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Ma K, Zhang K, Chen D, Wang C, Abdalla M, Zhang H, Tian R, Liu Y, Song L, Zhang X, Liu F, Liu G, Wang D. Real-world evidence: Risdiplam in a patient with spinal muscular atrophy type I with a novel splicing mutation and one SMN2 copy. Hum Mol Genet 2024; 33:1120-1130. [PMID: 38520738 PMCID: PMC11190614 DOI: 10.1093/hmg/ddae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Spinal muscular atrophy (SMA), which results from the deletion or/and mutation in the SMN1 gene, is an autosomal recessive neuromuscular disorder that leads to weakness and muscle atrophy. SMN2 is a paralogous gene of SMN1. SMN2 copy number affects the severity of SMA, but its role in patients treated with disease modifying therapies is unclear. The most appropriate individualized treatment for SMA has not yet been determined. Here, we reported a case of SMA type I with normal breathing and swallowing function. We genetically confirmed that this patient had a compound heterozygous variant: one deleted SMN1 allele and a novel splice mutation c.628-3T>G in the retained allele, with one SMN2 copy. Patient-derived sequencing of 4 SMN1 cDNA clones showed that this intronic single transversion mutation results in an alternative exon (e)5 3' splice site, which leads to an additional 2 nucleotides (AG) at the 5' end of e5, thereby explaining why the patient with only one copy of SMN2 had a mild clinical phenotype. Additionally, a minigene assay of wild type and mutant SMN1 in HEK293T cells also demonstrated that this transversion mutation induced e5 skipping. Considering treatment cost and goals of avoiding pain caused by injections and starting treatment as early as possible, risdiplam was prescribed for this patient. However, the patient showed remarkable clinical improvements after treatment with risdiplam for 7 months despite carrying only one copy of SMN2. This study is the first report on the treatment of risdiplam in a patient with one SMN2 copy in a real-world setting. These findings expand the mutation spectrum of SMA and provide accurate genetic counseling information, as well as clarify the molecular mechanism of careful genotype-phenotype correlation of the patient.
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Affiliation(s)
- Kai Ma
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
- Department of neurology, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Kaihui Zhang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Defang Chen
- The Office of operation management committee, Central Hospital Affiliated to Shandong First Medical University, Jiefang road NO. 105, Jinan, SD 250022, PR China
| | - Chuan Wang
- Science, Education and Foreign Affairs Section, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Mohnad Abdalla
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Haozheng Zhang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Rujin Tian
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Yang Liu
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
- Ophthalmology department, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Li Song
- Pediatric Hematology and Oncology, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Xinyi Zhang
- Intensive Care Unit, The Second People’s Hospital of Shandong Province, Duanxing west road NO. 4, Jinan, SD 250022, PR China
| | - Fangfang Liu
- Department of Ultrasound, Central Hospital Affiliated to Shandong First Medical University, Jiefang road NO. 105, Jinan, SD 250022, PR China
| | - Guohua Liu
- Ophthalmology department, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
| | - Dong Wang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jingshi road NO. 23976, Jinan, SD 250022, PR China
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Rabea F, El Naofal M, Chekroun I, Khalaf M, Zaabi NA, AlZaabi K, ElHalik M, Dash S, El Saba Y, Ali A, Abraham S, Fathi K, Shekhy J, Aswad SG, Elbashir H, Alkuraya F, Loney T, Alsheikh-Ali A, Khayat AA, Abou Tayoun A. Spinal muscular atrophy genetic epidemiology and the case for premarital genomic screening in Arab populations. COMMUNICATIONS MEDICINE 2024; 4:119. [PMID: 38879606 PMCID: PMC11180197 DOI: 10.1038/s43856-024-00548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a fatal autosomal recessive disorder for which several treatment options, including a gene therapy, have become available. SMA incidence has not been well-characterized in most Arab countries where rates of consanguinity are high. Understanding SMA disease epidemiology has important implications for screening, prevention, and treatment in those populations. METHODS We perform SMA diagnostic testing in a clinical multi-national patient cohort (N = 171) referred for hypotonia and/or muscle weakness. In addition, we carry out genetic newborn screening for SMA on 1502 healthy Emirati newborns to estimate the carrier frequency and incidence of the disease in the United Arab Emirates. RESULTS Patients referred for SMA genetic testing are mostly Arabs (82%) representing 18 countries. The overall diagnostic yield is 33.9%, which is higher (>50%) for certain nationalities. Most patients (71%) has two SMN2 copies and earlier disease onset. For the first time, we estimate SMA carrier frequency (1.3%) and incidence of the disease (1 in 7122 live births) in the United Arab Emirates. Using birth and marriage rates in two Arab populations (United Arab Emirates and Saudi Arabia), as well as disease incidence in both countries, we show that, besides preventing new cases, premarital genetic screening could potentially result in around $8 to $324 million annual cost savings, respectively, relative to postnatal treatment. CONCLUSIONS The SMA carrier frequency and incidence we document suggests high potential benefit for universal implementation of premarital genomic screening for a wide range of recessive disorders in Arab populations.
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Affiliation(s)
- Fatma Rabea
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Maha El Naofal
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Ikram Chekroun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Mona Khalaf
- Neonatology Department, Al Qassimi Women's & Children's Hospital, Emirates Health Services, Sharjah, UAE
| | - Nuha Al Zaabi
- Pediatric Department, Fujairah Hospital, Emirates Health Services, Fujairah, UAE
| | - Khawla AlZaabi
- Pediatric Department, Kalba Hospital, Emirates Health Services, Sharjah, UAE
| | - Mahmoud ElHalik
- Neonatal Section, Latifa Women & Children Hospital, Dubai Health, Dubai, UAE
| | - Swarup Dash
- Neonatal Section, Latifa Women & Children Hospital, Dubai Health, Dubai, UAE
| | - Yaser El Saba
- Department of Neonatology, Dubai Hospital, Dubai Health, Dubai, UAE
| | - Azhari Ali
- Neonatology Department, Umm Al Quwain Hospital, Emirates Health Services, Umm Al Quwain, UAE
| | - Smitha Abraham
- Department of Neonatology, Abdullah Bin Omran Hospital, Emirates Health Services, Ras Al Khaimah, UAE
| | - Khansa Fathi
- Neonatology Department, Al Dhaid Hospital, Emirates Health Services, Sharjah, UAE
| | - Jwan Shekhy
- Neonatology Department, Khorfakkan Hospital, Emirates Health Services, Sharjah, UAE
| | - Saad G Aswad
- General-Obs/Gyno Clinic, Tawam Hospital, Al Ain City, Abu Dhabi, UAE
| | - Haitham Elbashir
- Neurosceince Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE
| | - Fowzan Alkuraya
- Departement of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tom Loney
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE
| | | | - Ahmad Abou Tayoun
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Health, Dubai, UAE.
- Al Jalila Genomics Center of Excellence, Al Jalila Children's Specialty Hospital, Dubai Health, Dubai, UAE.
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Tan L, Qi Y, Zhao P, Cheng L, Yu G, Zhao D, Song YX, Xiang YG. Clinical application value of pre-pregnancy carrier screening in Chinese Han childbearing population. Mol Genet Genomic Med 2024; 12:e2425. [PMID: 38562051 PMCID: PMC10985407 DOI: 10.1002/mgg3.2425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/29/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND To explore the clinical application value of pre-conception expanded carrier screening (PECS) in the Chinese Han ethnicity population of childbearing age. METHODS The results of genetic testing of infertile parents who underwent PECS in the Reproductive Medicine Center of the Second Affiliated Hospital of Zhengzhou University, China, from September 2019 to December 2021, were retrospectively analyzed. The carrier rate of single gene disease, the detection rate of high-risk parents, and the clinical outcome of high-risk parents were statistically analyzed. RESULTS A total of 1372 Chinese Han ethnicity patients underwent PECS, among which 458 patients underwent the extended 108-gene test, their overall carrier rate was 31.7%, and the detection rate of high-risk parents was 0.3%. The highest carrier rates were SLC22A (2.4%), ATP7B (2.4%), MMACHC (2.2%), PAH (1.8%), GALC (1.8%), MLC1 (1.3%), UNC13D (1.1%), CAPN3 (1.1%), and PKHD1 (1.1%). There were 488 women with fragile X syndrome-FMR1 gene detection, and 6 patients (1.2%) had FMR1 gene mutation. A total of 426 patients were screened for spinal muscular atrophy-SMN1, and the carrier rate was 3.5%, and the detection rate of parents' co-carrier was 0.5%. CONCLUSION Monogenic recessive hereditary diseases had a high carrier rate in the population. Pre-pregnancy screening could provide good prenatal and postnatal care guidance for patients and preimplantation genetic testing for monogenic/single gene disorders (PGT-M) and prenatal diagnosis could provide more precise reproductive choices for high-risk parents.
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Affiliation(s)
- Li Tan
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yuefan Qi
- Department of Medical ImagingThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Peijuan Zhao
- Department of Reproductive GeneticsPingdingshan Maternal and Child Health HospitalPingdingshanChina
| | - LanLan Cheng
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Guo Yu
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Dongmei Zhao
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yu Xia Song
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yun Gai Xiang
- Department of Reproductive Medical CenterThe Second Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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Zhang L, Mo J, Zhou L, Xu X, Xu Z, Zhang L, Wu W. Carrier screening for spinal muscular atrophy in 22913 Chinese reproductive age women. Mol Genet Genomic Med 2024; 12:e2359. [PMID: 38284446 PMCID: PMC10795085 DOI: 10.1002/mgg3.2359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND To determine the carrier frequency of, and evaluate a carrier screening program for, spinal muscular atrophy (SMA) in reproductive age women in Shenzhen area. METHODS A staged screening procedure was used to perform carrier screening for SMA in 22,913 Chinese reproductive age women between 2019 and 2022 in Shenzhen area of China. First, the copy number of exon 7 in the SMN1 gene were detected in women of reproductive age using real-time quantitative polymerase chain reaction. If SMA carriers were detected, their spouses were then recommended to test. Prenatal diagnosis was carried out in couples who were both carriers. RESULTS A total of 389 women were found to be SMA carriers (1.70%, 95% CI: 1.53%-1.87%), indicating the carrier prevalence was approximately 1:59. Despite the proportion of nonpregnant women increased from 37.96% in 2019 to 58.18% in 2022 (p < 0.05) among the 22,913 reproductive age women, the recall rate of spouses was still not high (62.21%, 95% CI: 57.39%-67.03%). Eight partners were found to be SMA carriers and two fetuses were determined to have SMA with no copies of the SMN1 gene. CONCLUSION Although the acceptability and awareness of SMA carrier screening in Chinese population has increased in recent years, it still fails to reach the ideal expectation. Our experience may provide a basis for and facilitate the popularization of SMA carrier screening in Shenzhen area.
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Affiliation(s)
- Lijun Zhang
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Junluan Mo
- Shenzhen Center for Chronic Disease ControlShenzhenGuangdongChina
| | - Lu Zhou
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Xiaoxin Xu
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Zhiyong Xu
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Lei Zhang
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
| | - Weiqing Wu
- Department of Medical GeneticsAffiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical UniversityShenzhenGuangdongChina
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5
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Ibrahim F, Velayutham D, Alsharshani M, AlAlami U, AlDewik M, Abuarja T, Al Rifai H, Al‐Dewik NI. Studying carrier frequency of spinal muscular atrophy in the State of Qatar and comparison to other ethnic groups: Pilot study. Mol Genet Genomic Med 2023; 11:e2184. [PMID: 37964750 PMCID: PMC10724519 DOI: 10.1002/mgg3.2184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive disease caused by mutations and deletions in SMN1 at exon 7. The carrier frequency for SMN1 mutations ranges from 2 to 4% in the general population. METHODS We examined allelic, genotypic relatedness and copy number (CN) variations and frequencies of SMN1 and SMN2, in 13,426 samples from Qatar biobank (QBB) to provide a precise estimation of SMA carrier frequency in Qatar in comparison to other populations. RESULTS The SMA carrier frequency was found to be (2.8%) and the rs143838139 was found in 491/13426 (3.66%) of individuals. The SNP rs121909192, which is a pathogenic risk factor, was found in 321/13500 (2.38%). In Addition 242/11379 (2.13%) had two copies of SMN1 and the rs143838139, which may explain the (2 + 0) silent carrier. Additionally, two participants were found to be SMA type 4 with 0 and 4 copy numbers in SMN1 and SMN2, respectively. CONCLUSION The SMA carrier frequency in Qatar was found to be comparable to Saudi Arabia and Caucasians. The likely pathogenic variant, rs121909192, was found to be significantly higher when compering with other in our study. The rs143838139 variant, which has a strong association with the silent carrier genotype, has been found. Consequently, testing for this SNP may enhance the precision of evaluating the likelihood of a patient having an affected child. We conclude that the frequency of SMA carriers varies within the Qatar population and other ethnic groups.
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Affiliation(s)
- Faisal Ibrahim
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine and Pathology (DLMP)Hamad Medical Corporation (HMC)DohaQatar
| | - Dinesh Velayutham
- Liberal Arts and ScienceHamad Bin Khalifa University (HBKU)DohaQatar
| | - Mohamed Alsharshani
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine and Pathology (DLMP)Hamad Medical Corporation (HMC)DohaQatar
| | - Usama AlAlami
- School of Life ScienceManipal Academy of Higher Education (MAHE)DubaiUAE
| | - Manar AlDewik
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
| | - Tala Abuarja
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
| | - Hilal Al Rifai
- Department of Pediatrics and Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness and Research CenterHamad Medical CorporationDohaQatar
| | - Nader I. Al‐Dewik
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
- Department of Pediatrics and Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness and Research CenterHamad Medical CorporationDohaQatar
- Translational Research Institute (TRI)Hamad Medical Corporation (HMC)DohaQatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS)Hamad Bin Khalifa University (HBKU)DohaQatar
- College of Health and Life SciencesHamad Bin Khalifa University, Education CityDohaQatar
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Al Jumah M, Al Rajeh S, Eyaid W, Al‐Jedai A, Al Mudaiheem H, Al Shehri A, Hussein M, Al Abdulkareem I. Spinal muscular atrophy carrier frequency in Saudi Arabia. Mol Genet Genomic Med 2022; 10:e2049. [PMID: 36062320 PMCID: PMC9651606 DOI: 10.1002/mgg3.2049] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/23/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Spinal Muscular Dystrophy (SMA) is one of the leading causes of death in infants and young children from heritable diseases. Although no large-scale popultion-based studies have been done in Saudi Arabia, it is reported that the incidence of SMA is higher in the Saudi population partly because of the high degree of consanguineous marriages. METHODS The final analysis included 4198 normal volunteers aged between 18 and 25 years old, 54.7% males, and 45.3% females. Whole blood was spotted directly from finger pricks onto IsoCode StixTM and genomic DNA was isolated using one triangle from the machine. To discern the SMN1 copy number independently from SMN2, Multiplex PCR with Dral restriction fragment analysis was completed. We used the carrier frequency and population-level data to estimate the prevalence of SMA in the population using the life-table method. RESULTS This data analysis showed the presence of one copy of the SMN1 gene in 108 samples and two copies in 4090 samples, which resulted from a carrier frequency of 2.6%. The carrier frequency was twofold in females reaching 3.7% compared to 1.6% in males. 27% of participants were children of first-cousin marriages. We estimated the birth incidence of SMA to be 32 per 100,000 birth and the total number of people living with SMA in the Kingdom of Saudi Arabia to be 2265 of which 188 are type I, 1213 are type II, and 8,64 are type III. CONCLUSION The SMA carrier rate of 2.6% in Saudi control subjects is slightly higher than the reported global frequency of 1.25 to 2% with links to the high degree of consanguinity.
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Affiliation(s)
- Mohammed Al Jumah
- King Abdullah International Medical Research CentreRiyadhSaudi Arabia,Neurology DepartmentKing Fahd Medical City HospitalRiyadhSaudi Arabia
| | - Saad Al Rajeh
- Neurology DivisionKing Saud UniversityRiyadhSaudi Arabia
| | - Wafaa Eyaid
- Department of Pediatrics, Genetics divisionKing Abdul Aziz Medical CityRiyadhSaudi Arabia
| | - Ahmed Al‐Jedai
- Deputyship of Therapeutic AffairsMinistry of HealthRiyadhSaudi Arabia
| | | | - Ali Al Shehri
- Neuromuscular Integrated practice Unit, Neuroscience CentreKing Faisal Specialist Hospital and Research CentreRiyadhSaudi Arabia
| | - Mohammed Hussein
- Neurology DepartmentKing Fahd Medical City HospitalRiyadhSaudi Arabia
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Megarbane A, Bizzari S, Deepthi A, Sabbagh S, Mansour H, Chouery E, Hmaimess G, Jabbour R, Mehawej C, Alame S, Hani A, Hasbini D, Ghanem I, Koussa S, Al-Ali MT, Obeid M, Talea DB, Lefranc G, Levy N, Leturcq F, El Hayek S, Delague V, Urtizberea A. A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort. J Neuromuscul Dis 2021; 9:193-210. [PMID: 34602496 PMCID: PMC8842757 DOI: 10.3233/jnd-210652] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Clinical and molecular data on the occurrence and frequency of inherited neuromuscular disorders (NMD) in the Lebanese population is scarce. OBJECTIVE This study aims to provide a retrospective overview of hereditary NMDs based on our clinical consultations in Lebanon. METHODS Clinical and molecular data of patients referred to a multi-disciplinary consultation for neuromuscular disorders over a 20-year period (1999-2019) was reviewed. RESULTS A total of 506 patients were diagnosed with 62 different disorders encompassing 10 classes of NMDs. 103 variants in 49 genes were identified. In this cohort, 81.4%of patients were diagnosed with motor neuron diseases and muscular dystrophies, with almost half of these described with spinal muscular atrophy (SMA) (40.3%of patients). We estimate a high SMA incidence of 1 in 7,500 births in Lebanon. Duchenne and Becker muscular dystrophy were the second most frequently diagnosed NMDs (17%of patients). The latter disorders were associated with the highest number of variants (39) identified in this study. A highly heterogeneous presentation of Limb Girdle Muscular Dystrophy and Charcot-Marie-Tooth disease was notably identified. The least common disorders (5.5%of patients) involved congenital, metabolic, and mitochondrial myopathies, congenital myasthenic syndromes, and myotonic dystrophies. A review of the literature for selected NMDs in Lebanon is provided. CONCLUSIONS Our study indicates a high prevalence and underreporting of heterogeneous forms of NMDs in Lebanon- a major challenge with many novel NMD treatments in the pipeline. This report calls for a regional NMD patient registry.
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Affiliation(s)
- Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.,Institut Jérôme Lejeune, Paris, France
| | | | | | - Sandra Sabbagh
- Department of Pediatrics, Hôtel Dieu de France Hospital, Beirut, Lebanon
| | - Hicham Mansour
- Department of Pediatrics, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Ghassan Hmaimess
- Department of Pediatrics, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Rosette Jabbour
- Department of Neurology, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Saada Alame
- Department of Neuropediatrics, Lebanese University, Beirut, Lebanon
| | - Abeer Hani
- Departments of Pediatrics and Neurology, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Dana Hasbini
- Department of Pediatric Neurology, Rafic Hariri University Hospital, Beirut, Lebanon
| | - Ismat Ghanem
- Department of Orthopedics, Hotel Dieu de France Hospital, Beirut, Lebanon
| | - Salam Koussa
- Department of Neurology, Geitaoui Lebanese University Hospital, Beirut, Lebanon
| | | | - Marc Obeid
- Genetic laboratory, American University of Science and Technology, Lebanon
| | - Diana Bou Talea
- Genetic laboratory, American University of Science and Technology, Lebanon
| | - Gerard Lefranc
- Institut de Génétique Humaine, UMR 9002 CNRS-Université de Montpellier, France
| | - Nicolas Levy
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
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8
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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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Nilay M, Moirangthem A, Saxena D, Mandal K, Phadke SR. Carrier frequency of SMN1-related spinal muscular atrophy in north Indian population: The need for population based screening program. Am J Med Genet A 2020; 185:274-277. [PMID: 33051992 DOI: 10.1002/ajmg.a.61918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/21/2020] [Accepted: 09/27/2020] [Indexed: 11/08/2022]
Abstract
Chromosome 5q related Spinal muscular atrophy (SMA) is an autosomal recessive, progressive, neuromuscular disorder most commonly caused by homozygous deletion of exon 7 or exon 7 and 8 of SMN1 gene. Being the leading genetic cause of infant mortality, studies of its prevalence and incidence are necessary. Carrier testing for the common pathogenic variant for SMA is offered to the couples visiting our tertiary care hospital in North India. Subjects were tested for SMA carrier status by Multiplex Ligation-dependent Probe amplification (MLPA) technique for deletion of exons 7 and 8 of SMN1 gene. The retrospective data of individuals tested for SMA carrier status in last 4 years (2016-2019) was evaluated. Six hundred and six individuals without family history of SMA or carrier of SMA who were subjected to MLPA based screening for SMA carrier status were included in the study. The carrier frequency of SMN1 deletion (deletion of exon 7 and/or exon 8) was found to be 1 in 38 (16 out of 606). The catchment area of our medical genetics clinic covering the state of Uttar Pradesh (16.5% of Indian population according to censusindia.gov.in, 2011) and neighboring states, showing SMA carrier frequency of 1:38 in a cohort with no prior positive family history has important significance for policy making.
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Affiliation(s)
- Mayank Nilay
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Hassan HA, Zaki MS, Issa MY, El-Bagoury NM, Essawi ML. Genetic pattern of SMN1, SMN2, and NAIP genes in prognosis of SMA patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-019-0044-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Spinal muscular atrophy (SMA) is the most common autosomal recessive disorder in humans after cystic fibrosis. It is classified into five clinical grades based on age of onset and severity of the disease. Although SMN1 was identified as the SMA disease-determining gene, modifier genes mapped to 5q13 were affirmed to play a crucial role in determination of disease severity and used as a target for SMA therapy. In this study, we determined SMN2 copy number and NAIP deletion status in SMA Egyptian patients with different clinical phenotypes and had homozygous deletion of SMN1. We aimed at finding a prognostic genetic pattern including SMN1, SMN2, and NAIP gene genotypes to determine the clinical SMA type of the patient to help in genetic counseling and prenatal diagnosis.
Results
Copy number variations (CNVs) of exon 7 of SMN2 gene were significantly decreased with the increase in disease severity. Homozygous deletion of exon 5 of NAIP was detected in 60% (12/20) of type I SMA and in 73% (8/11) of type III SMA cases. Combining the data of the SMN2 and NAIP genes showed 8 genotypes. Patients with D2 genotype (0 copies of NAIP and 2 copies of SMN2) were likely to have type I SMA. Type II SMA patients mostly had no homozygous deletion of NAIP and 2 copies of SMN2. However, patients with N3 genotype (> 1 copy of NAIP and 3 copies of SMN2) and patients with D3 genotype (0 copies of NAIP and > 3 copies of SMN2) had type III SMA.
Conclusion
SMN2 and NAIP are the most important modifier genes whose copy numbers can affect the severity of SMA. We concluded that the combination of modifier genes to provide prognostic genetic pattern for phenotype determination is preferable than using CNVs of exon 7 of SMN2 gene only. CNVs of exon 7 of SMN2 are of high importance to predict patients’ response to genetic therapy. On the other hand, deletion of exon5 of NAIP gene alone is not a sufficient predictor of SMA severity.
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11
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Adadi N, Sahli M, Egéa G, Ratbi I, Taoudi M, Zniber L, Jdioui W, El Mouatassim S, Sefiani A. Post-mortem diagnosis of Pompe disease by exome sequencing in a Moroccan family: a case report. J Med Case Rep 2018; 12:322. [PMID: 30371346 PMCID: PMC6205784 DOI: 10.1186/s13256-018-1855-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 09/21/2018] [Indexed: 11/21/2022] Open
Abstract
Background Pompe disease is an autosomal recessive lysosomal storage disorder characterized by progressive myopathy with proximal muscle weakness, respiratory muscle dysfunction, and cardiomyopathy. Its prevalence ranges between 1/9000 and 1/40,000. It is caused by compound heterozygous or homozygous mutations in the GAA gene, which encodes for the lysosomal enzyme alpha-glucosidase, required for the degrading of lysosomal glycogen. Case presentation In this study, we report the case of a Moroccan consanguineous family with hypertrophic cardiomyopathy and sudden cardiac deaths at an early age; our patient was a 7-month-old Moroccan girl. Whole exome sequencing identified the deleterious homozygous mutation c.236_246delCCACACAGTGC (p.Pro79ArgfsX13) of GAA gene leading to a post-mortem diagnosis of Pompe disease. Conclusion The identification of the genetic substrate in our patient, the daughter, confirmed the clinical diagnosis of Pompe disease and allowed us to provide appropriate genetic counseling to the family for future pregnancies.
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Affiliation(s)
- Najlae Adadi
- Centre de Génomique Humaine, Faculté de Médecine et Pharmacie, Mohammed V University, Rabat, Morocco. .,Department of Medical Genetics, National Institute of Health, BP 769 Agdal, 10090, Rabat, Morocco.
| | - Maryem Sahli
- Centre de Génomique Humaine, Faculté de Médecine et Pharmacie, Mohammed V University, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, BP 769 Agdal, 10090, Rabat, Morocco
| | - Grégory Egéa
- Département de Génétique Moléculaire, Laboratoire Biomnis, Lyon, France
| | - Ilham Ratbi
- Centre de Génomique Humaine, Faculté de Médecine et Pharmacie, Mohammed V University, Rabat, Morocco
| | - Mohamed Taoudi
- Département de Génétique Moléculaire, Laboratoire Biomnis, Lyon, France
| | | | - Wafaa Jdioui
- Centre de Génomique Humaine, Faculté de Médecine et Pharmacie, Mohammed V University, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, BP 769 Agdal, 10090, Rabat, Morocco
| | - Said El Mouatassim
- Département de Génétique Moléculaire, Laboratoire Biomnis, Lyon, France.,Appolonbioteck, Brignais, France
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine, Faculté de Médecine et Pharmacie, Mohammed V University, Rabat, Morocco.,Department of Medical Genetics, National Institute of Health, BP 769 Agdal, 10090, Rabat, Morocco
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Using Systems Biology and Mathematical Modeling Approaches in the Discovery of Therapeutic Targets for Spinal Muscular Atrophy. ADVANCES IN NEUROBIOLOGY 2018. [PMID: 30334226 DOI: 10.1007/978-3-319-94593-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Systems biology uses a combination of experimental and mathematical approaches to investigate the complex and dynamic interactions with a given system or biological process. Systems biology integrates genetics, signal transduction, biochemistry and cell biology with mathematical modeling. It can be used to identify novel pathways implicated in diseases as well as to understand the mechanisms by which a specific gene is regulated. This review describes the development of mathematical models for the regulation of an endogenous modifier gene, SMN2, in spinal muscular atrophy-an early-onset motor neuron disease that is a leading genetic cause of infant mortality worldwide-by cAMP signaling. These mathematical models not only can aid in understanding how SMN2 expression is regulated but they can also be used to examine the best ways to manipulate cAMP signaling to maximally increase SMN2 expression. These models will lead to the development of therapeutic strategies for treating SMA. This systems biology approach can also be applied to other neurological diseases, particularly those in which a disease-causing gene or a modifier gene has been identified.
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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: 370] [Impact Index Per Article: 52.9] [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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14
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Butchbach MER. Copy Number Variations in the Survival Motor Neuron Genes: Implications for Spinal Muscular Atrophy and Other Neurodegenerative Diseases. Front Mol Biosci 2016; 3:7. [PMID: 27014701 PMCID: PMC4785180 DOI: 10.3389/fmolb.2016.00007] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/25/2016] [Indexed: 12/11/2022] Open
Abstract
Proximal spinal muscular atrophy (SMA), a leading genetic cause of infant death worldwide, is an early-onset, autosomal recessive neurodegenerative disease characterized by the loss of spinal α-motor neurons. This loss of α-motor neurons is associated with muscle weakness and atrophy. SMA can be classified into five clinical grades based on age of onset and severity of the disease. Regardless of clinical grade, proximal SMA results from the loss or mutation of SMN1 (survival motor neuron 1) on chromosome 5q13. In humans a large tandem chromosomal duplication has lead to a second copy of the SMN gene locus known as SMN2. SMN2 is distinguishable from SMN1 by a single nucleotide difference that disrupts an exonic splice enhancer in exon 7. As a result, most of SMN2 mRNAs lack exon 7 (SMNΔ7) and produce a protein that is both unstable and less than fully functional. Although only 10–20% of the SMN2 gene product is fully functional, increased genomic copies of SMN2 inversely correlates with disease severity among individuals with SMA. Because SMN2 copy number influences disease severity in SMA, there is prognostic value in accurate measurement of SMN2 copy number from patients being evaluated for SMA. This prognostic value is especially important given that SMN2 copy number is now being used as an inclusion criterion for SMA clinical trials. In addition to SMA, copy number variations (CNVs) in the SMN genes can affect the clinical severity of other neurological disorders including amyotrophic lateral sclerosis (ALS) and progressive muscular atrophy (PMA). This review will discuss how SMN1 and SMN2 CNVs are detected and why accurate measurement of SMN1 and SMN2 copy numbers is relevant for SMA and other neurodegenerative diseases.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, DE, USA; Department of Biological Sciences, University of DelawareNewark, DE, USA; Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, PA, USA
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15
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Stabley DL, Harris AW, Holbrook J, Chubbs NJ, Lozo KW, Crawford TO, Swoboda KJ, Funanage VL, Wang W, Mackenzie W, Scavina M, Sol-Church K, Butchbach MER. SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR. Mol Genet Genomic Med 2015; 3:248-57. [PMID: 26247043 PMCID: PMC4521962 DOI: 10.1002/mgg3.141] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 02/22/2015] [Accepted: 02/26/2015] [Indexed: 11/22/2022] Open
Abstract
Proximal spinal muscular atrophy (SMA) 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 mutation of survival motor neuron 1 (SMN1). In the human genome, a large duplication of the SMN-containing region gives rise to a second copy of this gene (SMN2) that is distinguishable by a single nucleotide change in exon 7. Within the SMA population, there is substantial variation in SMN2 copy number; in general, those individuals with SMA who have a high SMN2 copy number have a milder disease. Because SMN2 functions as a disease modifier, its accurate copy number determination may have clinical relevance. In this study, we describe the development of an assay to assess SMN1 and SMN2 copy numbers in DNA samples using an array-based digital PCR (dPCR) system. This dPCR assay 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 copy number and disease severity. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 copy numbers from SMA samples.
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Affiliation(s)
- Deborah L Stabley
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Ashlee W Harris
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Jennifer Holbrook
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Nicholas J Chubbs
- Department of Biological Sciences, University of DelawareNewark, Delaware
| | - Kevin W Lozo
- Department of Biological Sciences, University of DelawareNewark, Delaware
| | - Thomas O Crawford
- Department of Neurology, Johns Hopkins UniversityBaltimore, Maryland
- Department of Pediatrics, Johns Hopkins UniversityBaltimore, Maryland
| | - Kathryn J Swoboda
- Neurogenetics Research Program, Center for Human Genetics Research, Massachusetts General HospitalBoston, Massachusetts
| | - Vicky L Funanage
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
| | - Wenlan Wang
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
| | - William Mackenzie
- Division of Orthopedics, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Mena Scavina
- Division of Neurology, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Katia Sol-Church
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Biological Sciences, University of DelawareNewark, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
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16
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Schrodi SJ, DeBarber A, He M, Ye Z, Peissig P, Van Wormer JJ, Haws R, Brilliant MH, Steiner RD. Prevalence estimation for monogenic autosomal recessive diseases using population-based genetic data. Hum Genet 2015; 134:659-69. [PMID: 25893794 DOI: 10.1007/s00439-015-1551-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/05/2015] [Indexed: 01/28/2023]
Abstract
Genetic methods can complement epidemiological surveys and clinical registries in determining prevalence of monogenic autosomal recessive diseases. Several large population-based genetic databases, such as the NHLBI GO Exome Sequencing Project, are now publically available. By assuming Hardy-Weinberg equilibrium, the frequency of individuals homozygous in the general population for a particular pathogenic allele can be directly calculated from a sample of chromosomes where some harbor the pathogenic allele. Further assuming that the penetrance of the pathogenic allele(s) is known, the prevalence of recessive phenotypes can be determined. Such work can inform public health efforts for rare recessive diseases. A Bayesian estimation procedure has yet to be applied to the problem of estimating disease prevalence from large population-based genetic data. A Bayesian framework is developed to derive the posterior probability density of monogenic, autosomal recessive phenotypes. Explicit equations are presented for the credible intervals of these disease prevalence estimates. A primary impediment to performing accurate disease prevalence calculations is the determination of truly pathogenic alleles. This issue is discussed, but in many instances remains a significant barrier to investigations solely reliant on statistical interrogation--functional studies can provide important information for solidifying evidence of variant pathogenicity. We also discuss several challenges to these efforts, including the population structure in the sample of chromosomes, the treatment of allelic heterogeneity, and reduced penetrance of pathogenic variants. To illustrate the application of these methods, we utilized recently published genetic data collected on a large sample from the Schmiedeleut Hutterites. We estimate prevalence and calculate 95% credible intervals for 13 autosomal recessive diseases using these data. In addition, the Bayesian estimation procedure is applied to data from a central European study of hereditary fructose intolerance. The methods described herein show a viable path to robustly estimating both the expected prevalence of autosomal recessive phenotypes and corresponding credible intervals using population-based genetic databases that have recently become available. As these genetic databases increase in number and size with the advent of cost-effective next-generation sequencing, we anticipate that these methods and approaches may be helpful in recessive disease prevalence calculations, potentially impacting public health management, health economic analyses, and treatment of rare diseases.
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Affiliation(s)
- Steven J Schrodi
- Center for Human Genetics, Marshfield Clinic Research Foundation, 1000 N Oak Ave-MLR, Marshfield, WI, 54449, USA,
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17
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Maeda M, Harris AW, Kingham BF, Lumpkin CJ, Opdenaker LM, McCahan SM, Wang W, Butchbach MER. Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells. PLoS One 2014; 9:e106818. [PMID: 25191843 PMCID: PMC4156416 DOI: 10.1371/journal.pone.0106818] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/01/2014] [Indexed: 01/20/2023] Open
Abstract
Proximal spinal muscular atrophy (SMA) is an early onset, autosomal recessive motor neuron disease caused by loss of or mutation in SMN1 (survival motor neuron 1). Despite understanding the genetic basis underlying this disease, it is still not known why motor neurons (MNs) are selectively affected by the loss of the ubiquitously expressed SMN protein. Using a mouse embryonic stem cell (mESC) model for severe SMA, the RNA transcript profiles (transcriptomes) between control and severe SMA (SMN2+/+;mSmn−/−) mESC-derived MNs were compared in this study using massively parallel RNA sequencing (RNA-Seq). The MN differentiation efficiencies between control and severe SMA mESCs were similar. RNA-Seq analysis identified 3,094 upregulated and 6,964 downregulated transcripts in SMA mESC-derived MNs when compared against control cells. Pathway and network analysis of the differentially expressed RNA transcripts showed that pluripotency and cell proliferation transcripts were significantly increased in SMA MNs while transcripts related to neuronal development and activity were reduced. The differential expression of selected transcripts such as Crabp1, Crabp2 and Nkx2.2 was validated in a second mESC model for SMA as well as in the spinal cords of low copy SMN2 severe SMA mice. Furthermore, the levels of these selected transcripts were restored in high copy SMN2 rescue mouse spinal cords when compared against low copy SMN2 severe SMA mice. These findings suggest that SMN deficiency affects processes critical for normal development and maintenance of MNs.
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Affiliation(s)
- Miho Maeda
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Ashlee W. Harris
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
| | - Brewster F. Kingham
- Sequencing and Genotyping Center, University of Delaware, Newark, Delaware, United States of America
| | - Casey J. Lumpkin
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Lynn M. Opdenaker
- Center for Translational Cancer Research, University of Delaware, Newark, Delaware, United States of America
| | - Suzanne M. McCahan
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Bioinformatics Core Facility, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Wenlan Wang
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Matthew E. R. Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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19
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Abstract
UNLABELLED Spinal muscle atrophy (SMA) is autosomal recessive and one of the most common inherited lethal diseases in childhood. The spectrum of symptoms of SMA is continuous and varies from neonatal death to progressive symmetrical muscle weakness first appearing in adulthood. The disease is produced by degeneration of spinal motor neurons and can be described in three or more categories: SMA I with onset of symptoms before 6 months of age; SMAII with onset between 6 and 18 months and SMA III, which presents later in childhood. Genetics: The disease is in more than 95% of cases caused by a homozygous deletion in survival motor neuron gene 1 (SMN1). PATHOPHYSIOLOGY The loss of full-length functioning SMN protein leads to a degeneration of anterior spinal motor neurons which causes muscle weakness. Anesthetic risks: Airway: Tracheal intubation can be difficult. Respiration: Infants with SMA I almost always need postoperative respiratory support. Patients with SMA II sometimes need support, while SMA III patients seldom need support. Circulation: Circulatory problems during anesthesia are rare. Anesthetic drugs: Neuromuscular blockers: Patients with SMA may display increased sensitivity to and prolonged effect of nondepolarizing neuromuscular blockers. Intubation without muscle relaxation should be considered. Succinylcholine should be avoided. Opioids: These should be titrated carefully. Anesthetic techniques: All types of anesthetic technique have been used. Although none is absolutely contraindicated, none is perfect: anesthesia must be individualized. CONCLUSION The perioperative risks can be considerable and are mainly related to the respiratory system, from respiratory failure to difficult/impossible intubation.
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Affiliation(s)
- Gunilla Islander
- Department of Intensive and Perioperative Care, Skåne University Hospital, Lund, Sweden.
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