294-302. [PMID: 33036822 DOI: 10.1016/j.braindev.2020.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/26/2020] [Accepted: 09/08/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a neuromuscular disease caused by homozygous deletion of SMN1 exons 7 and 8. However, exon 8 is retained in some cases, where SMN2 exon 7 recombines with SMN1 exon 8, forming a hybrid SMN gene. It remains unknown how the hybrid SMN gene contribute to the SMA phenotype. METHOD We analyzed 515 patients with clinical suspicion for SMA. SMN1 exons 7 and 8 deletion was detected by PCR followed by enzyme digestion. Hybrid SMN genes were further analyzed by nucleotide sequencing. SMN2 copy number was determined by real-time PCR. RESULTS SMN1 exon 7 was deleted in 228 out of 515 patients, and SMN1 exon 8 was also deleted in 204 out of the 228 patients. The remaining 24 patients were judged to carry a hybrid SMN gene. In the patients with SMN1 exon 7 deletion, the frequency of the severe phenotype was significantly lower in the patients with hybrid SMN gene than in the patients without hybrid SMN gene. However, as for the distribution of SMN2 exon 7 copy number among the clinical phenotypes, there was no significant difference between both groups of SMA patients with or without hybrid SMN gene. CONCLUSION Hybrid SMN genes are not rare in Japanese SMA patients, and it appears to be associated with a less severe phenotype. The phenotype of patients with hybrid SMN gene was determined by the copy number of SMN2 exon 7, as similarly for the patients without hybrid SMN gene.
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Affiliation(s)
- Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan; Faculty of Medical Rehabilitation, Kobe Gakuin University, Kobe, Japan.
| | - Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Takenori Tozawa
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Tomohiro Chiyonobu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Misaki Yamadera
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan.
| | - Kentaro Okamoto
- Department of Pediatrics, Ehime Prefectural Imabari Hospital, Ehime, Japan.
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya, Japan.
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan.
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan.
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Detection of SMN1 to SMN2 gene conversion events and partial SMN1 gene deletions using array digital PCR. Neurogenetics 2021; 22:53-64. [PMID: 33415588 DOI: 10.1007/s10048-020-00630-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/26/2020] [Indexed: 12/15/2022]
Abstract
Proximal spinal muscular atrophy (SMA), a leading genetic cause of infant death worldwide, is an early-onset motor neuron disease characterized by loss of α-motor neurons and associated muscle atrophy. SMA is caused by deletion or other disabling mutations of survival motor neuron 1 (SMN1) but retention of one or more copies of the paralog SMN2. Within the SMA population, there is substantial variation in SMN2 copy number (CN); in general, those individuals with SMA who have a high SMN2 CN have a milder disease. Because SMN2 functions as a disease modifier, its accurate CN determination may have clinical relevance. In this study, we describe the development of array digital PCR (dPCR) to quantify SMN1 and SMN2 CNs in DNA samples using probes that can distinguish the single nucleotide difference between SMN1 and SMN2 in exon 8. This set of dPCR assays can accurately and reliably measure the number of SMN1 and SMN2 copies in DNA samples. In a cohort of SMA patient-derived cell lines, the assay confirmed a strong inverse correlation between SMN2 CN and disease severity. We can detect SMN1-SMN2 gene conversion events in DNA samples by comparing CNs at exon 7 and exon 8. Partial deletions of SMN1 can also be detected with dPCR by comparing CNs at exon 7 or exon 8 with those at intron 1. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 CNs from SMA samples as well as identify gene conversion events and partial deletions of SMN1.
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Cuscó I, Bernal S, Blasco-Pérez L, Calucho M, Alias L, Fuentes-Prior P, Tizzano EF. Practical guidelines to manage discordant situations of SMN2 copy number in patients with spinal muscular atrophy. NEUROLOGY-GENETICS 2020; 6:e530. [PMID: 33324756 PMCID: PMC7713720 DOI: 10.1212/nxg.0000000000000530] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/29/2020] [Indexed: 12/26/2022]
Abstract
Objective Assessment of SMN2 copy number in patients with spinal muscular atrophy (SMA) is essential to establish careful genotype-phenotype correlations and predict disease evolution. This issue is becoming crucial in the present scenario of therapeutic advances with the perspective of SMA neonatal screening and early diagnosis to initiate treatment, as this value is critical to stratify patients for clinical trials and to define those eligible to receive medication. Several technical pitfalls and interindividual variations may account for reported discrepancies in the estimation of SMN2 copy number and establishment of phenotype-genotype correlations. Methods We propose a management guide based on a sequence of specified actions once SMN2 copy number is determined for a given patient. Regardless of the method used to estimate the number of SMN2 copies, our approach focuses on the manifestations of the patient to recommend how to proceed in each case. Results We defined situations according to SMN2 copy number in a presymptomatic scenario of screening, in which we predict the possible evolution, and when a symptomatic patient is genetically confirmed. Unexpected discordant cases include patients having a single SMN2 copy but noncongenital disease forms, 2 SMN2 copies compatible with type II or III SMA, and 3 or 4 copies of the gene showing more severe disease than expected. Conclusions Our proposed guideline would help to systematically identify discordant SMA cases that warrant further genetic investigation. The SMN2 gene, as the main modifier of SMA phenotype, deserves a more in-depth study to provide more accurate genotype-phenotype correlations.
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Affiliation(s)
- Ivon Cuscó
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Sara Bernal
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Laura Blasco-Pérez
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Maite Calucho
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Laura Alias
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Pablo Fuentes-Prior
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Eduardo F Tizzano
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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Jiang L, Lin R, Gallagher S, Zayac A, Butchbach MER, Hung P. Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument. Sci Rep 2020; 10:19892. [PMID: 33199817 PMCID: PMC7670453 DOI: 10.1038/s41598-020-76893-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 01/30/2023] Open
Abstract
Digital PCR (dPCR) technology has been proven to be highly sensitive and accurate in detecting copy number variations (CNV). However, a higher-order multiplexing dPCR assay for measuring SMN1 and SMN2 copy numbers in spinal muscular atrophy (SMA) samples has not been reported. Described here is a rapid multiplex SMA dPCR genotyping assay run on a fully integrated dPCR instrument with five optical channels. The hydrolysis probe-based multiplex dPCR assay quantifies SMN1, SMN2, and the total SMN (SMN1 + SMN2) while using RPPH1 gene as an internal reference control. The quadruplex assay was evaluated with characterized control DNA samples and validated with 15 blinded clinical samples from a previously published study. SMN1 and SMN2 copy numbers were completely concordant with previous results for both the control and blinded samples. The dPCR-based SMA copy number determination was accomplished in 90 min with a walk-away workflow identical to real-time quantitative PCR (qPCR). In summary, presented here is a simple higher-order multiplexing solution on a novel digital PCR platform to meet the growing demand for SMA genotyping and prognostics.
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Affiliation(s)
- Lingxia Jiang
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA.
| | - Robert Lin
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Steve Gallagher
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Andrew Zayac
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paul Hung
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
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19
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Lopez-Lopez D, Loucera C, Carmona R, Aquino V, Salgado J, Pasalodos S, Miranda M, Alonso Á, Dopazo J. SMN1 copy-number and sequence variant analysis from next-generation sequencing data. Hum Mutat 2020; 41:2073-2077. [PMID: 33058415 PMCID: PMC7756735 DOI: 10.1002/humu.24120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/17/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022]
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular autosomal recessive disorder affecting 1/10,000 live births. Most SMA patients present homozygous deletion of SMN1, while the vast majority of SMA carriers present only a single SMN1 copy. The sequence similarity between SMN1 and SMN2, and the complexity of the SMN locus makes the estimation of the SMN1 copy-number by next-generation sequencing (NGS) very difficult. Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data. Moreover, SMAca takes advantage of the knowledge of certain variants specific to SMN1 duplication to also identify silent carriers. This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation. This combination makes it especially suitable to be integrated into production NGS pipelines. Source code and documentation are available at https://www.github.com/babelomics/SMAca.
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Affiliation(s)
- Daniel Lopez-Lopez
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain.,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain.,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain
| | - Rosario Carmona
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Virginia Aquino
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Josefa Salgado
- Genomic Medicine, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, Spain
| | - Sara Pasalodos
- Genomic Medicine, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, Spain
| | - María Miranda
- Genomic Medicine, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, Spain
| | - Ángel Alonso
- Genomic Medicine, Navarrabiomed, Complejo Hospitalario de Navarra (CHN)-Universidad Pública de Navarra (UPNA), IDISNA, Pamplona, Spain
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain.,Computational Systems Medicine, Institute of Biomedicine of Seville (IBIS), Hospital Virgen del Rocio, Sevilla, Spain.,Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), FPS, Hospital Virgen del Rocío, Sevilla, Spain.,FPS/ELIXIR-es, Hospital Virgen del Rocío, Sevilla, Spain
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20
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Kirschner J, Becker J, Schorling D, Pechmann A, Wirth B. Author response: Discrepancy in redetermination of SMN2 copy numbers in children with SMA. Neurology 2020; 95:145. [PMID: 32690781 DOI: 10.1212/wnl.0000000000009908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Wadman RI, Jansen MD, Stam M, Wijngaarde CA, Curial CAD, Medic J, Sodaar P, Schouten J, Vijzelaar R, Lemmink HH, van den Berg LH, Groen EJN, van der Pol WL. Intragenic and structural variation in the SMN locus and clinical variability in spinal muscular atrophy. Brain Commun 2020; 2:fcaa075. [PMID: 32954327 PMCID: PMC7425299 DOI: 10.1093/braincomms/fcaa075] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 11/15/2022] Open
Abstract
Clinical severity and treatment response vary significantly between patients with spinal muscular atrophy. The approval of therapies and the emergence of neonatal screening programmes urgently require a more detailed understanding of the genetic variants that underlie this clinical heterogeneity. We systematically investigated genetic variation other than SMN2 copy number in the SMN locus. Data were collected through our single-centre, population-based study on spinal muscular atrophy in the Netherlands, including 286 children and adults with spinal muscular atrophy Types 1–4, including 56 patients from 25 families with multiple siblings with spinal muscular atrophy. We combined multiplex ligation-dependent probe amplification, Sanger sequencing, multiplexed targeted resequencing and digital droplet polymerase chain reaction to determine sequence and expression variation in the SMN locus. SMN1, SMN2 and NAIP gene copy number were determined by multiplex ligation-dependent probe amplification. SMN2 gene variant analysis was performed using Sanger sequencing and RNA expression analysis of SMN by droplet digital polymerase chain reaction. We identified SMN1–SMN2 hybrid genes in 10% of spinal muscular atrophy patients, including partial gene deletions, duplications or conversions within SMN1 and SMN2 genes. This indicates that SMN2 copies can vary structurally between patients, implicating an important novel level of genetic variability in spinal muscular atrophy. Sequence analysis revealed six exonic and four intronic SMN2 variants, which were associated with disease severity in individual cases. There are no indications that NAIP1 gene copy number or sequence variants add value in addition to SMN2 copies in predicting the clinical phenotype in individual patients with spinal muscular atrophy. Importantly, 95% of spinal muscular atrophy siblings in our study had equal SMN2 copy numbers and structural changes (e.g. hybrid genes), but 60% presented with a different spinal muscular atrophy type, indicating the likely presence of further inter- and intragenic variabilities inside as well as outside the SMN locus. SMN2 gene copies can be structurally different, resulting in inter- and intra-individual differences in the composition of SMN1 and SMN2 gene copies. This adds another layer of complexity to the genetics that underlie spinal muscular atrophy and should be considered in current genetic diagnosis and counselling practices.
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Affiliation(s)
- Renske I Wadman
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Marc D Jansen
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Marloes Stam
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Camiel A Wijngaarde
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Chantall A D Curial
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jelena Medic
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Peter Sodaar
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jan Schouten
- MRC Holland BV, 1057 DL Amsterdam, the Netherlands
| | | | - Henny H Lemmink
- Department of Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Leonard H van den Berg
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ewout J N Groen
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - W Ludo van der Pol
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
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22
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Chen X, Sanchis-Juan A, French CE, Connell AJ, Delon I, Kingsbury Z, Chawla A, Halpern AL, Taft RJ, Bentley DR, Butchbach MER, Raymond FL, Eberle MA. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med 2020; 22:945-953. [PMID: 32066871 PMCID: PMC7200598 DOI: 10.1038/s41436-020-0754-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/21/2022] Open
Abstract
Purpose Spinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics. Methods We developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2. Results We characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers. Conclusion This SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.
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Affiliation(s)
| | - Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Courtney E French
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Andrew J Connell
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Isabelle Delon
- East Midlands and East of England NHS Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | | | | | | | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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