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Costa-Roger M, Blasco-Pérez L, Gerin L, Codina-Solà M, Leno-Colorado J, Gómez-García De la Banda M, Garcia-Uzquiano R, Saugier-Veber P, Drunat S, Quijano-Roy S, Tizzano EF. Complex SMN Hybrids Detected in a Cohort of 31 Patients With Spinal Muscular Atrophy. Neurol Genet 2024; 10:e200175. [PMID: 39035824 PMCID: PMC11259531 DOI: 10.1212/nxg.0000000000200175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/06/2024] [Indexed: 07/23/2024]
Abstract
Background and Objectives Spinal muscular atrophy (SMA) is a recessive neuromuscular disorder caused by the loss or presence of point pathogenic variants in the SMN1 gene. The main positive modifier of the SMA phenotype is the number of copies of the SMN2 gene, a paralog of SMN1, which only produces around 10%-15% of functional SMN protein. The SMN2 copy number is inversely correlated with phenotype severity; however, discrepancies between the SMA type and the SMN2 copy number have been reported. The presence of SMN2-SMN1 hybrids has been proposed as a possible modifier of SMA disease. Methods We studied 31 patients with SMA, followed at a single center and molecularly diagnosed by Multiplex Ligand-Dependent Probe Amplification (MLPA), with a specific next-generation sequencing protocol to investigate their SMN2 genes in depth. Hybrid characterization also included bioinformatics haplotype phasing and specific PCRs to resolve each SMN2-SMN1 hybrid structure. Results We detected SMN2-SMN1 hybrid genes in 45.2% of the patients (14/31), the highest rate reported to date. This represents a total of 25 hybrid alleles, with 9 different structures, of which only 4 are detectable by MLPA. Of particular interest were 2 patients who presented 4 SMN2-SMN1 hybrid copies each and no pure SMN2 copies, an event reported here for the first time. No clear trend between the presence of hybrids and a milder phenotype was observed, although 5 of the patients with hybrid copies showed a better-than-expected phenotype. The higher hybrid detection rate in our cohort may be due to both the methodology applied, which allows an in-depth characterization of the SMN genes and the ethnicity of the patients, mainly of African origin. Discussion Although hybrid genes have been proposed to be beneficial for patients with SMA, our work revealed great complexity and variability between hybrid structures; therefore, each hybrid structure should be studied independently to determine its contribution to the SMA phenotype. Large-scale studies are needed to gain a better understanding of the function and implications of SMN2-SMN1 hybrid copies, improving genotype-phenotype correlations and prediction of the evolution of patients with SMA.
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Affiliation(s)
- Mar Costa-Roger
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Laura Blasco-Pérez
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Lorene Gerin
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Marta Codina-Solà
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Jordi Leno-Colorado
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Marta Gómez-García De la Banda
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Rocio Garcia-Uzquiano
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Pascale Saugier-Veber
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Séverine Drunat
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Susana Quijano-Roy
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
| | - Eduardo F Tizzano
- From the Medicine Genetics Group (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Vall d'Hebron Research Institute (VHIR); Department of Clinical and Molecular Genetics (M.C.-R., L.B.-P., M.C.-S., J.L.-C., E.F.T.), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Neuromuscular Unit (L.G., M.G.-G.D.B., R.G.-U., P.S.-V., S.D., S.Q.-R.), Pediatric Neurology and ICU Department, Raymond Poincaré Hospital (UVSQ), AP-HP Université Paris-Saclay, Garches; and Laboratoire END-ICAP - UMR 1179 (INSERM/UVSQ) (S.Q.-R.), Equipe 1 Biothérapies des maladies neuromusculaires, Montigny-Le-Bretonneux, France
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Bai J, Qu Y, OuYang S, Jiao H, Wang Y, Li J, Huang W, Zhao Y, Peng X, Wang D, Jin Y, Wang H, Song F. Novel Alu-mediated deletions of the SMN1 gene were identified by ultra-long read sequencing technology in patients with spinal muscular atrophy. Neuromuscul Disord 2023; 33:382-390. [PMID: 37023488 DOI: 10.1016/j.nmd.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by biallelic variants of the survival motor neuron 1 (SMN1) gene. In this study, our aim was to make a molecular diagnosis in two patients with SMA carrying only one SMN1 copy number. Using ultra-long read sequencing (Ultra-LRS), 1415 bp deletion and 3348 bp deletion of the SMN1 gene were identified in patient 1 and the father of patient 2, respectively. Ultra-LRS revealed two novel deletions, starting from the SMN1 promoter to intron 1. It also accurately provided the location of the deletion breakpoints in the SMN1 gene: chr5 g.70,924,798-70,926,212 for a 1415 bp deletion; chr5 g.70,922,695-70,926,042 for a 3348 bp deletion. By analyzing the breakpoint junctions, we identified that these genomic sequences were composed of Alu sequences, including AluJb, AluYm1, AluSq, and AluYm1, indicating that Alu-mediated rearrangements are a mechanism of SMN1 deletion events. In addition, full-length SMN1 transcripts and SMN protein in patient 1 were significantly decreased (p < 0.01), suggesting that a 1415 bp deletion that included the transcription and translation initiation sites of the SMN1 gene had severe consequences for SMN expression. Ultra-LRS can easily distinguish highly homozygous genes compared to other detection technologies, which is useful for detecting SMN1 intragenic mutations, to quickly discover structural rearrangements and to precisely present the breakpoint positions.
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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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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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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: 28] [Impact Index Per Article: 9.3] [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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Kumar B, Barton S, Kordowska J, Eaton RB, Counihan AM, Hale JE, Comeau AM. Novel Modification of a Confirmatory SMA Sequencing Assay that Can Be Used to Determine SMN2 Copy Number. Int J Neonatal Screen 2021; 7:ijns7030047. [PMID: 34449530 PMCID: PMC8395917 DOI: 10.3390/ijns7030047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 01/04/2023] Open
Abstract
Promising treatments for spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, prompted calls for inclusion in newborn screening (NBS). In January 2018, the New England Newborn Screening Program (NENSP) began statewide screening for SMA using a tiered algorithm looking for the absence of SMN1 Exon 7. When results from the first and second tier needed reconciliation, we developed and validated a third tier DNA sequencing assay to ensure the presence or absence of SMN1 Exon 7. All nine infants referred to specialty centers through NBS showed single base substitution of c.840C>T, and were confirmed to have SMA. Further, a minor sequencing protocol modification allowed the estimation of SMN2 copy number in SMA affected patients; we developed and validated a copy-number assay yielding 100% match with seven previously characterized specimens of SMA patients. All nine SMA-affected infants found through NBS were also assayed for SMN2 copy number. Results were comparable but not 100% matched with those that were reported by independent diagnostic laboratories. In conclusion, a sequencing protocol confirms NBS findings from real-time qPCR, and its modified application allows NBS programs that have sequencing capabilities to provide SMN2 copy numbers without the need for additional instrumentation.
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Affiliation(s)
- Binod Kumar
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
- Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Correspondence: ; Tel.: +1-774-455-4657
| | - Samantha Barton
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
| | - Jolanta Kordowska
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
| | - Roger B. Eaton
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
- Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anne M. Counihan
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
| | - Jaime E. Hale
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
| | - Anne Marie Comeau
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA 01605, USA; (S.B.); (J.K.); (R.B.E.); (A.M.C.); (J.E.H.); (A.M.C.)
- Division of Genetics, Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Milligan JN, Larson JL, Filipovic-Sadic S, Laosinchai-Wolf W, Huang YW, Ko TM, Abbott KM, Lemmink HH, Toivonen M, Schleutker J, Gentile C, Van Deerlin VM, Zhu H, Latham GJ. Multisite Evaluation and Validation of a Sensitive Diagnostic and Screening System for Spinal Muscular Atrophy that Reports SMN1 and SMN2 Copy Number, along with Disease Modifier and Gene Duplication Variants. J Mol Diagn 2021; 23:753-764. [PMID: 33798739 DOI: 10.1016/j.jmoldx.2021.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
Spinal muscular atrophy is a severe autosomal recessive disease caused by disruptions in the SMN1 gene. The nearly identical SMN2 gene copy number is associated with disease severity. SMN1 duplication markers, such as c.∗3+80T>G and c.∗211_∗212del, can assess residual carrier risk. An SMN2 disease modifier (c.859G>C) can help inform prognostic outcomes. The emergence of multiple precision gene therapies for spinal muscular atrophy requires accurate and rapid detection of SMN1 and SMN2 copy numbers to enable early treatment and optimal patient outcomes. We developed and evaluated a single-tube PCR/capillary electrophoresis assay system that quantifies SMN1/2 copy numbers and genotypes three additional clinically relevant variants. Analytical validation was performed with human cell lines and whole blood representing varying SMN1/2 copies on four capillary electrophoresis instrument models. In addition, four independent laboratories used the assay to test 468 residual clinical genomic DNA samples. The results were ≥98.3% concordant with consensus SMN1/2 exon 7 copy numbers, determined using multiplex ligation-dependent probe amplification and droplet digital PCR, and were 100% concordant with Sanger sequencing for the three variants. Furthermore, copy number values were 98.6% (SMN1) and 97.1% (SMN2) concordant to each laboratory's own reference results.
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Affiliation(s)
| | | | | | | | - Ya-Wen Huang
- GenePhile Bioscience Laboratory, Ko's Obstetrics and Gynecology Clinic, Taipei City, Taiwan
| | - Tsang-Ming Ko
- GenePhile Bioscience Laboratory, Ko's Obstetrics and Gynecology Clinic, Taipei City, Taiwan
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Henny H Lemmink
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Minna Toivonen
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Johanna Schleutker
- Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland; Institute of Biomedicine, University of Turku, Turun yliopisto, Finland
| | - Caren Gentile
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Huiping Zhu
- Research and Development, Asuragen Inc., Austin, Texas
| | - Gary J Latham
- Research and Development, Asuragen Inc., Austin, Texas
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8
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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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9
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Park JE, Yun SA, Roh EY, Yoon JH, Shin S, Ki CS. Carrier Frequency of Spinal Muscular Atrophy in a Large-scale Korean Population. Ann Lab Med 2020; 40:326-330. [PMID: 32067433 PMCID: PMC7054693 DOI: 10.3343/alm.2020.40.4.326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/29/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by progressive proximal muscle weakness and atrophy. Given the recent introduction of gene therapies, knowledge of the SMA carrier frequency in various populations has become important for developing screening programs for this disease. In total, 1,581 anonymous DNA samples from an umbilical cord blood bank were tested for SMN1 and SMN2 gene copies using a multiplex ligation-dependent probe amplification assay. Twenty-nine of the 1,581 newborns [1.83%; 95% confidence interval (CI), 1.25–2.66%] were SMA carriers with one copy of SMN1, and no homozygous SMN1 deletion was detected. The carrier frequency in this population was estimated to be 1,834 per 100,000 (95% CI, 1,254–2,659) or 1 in 55 (95% CI, 1/79–1/38). Our data indicate that SMA carriers are not uncommon in the Korean population and may serve as a reference for designing a population screening program in Korea.
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Affiliation(s)
- Jong Eun Park
- Department of Laboratory Medicine, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Boramae Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Boramae Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Boramae Hospital, Seoul National University College of Medicine, Seoul, Korea.
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10
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Hryshchenko NV, Yurchenko AA, Karaman HS, Livshits LA. Genetic Modifiers of the Spinal Muscular Atrophy Phenotype. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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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: 68] [Impact Index Per Article: 17.0] [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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12
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Transmission characteristics of SMN from 227 spinal muscular atrophy core families in China. J Hum Genet 2020; 65:469-473. [PMID: 32051521 DOI: 10.1038/s10038-020-0730-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/05/2020] [Accepted: 01/26/2020] [Indexed: 11/09/2022]
Abstract
To define the relationship between the survival motor neuron 1 gene (SMN1) and SMN2, and explore the variability of these two genes within the generations, SMN1 and SMN2 copy numbers were determined for 227 SMA families. The association analysis indicated that there was a negative correlation between the copy number of SMN1 and SMN2 (Spearman = -0.472, P < 0.001) in 227 SMA children and 454 of their parents. The average SMN copies from father and mother in each SMA family were used to represent the copy number in the parent's generation. Subsequently, SMN transmission analysis showed that the similar distribution trend of SMN1 and SMN2 copy number was not only in the SMA children and their parents' generation but also in the non-SMA families. Moreover, when the SMN2 copy number was one in the parent's generation, 75% of their SMA children had type I and 25% of them had type II/III. However, when the SMN2 copies were three in the parent's generation, all of their SMA children were type II/III. Therefore, the diversity of SMN copies was mostly inherited and the SMN2 copy number in the parent's generation could predict the disease severity of SMA children to some extent.
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13
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Chien YH, Chiang SC, Weng WC, Lee NC, Lin CJ, Hsieh WS, Lee WT, Jong YJ, Ko TM, Hwu WL. Presymptomatic Diagnosis of Spinal Muscular Atrophy Through Newborn Screening. J Pediatr 2017; 190:124-129.e1. [PMID: 28711173 DOI: 10.1016/j.jpeds.2017.06.042] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/15/2017] [Accepted: 06/16/2017] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To demonstrate the feasibility of presymptomatic diagnosis of spinal muscular atrophy (SMA) through newborn screening (NBS). STUDY DESIGN We performed a screening trial to assess all newborns who underwent routine newborn metabolic screening at the National Taiwan University Hospital newborn screening center between November 2014 and September 2016. A real-time polymerase chain reaction (RT-PCR) genotyping assay for the SMN1/SMN2 intron 7 c.888+100A/G polymorphism was performed to detect homozygous SMN1 deletion using dried blood spot (DBS) samples. Then the exon 7 c.840C>T mutation and SMN2 copy number were determined by both droplet digital PCR (ddPCR) using the original screening DBS and multiplex ligation-dependent probe amplification (MLPA) using a whole blood sample. RESULTS Of the 120 267 newborns, 15 tested positive according to the RT-PCR assay. The DBS ddPCR assay excluded 8 false-positives, and the other 7 patients were confirmed by the MLPA assay. Inclusion of the second-tier DBS ddPCR screening assay resulted in a positive prediction value of 100%. The incidence of SMA was 1 in 17 181 (95% CI, 1 in 8323 to 1 in 35 468). Two of the 3 patients with 2 copies of SMN2 and all 4 patients with 3 or 4 copies of SMN2 were asymptomatic at the time of diagnosis. Five of the 8 false-positives were caused by intragenic recombination between SMN1 and SMN2. CONCLUSION Newborn screening can detect patients affected by SMA before symptom onset and enable early therapeutic intervention. A combination of a RT-PCR and a second-tier ddPCR can accurately diagnose SMA from DBS samples with no false-positives. TRIAL REGISTRATION ClinicalTrials.gov NCT02123186.
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Affiliation(s)
- Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Shu-Chuan Chiang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chin Weng
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ching-Jie Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wu-Shiun Hsieh
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yuh-Jyh Jong
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics and Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Tsang-Ming Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics and Gynecology, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan.
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14
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Spinal muscular atrophy carriers with two SMN1 copies. Brain Dev 2017; 39:851-860. [PMID: 28676237 DOI: 10.1016/j.braindev.2017.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder. Over 95% of SMA patients have homozygous deletions of the SMA-causative gene, SMN1. Thus, SMA carriers are usually diagnosed based on SMN1 copy number, with one copy indicating SMA carrier status. However, two SMN1 copies do not always exclude carrier status. In this study, we identified SMA carriers with two SMN1 copies. SUBJECTS AND METHODS From 33 families, 65 parents of genetically confirmed SMA patients were tested to determine SMA carrier status. Molecular genetic analyses, including multiplex ligation-dependent probe amplification (MLPA) assay, were performed using blood samples from family members. RESULTS Of the 65 parents, three parents from three families had two SMN1 copies. Accordingly, the frequency of carriers with two SMN1 copies was 4.6%. Two of these families were further studied. Patient 1 was homozygous for SMN1 deletion. Patient 1's mother had two SMN1 copies on one chromosome, with deletion of SMN1 on the other chromosome ([2+0] genotype). Patient 1 inherited SMN1-deleted chromosomes from both parents. Patient 2 was compound heterozygous for two SMN1 mutations: whole-gene deletion and intragenic missense mutation, c.826T>C (p.Tyr276His). Patient 2's father had two SMN1 copies with the same intragenic mutation in one copy ([1+1d] genotype, d intragenic mutation). Patient 2 inherited the chromosome with an SMN1 mutation from the father and SMN1-deleted chromosome from the mother. CONCLUSION SMA carriers with two SMN1 copies may be rare, but its possibility should be taken into consideration in carrier testing and counseling for SMA families or population-based carrier screening.
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15
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Verhaart IEC, Robertson A, Wilson IJ, Aartsma-Rus A, Cameron S, Jones CC, Cook SF, Lochmüller H. Prevalence, incidence and carrier frequency of 5q-linked spinal muscular atrophy - a literature review. Orphanet J Rare Dis 2017; 12:124. [PMID: 28676062 PMCID: PMC5496354 DOI: 10.1186/s13023-017-0671-8] [Citation(s) in RCA: 362] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022] Open
Abstract
Spinal muscular atrophy linked to chromosome 5q (SMA) is a recessive, progressive, neuromuscular disorder caused by bi-allelic mutations in the SMN1 gene, resulting in motor neuron degeneration and variable presentation in relation to onset and severity. A prevalence of approximately 1-2 per 100,000 persons and incidence around 1 in 10,000 live births have been estimated with SMA type I accounting for around 60% of all cases. Since SMA is a relatively rare condition, studies of its prevalence and incidence are challenging. Most published studies are outdated and therefore rely on clinical rather than genetic diagnosis. Furthermore they are performed in small cohorts in small geographical regions and only study European populations. In addition, the heterogeneity of the condition can lead to delays and difficulties in diagnosing the condition, especially outside of specialist clinics, and contributes to the challenges in understanding the epidemiology of the disease. The frequency of unaffected, heterozygous carriers of the SMN1 mutations appears to be higher among Caucasian and Asian populations compared to the Black (Sub-Saharan African ancestry) population. However, carrier frequencies cannot directly be translated into incidence and prevalence, as very severe (death in utero) and very mild (symptom free in adults) phenotypes carrying bi-allelic SMN1 mutations exist, and their frequency is unknown. More robust epidemiological data on SMA covering larger populations based on accurate genetic diagnosis or newborn screening would be helpful to support planning of clinical studies, provision of care and therapies and evaluation of outcomes.
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Affiliation(s)
- Ingrid E. C. Verhaart
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Agata Robertson
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ian J. Wilson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Annemieke Aartsma-Rus
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Shona Cameron
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
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16
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Wei X, Tan H, Yang P, Zhang R, Tan B, Zhang Y, Mei L, Liang D, Wu L. Notable Carrier Risks for Individuals Having Two Copies of SMN1 in Spinal Muscular Atrophy Families with 2-copy Alleles: Estimation Based on Chinese Meta-analysis Data. J Genet Couns 2016; 26:72-78. [DOI: 10.1007/s10897-016-9980-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 05/24/2016] [Indexed: 01/29/2023]
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17
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Fang P, Li L, Zeng J, Zhou WJ, Wu WQ, Zhong ZY, Yan TZ, Xie JS, Huang J, Lin L, Zhao Y, Xu XM. Molecular characterization and copy number of SMN1, SMN2 and NAIP in Chinese patients with spinal muscular atrophy and unrelated healthy controls. BMC Musculoskelet Disord 2015; 16:11. [PMID: 25888055 PMCID: PMC4328246 DOI: 10.1186/s12891-015-0457-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is caused by SMN1 dysfunction, and the copy number of SMN2 and NAIP can modify the phenotype of SMA. The aim of this study was to analyze the copy numbers and gene structures of SMA-related genes in Chinese SMA patients and unrelated healthy controls. METHODS Forty-two Chinese SMA patients and two hundred and twelve unrelated healthy Chinese individuals were enrolled in our study. The copy numbers and gene structures of SMA-related genes were measured by MLPA assay. RESULTS We identified a homozygous deletion of SMN1 in exons 7 and 8 in 37 of 42 patients (88.1%); the other 5 SMA patients (11.9%) had a single copy of SMN1 exon 8. The proportions of the 212 unrelated healthy controls with different copy numbers for the normal SMN1 gene were 1 copy in 4 individuals (1.9%), 2 copies in 203 (95.7%) and 3 copies in 5 (2.4%). Three hybrid SMN genes and five genes that lack partial sequences were found in SMA patients and healthy controls. Distributions of copy numbers for normal SMN2 and NAIP were significantly different (P < 0.001) in people with and without SMA. CONCLUSION The copy numbers and gene structures of SMA-related genes were different in Chinese SMA patients and healthy controls.
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Affiliation(s)
- Ping Fang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
| | - Liang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
| | - Jian Zeng
- Department of Clinical Laboratory, The Fuzhou General Hospital, Nanjing Military Command, Fuzhou, Fujian, People's Republic of China.
| | - Wan-Jun Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
| | - Wei-Qing Wu
- Prenatal Diagnosis Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, People's Republic of China.
| | - Ze-Yan Zhong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
| | - Ti-Zhen Yan
- Liuzhou Key Laboratory of birth defects prevention and control, Liuzhou Municipal Maternity and Child Healthcare Hospital, Liuzhou, Guangxi, People's Republic of China.
| | - Jian-Sheng Xie
- Prenatal Diagnosis Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, People's Republic of China.
| | - Jing Huang
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong, People's Republic of China.
| | - Li Lin
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
| | - Ying Zhao
- Prenatal Diagnostic Center, Dongguan Maternal and Children Health Hospital, Dongguan, Guangdong, People's Republic of China.
| | - Xiang-Min Xu
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Avenue North1838, Guangzhou, Guangdong, People's Republic of China.
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18
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Kekou K, Sofocleous C, Konstantinidis G, Fryssira H, Mavrou A, Kitsiou S, Kanavakis E. SMA prenatal diagnosis: a modified protocol to help differentiation between deletions and gene conversion. Mol Cell Probes 2014; 29:71-3. [PMID: 25308401 DOI: 10.1016/j.mcp.2014.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 09/17/2014] [Accepted: 10/01/2014] [Indexed: 11/28/2022]
Abstract
In SMA, unusual findings such as deletions restricted only to SMN1 exon 8, inspite of honozygous SMN1 exons 7-8 deletions in the family, may obscure final diagnosis. Application of a modified PCR procedure allowed discrimination between a deletion or a gene conversion event in a case of prenatal diagnosis.
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Affiliation(s)
- K Kekou
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece.
| | - C Sofocleous
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
| | - G Konstantinidis
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
| | - H Fryssira
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
| | - A Mavrou
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
| | - S Kitsiou
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
| | - E Kanavakis
- Department of Medical Genetics, Athens University, "Aghia Sophia" Children's Hospital, Hellas, Greece
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19
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Hwang HS, Shin GW, Jung GY, Jung GY. A simple and precise diagnostic method for spinal muscular atrophy using a quantitative SNP analysis system. Electrophoresis 2014; 35:3402-7. [PMID: 25113913 DOI: 10.1002/elps.201400207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/21/2014] [Accepted: 08/04/2014] [Indexed: 11/06/2022]
Abstract
A simple and precise diagnostic method for spinal muscular atrophy (SMA) using high-resolution CE-based single-strand conformation polymorphism (CE-SSCP) was developed in this study. SMA is a common genetic disorder caused by an abnormality in the relative copy numbers of SMN1 and its centromeric copy SMN2, which differ only in two nucleotides, namely at exons 7 and 8. Therefore, the precise discrimination of the differences in sequence as well as their relative quantities is crucial for the diagnosis of SMA. Multiplex ligation-dependent probe amplification and sequence-sensitive DNA separation using hydroxyethyl cellulose and hydroxypropyl cellulose blended polymer matrix are currently the available methods used in the diagnosis of SMA. However, these methods are limited by their extended hybridization step and low resolution. In this study, the simultaneous discrimination of SMN exons 7 and 8 was successfully demonstrated using high-resolution CE-SSCP. Unlike the previously reported alternative method, single base differing amplicons were baseline-separated because of its extraordinary resolution, thus providing accurate and precise quantification of each paralog.
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Affiliation(s)
- Hee Sung Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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20
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Sangaré M, Hendrickson B, Sango HA, Chen K, Nofziger J, Amara A, Dutra A, Schindler AB, Guindo A, Traoré M, Harmison G, Pak E, Yaro FN, Bricceno K, Grunseich C, Chen G, Boehm M, Zukosky K, Bocoum N, Meilleur KG, Daou F, Bagayogo K, Coulibaly YI, Diakité M, Fay MP, Lee HS, Saad A, Gribaa M, Singleton AB, Maiga Y, Auh S, Landouré G, Fairhurst RM, Burnett BG, Scholl T, Fischbeck KH. Genetics of low spinal muscular atrophy carrier frequency in sub-Saharan Africa. Ann Neurol 2014; 75:525-32. [PMID: 24515897 PMCID: PMC4112719 DOI: 10.1002/ana.24114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022]
Abstract
Objective Spinal muscular atrophy (SMA) is one of the most common severe hereditary diseases of infancy and early childhood in North America, Europe, and Asia. SMA is usually caused by deletions of the survival motor neuron 1 (SMN1) gene. A closely related gene, SMN2, modifies the disease severity. SMA carriers have only 1 copy of SMN1 and are relatively common (1 in 30–50) in populations of European and Asian descent. SMN copy numbers and SMA carrier frequencies have not been reliably estimated in Malians and other sub‐Saharan Africans. Methods We used a quantitative polymerase chain reaction assay to determine SMN1 and SMN2 copy numbers in 628 Malians, 120 Nigerians, and 120 Kenyans. We also explored possible mechanisms for SMN1 and SMN2 copy number differences in Malians, and investigated their effects on SMN mRNA and protein levels. Results The SMA carrier frequency in Malians is 1 in 209, lower than in Eurasians. Malians and other sub‐Saharan Africans are more likely to have ≥3 copies of SMN1 than Eurasians, and more likely to lack SMN2 than Europeans. There was no evidence of gene conversion, gene locus duplication, or natural selection from malaria resistance to account for the higher SMN1 copy numbers in Malians. High SMN1 copy numbers were not associated with increased SMN mRNA or protein levels in human cell lines. Interpretation SMA carrier frequencies are much lower in sub‐Saharan Africans than in Eurasians. This finding is important to consider in SMA genetic counseling in individuals with black African ancestry. Ann Neurol 2014;75:525–532
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Affiliation(s)
- Modibo Sangaré
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD; Institute of Biomedical Sciences, George Washington University, Washington, DC
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21
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Survival of motor neuron protein downregulates miR-9 expression in patients with spinal muscular atrophy. Kaohsiung J Med Sci 2014; 30:229-34. [PMID: 24751385 DOI: 10.1016/j.kjms.2013.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 09/26/2013] [Indexed: 11/23/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a lethal hereditary disease caused by homozygous absence of the survival of the motor neuron (SMN) 1 gene (SMN1), and it is the leading genetic cause of infant mortality. The severity of SMA is directly correlated with SMN protein levels in affected patients; however, the cellular regulatory mechanisms for SMN protein expression are not completely understood. In this study, we investigated the regulatory effects between SMN expression and miR-9a, a downstream noncoding small RNA. Using an inducible SMN short hairpin RNA interference (shRNAi) system in NSC 34 and human skin fibroblast cells, cellular miR-9 levels and SMN protein repression were time-dependently upregulated. Conversely, cellular miR-9 levels decreased when HeLa cells were transfected with SMN protein fused with green fluorescent protein. In SMA-like mice spinal cords and human primary skin fibroblasts isolated from patients with different degrees of SMA, human SMN exhibited a disease severity-dependent decrease, whereas cellular miR-9 levels increased. These results clearly suggested that cellular SMN proteins regulated miR-9 expression and that miR-9 expression was related to SMA severity. Thus, miR-9 may be a marker for SMA prognosis.
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Nurputra DK, Lai PS, Harahap NIF, Morikawa S, Yamamoto T, Nishimura N, Kubo Y, Takeuchi A, Saito T, Takeshima Y, Tohyama Y, Tay SKH, Low PS, Saito K, Nishio H. Spinal muscular atrophy: from gene discovery to clinical trials. Ann Hum Genet 2013; 77:435-63. [PMID: 23879295 DOI: 10.1111/ahg.12031] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 04/26/2013] [Indexed: 12/25/2022]
Abstract
Spinal muscular atrophy (SMA) is a common neuromuscular disorder with autosomal recessive inheritance, resulting in the degeneration of motor neurons. The incidence of the disease has been estimated at 1 in 6000-10,000 newborns with a carrier frequency of 1 in 40-60. SMA is caused by mutations of the SMN1 gene, located on chromosome 5q13. The gene product, survival motor neuron (SMN) plays critical roles in a variety of cellular activities. SMN2, a homologue of SMN1, is retained in all SMA patients and generates low levels of SMN, but does not compensate for the mutated SMN1. Genetic analysis demonstrates the presence of homozygous deletion of SMN1 in most patients, and allows screening of heterozygous carriers in affected families. Considering high incidence of carrier frequency in SMA, population-wide newborn and carrier screening has been proposed. Although no effective treatment is currently available, some treatment strategies have already been developed based on the molecular pathophysiology of this disease. Current treatment strategies can be classified into three major groups: SMN2-targeting, SMN1-introduction, and non-SMN targeting. Here, we provide a comprehensive and up-to-date review integrating advances in molecular pathophysiology and diagnostic testing with therapeutic developments for this disease including promising candidates from recent clinical trials.
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Affiliation(s)
- Dian K Nurputra
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
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