1
|
Bai J, Qu Y, Huang W, Meng W, Zhan J, Wang H, Hou W, Jin Y, Mao A, Song F. A high-fidelity long-read sequencing-based approach enables accurate and effective genetic diagnosis of spinal muscular atrophy. Clin Chim Acta 2024; 553:117743. [PMID: 38158006 DOI: 10.1016/j.cca.2023.117743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND We aimed to develop a high-fidelity long-read sequencing (LRS)-based approach to detect SMN gene variants in one step. It is challenging for conventional step-wise methods to simultaneously detect all kinds of variations between homologous SMN1 and SMN2. METHODS In this study, LRS was developed to analyze copy numbers (CNs), full sequences, and structure of SMN1 and SMN2. The results were compared with those from the step-wise methods in 202 samples from 67 families. RESULTS LRS achieved 100% (202/202) and 99.5% (201/202) accuracy for SMN1 and SMN2 CNs, respectively. It corrected SMN1 CNs from MLPA, which was caused by SNVs/indels that located in probe-binding region. LRS identified 23 SNVs/indels distributing throughout SMN1, including c.22dup and c.884A > T in trans-configuration, and a de novo variant c.41_42delinsC for the first time. LRS also identified a SMN2 variant c.346A > G. Moreover, it successfully determined Alu-mediated 8978-bp deletion encompassing exon 2a-5 and 1415-bp deletion disrupting exon 1, and the exact breakpoints of large deletions. Through haplotype-based pedigree trio analysis, LRS identified SMN1 2 + 0 carriers, and determined the distribution of SMN1 and SMN2 on two chromosomes. CONCLUSIONS LRS represents a more comprehensive and accurate diagnosis approach that is beneficial to early treatment and effective management of SMA.
Collapse
Affiliation(s)
- Jinli Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yujin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wenchen Huang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Jiahan Zhan
- Berry Genomics Corporation, Beijing 102200, China
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wenqi Hou
- Berry Genomics Corporation, Beijing 102200, China
| | - Yuwei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| |
Collapse
|
2
|
Hosseini Nami A, Kabiri M, Zafarghandi Motlagh F, Shirzadeh T, Bagherian H, Zeinali R, Karimi A, Zeinali S. Identification and in silico structural analysis for the first de novo mutation in the cystic fibrosis transmembrane conductance regulator protein in Iran: case report and developmental insight using microsatellite markers. Ther Adv Respir Dis 2024; 18:17534666241253990. [PMID: 38904297 PMCID: PMC11193346 DOI: 10.1177/17534666241253990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/19/2024] [Indexed: 06/22/2024] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by the inheritance of two mutant cystic fibrosis transmembrane conductance regulator (CFTR) alleles, one from each parent. Autosomal recessive disorders are rarely associated with germline mutations or mosaicism. Here, we propose a case of paternal germline mutation causing CF. The subject also had an identifiable maternal mutant allele. We identified the compound heterozygous variants in the proband through Sanger sequencing, and in silico studies predicted functional effects on the protein. Also, short tandem repeat markers revealed the de novo nature of the mutation. The maternal mutation in the CFTR gene was c.1000C > T. The de novo mutation was c.178G > A, p.Glu60Lys. This mutation is located in the lasso motif of the CFTR protein and, according to in silico structural analysis, disrupts the interaction of the lasso motif and R-domain, thus influencing protein function. This first reported case of de novo mutation in Asia has notable implications for molecular diagnostics, genetic counseling, and understanding the genetic etiology of recessive disorders in the Iranian population.
Collapse
Affiliation(s)
- Amin Hosseini Nami
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Mahboubeh Kabiri
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Tina Shirzadeh
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Hamideh Bagherian
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
| | - Razie Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), Tehran, Iran
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Ali Karimi
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Sirous Zeinali
- Dr. Zeinali’s Medical Genetics Lab, Kawsar Human Genetics Research Center (KHGRC), No. 41, Irna St., Valiasr St., Tehran, Iran
| |
Collapse
|
3
|
Li S, Han X, Zhang L, Xu Y, Chang C, Gao L, Zhan J, Hua R, Mao A, Wang Y. An Effective and Universal Long-Read Sequencing-Based Approach for SMN1 2 + 0 Carrier Screening through Family Trio Analysis. Clin Chem 2023; 69:1295-1306. [PMID: 37932106 DOI: 10.1093/clinchem/hvad152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Population-wide carrier screening for spinal muscular atrophy (SMA) is recommended by professional organizations to facilitate informed reproductive options. However, genetic screening for SMN1 2 + 0 carriers, accounting for 3%-8% of all SMA carriers, has been challenging due to the large gene size and long distance between the 2 SMN genes. METHODS Here we repurposed a previously developed long-read sequencing-based approach, termed comprehensive analysis of SMA (CASMA), to identify SMN1 2 + 0 carriers through haplotype analysis in family trios (CASMA-trio). Bioinformatics pipelines were developed for accurate haplotype analysis and SMN1 2 + 0 deduction. Seventy-nine subjects from 24 families composed of, at the minimum, 3 were enrolled, and CASMA-trio was employed to determine whether an index subject with 2 SMN1 copies was a 2 + 0 carrier in these families. For the proof-of-principle, SMN2 2 + 0 was also analyzed. RESULTS Among the 16 subjects with 2 SMN1 copies, CASMA-trio identified 5 subjects from 4 families as SMN1 2 + 0 carriers, which was consistent with pedigree analysis involving an affected proband. CASMA-trio also identified SMN2 2 + 0 in six out of 43 subjects with 2 SMN2 copies. Additionally, CASMA-trio successfully determined the distribution pattern of SMN1 and SMN2 genes on 2 alleles in all 79 subjects. CONCLUSIONS CASMA-trio represents an effective and universal approach for SMN1 2 + 0 carriers screening, as it does not reply on the presence of an affected proband, certain single-nucleotide polymorphisms, ethnicity-specific haplotypes, or complicated single-nucleotide polymorphism analysis across 3 generations. Incorporating CASMA-trio into existing SMA carrier screening programs will greatly reduce residual risk ratio.
Collapse
Affiliation(s)
- Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Liang Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chunxin Chang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Li Gao
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiahan Zhan
- Berry Genomics Corporation, Beijing 102200, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| |
Collapse
|
4
|
Gombosh M, Yogev Y, Hadar N, Proskorovski-Ohayon R, Aharoni S, Gradstein L, Birk OS. De-novo "germline second hit" loss-of-heterozygosity RBP3 deletion mutation causing recessive high myopia. Clin Genet 2023; 104:571-576. [PMID: 37308324 DOI: 10.1111/cge.14384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/27/2023] [Accepted: 05/28/2023] [Indexed: 06/14/2023]
Abstract
Knudson's "two hit" hypothesis, mostly associated with cancer, relates to a primary heterozygous germline mutation complemented by a somatic mutation in the second allele. When the somatic "second hit" is a deletion mutation, the heterozygosity due to the first hit is lost ("loss of heterozygosity"). As the rate of germline mutations is almost two orders of magnitude lower than that of somatic mutations, de-novo germline mutations causing autosomal recessive diseases in carriers of inherited heterozygous mutations are not common. We delineate a case of high myopia presenting at infancy with mild diminution of retinal responses. Exome sequencing identified a paternally inherited apparently homozygous missense mutation in RBP3. Chromosomal microarrays delineated a de-novo germline heterozygous deletion encompassing RBP3, verified through revision of WES data. Thus, we demonstrate an inherited RBP3 missense mutation complemented by a de-novo germline RBP3 deletion, causing loss of heterozygosity of the inherited mutation. We describe a novel RBP3 missense mutation, report the first isolated RBP3 deletion, and demonstrate infantile high myopia as an initial presentation of RBP3 disease. Notably, we highlight de-novo germline deletion mutations causing "loss of heterozygosity" of inherited heterozygous mutations, culminating in autosomal recessive diseases, and discuss the scarce literature.
Collapse
Affiliation(s)
- Maya Gombosh
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Noam Hadar
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Regina Proskorovski-Ohayon
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Sarit Aharoni
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Ben-Gurion University, Beer-Sheva, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, Israel
- Genetics Institute, Soroka Medical Center, Beer-Sheva, Israel
| |
Collapse
|
5
|
Alghamdi A, AlDossary S, Abdulaziz Alabdulqader W, Amer F, Ali M, Almomen M, Alghamdi F. Identifying Clinical and Genetic Characteristics of Spinal Muscular Atrophy Patients and Families in Saudi Arabia. Cureus 2023; 15:e46452. [PMID: 37927698 PMCID: PMC10623204 DOI: 10.7759/cureus.46452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
INTRODUCTION Spinal muscular atrophy (SMA) is an inherited, neuromuscular disease characterized by the deterioration of spinal motor neurons, causing progressive muscular atrophy and weakening. It is an autosomal recessive disease with the mutation of the survival motor neuron 1 (SMN1) gene as a hallmark. Evidence suggests that the SMN2 gene modulates the severity of the disease. SMA is classified based on the maximum motor function achieved. This study aims to describe the genetic makeup and characteristics of an SMA cohort in the Kingdom of Saudi Arabia (KSA). METHODS Data from families presenting with SMA children was collected between January 2018 and December 2020. Blood samples were collected from patients and family members. Genetic testing for SMA and mutations was performed at a European central lab. RESULTS AND DISCUSSION Seventeen families were enrolled in the study, including 52 children. Among 34 parents, 28 were carriers with heterozygous deletion (82.3%), one (2.9%) had no deletion detected by multiplex ligation-dependent probe amplification (MLPA) but had point mutation by sequencing, one (2.9%) had homozygous deletion and was symptomatic, three (8.8%) had no deletion or point mutation and were presumed to have 2+0, and one (2.9%) was not tested. CONCLUSION This study provides insight into the carrier mutational analysis of families with SMA disease manifestations in KSA. Further studies are needed to understand the burden and impact of SMA among the Saudi population.
Collapse
Affiliation(s)
- Alaa Alghamdi
- Primary Care and Population Health, King Fahad University Hospital, Dammam, SAU
| | - Shaikhah AlDossary
- Primary Care and Population Health, University College London, London, GBR
| | | | - Fawzia Amer
- Pediatric Neurology, King Fahad Specialist Hospital, Dammam, SAU
- Pediatric Neurology and Metabolic, Cairo University Children Hospital, Cairo, EGY
| | - Mona Ali
- Neurology, Neuroscience Center, King Fahad Specialist Hospital, Dammam, SAU
| | - Momen Almomen
- Pediatric Neurology, King Fahad Specialist Hospital, Dammam, SAU
| | - Fouad Alghamdi
- Pediatric Neurology, Neuroscience Center, King Fahad Specialist Hospital, Dammam, SAU
| |
Collapse
|
6
|
Davidson JE, Russell JS, Martinez NN, Mowat DR, Jones KJ, Kirk EP, Kariyawasam D, Farrar M, D’Silva A. The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers. Genes (Basel) 2023; 14:1403. [PMID: 37510307 PMCID: PMC10379112 DOI: 10.3390/genes14071403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Current carrier screening methods do not identify a proportion of carriers that may have children affected by spinal muscular atrophy (SMA). Additional genetic data is essential to inform accurate risk assessment and genetic counselling of SMA carriers. This study aims to quantify the various genotypes among parents of children with SMA. METHOD A retrospective cohort study was undertaken at Sydney Children's Hospital Network, the major SMA referral centre for New South Wales, Australia. Participants included children with genetically confirmed SMA born between 2005 and 2021. Data was collected on parent genotype inclusive of copy number of SMN1 exons 7 and 8. The number of SMN2 exon 7 copies were recorded for the affected children. Descriptive statistics were used to determine the proportion of carriers of 2+0 genotype classified as silent carriers. Chi-square test was used to correlate the association between parents with a heterozygous SMN1 exon 7 deletion and two copies of exon 8 and ≥3 SMN2 copy number in the proband. RESULTS SMA carrier testing was performed in 118/154 (76.6%) parents, incorporating 59 probands with homozygous SMN1 deletions and one proband with compound heterozygote pathogenic variants. Among parents with a child with SMA, 7.6% had two copies of SMN1 exon 7. When only probands with a homozygous SMN1 exon 7 deletion were included, 6.9% of parents had two copies of SMN1 exon 7. An association was observed between heterozygous deletion of SMN1 exon 7 with two copies of exon 8 in a parent and ≥3 SMN2 copy number in the affected proband (p = 0.07). CONCLUSIONS This study confirmed a small but substantial proportion of silent carriers not identified by conventional screening within an Australian context. Accordingly, the effectiveness of carrier screening for SMA is linked with genetic counselling to enable health literacy regarding high and low risk results and is complemented by new-born screening and maintaining clinical awareness for SMA. Gene conversion events may underpin the associations between parent carrier status and proband SMN2 copy number.
Collapse
Affiliation(s)
- Joanne E Davidson
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
| | - Jacqueline S Russell
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - Noelia Nunez Martinez
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - David R Mowat
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - Kristi J Jones
- Department of Clinical Genetics, The Children’s Hospital at Westmead, and Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Didu Kariyawasam
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Michelle Farrar
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Arlene D’Silva
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| |
Collapse
|
7
|
Huang Z, Yang Q, Ye J, Huang J, Lin J, Chen J, Liang Z, Cao Z. Screening and prenatal diagnosis of survival motor neuron gene deletion in pregnant women in Zhaoqing city, Guangdong Province. BMC Med Genomics 2023; 16:39. [PMID: 36859245 PMCID: PMC9976494 DOI: 10.1186/s12920-023-01468-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVE A total of 5,200 pregnant women in Zhaoqing city, Guangdong Province, were screened to identify spinal muscular atrophy (SMA) mutation carriers to guide the prevention of SMA and prevent the birth of children with SMA. METHODS Exons 7 and 8 (E7 and E8) of the survival motor neuron (SMN) 1 gene were detected in women using real-time fluorescence quantitative polymerase chain reaction. SMN1 and SMN2 copy numbers in those who were initially identified as carriers were verified via targeted region capture and next-generation sequencing. When both partners were identified as carriers, prenatal diagnosis of the fetus was performed. RESULTS Among the screened women, 75 SMA carriers (71 cases had both E7 and E8 heterozygous deletions and 4 cases only had an E7 heterozygous deletion) were identified, with a carrier frequency of 1.44% (95% confidence interval: 1.31-1.65%). Three couples where both spouses were identified as SMA carriers, and their three fetuses were subjected to prenatal genetic analysis. Of the three, one had homozygous deletions of E7 and E8 and the other two had heterozygous deletions of E7 and E8. After a detailed prenatal consultation, the former couple decided to terminate the pregnancy. CONCLUSION Through screening and prenatal diagnosis of pregnant women in Zhaoqing city, Guangdong Province, the incidence of SMA can be reduced, prevention of birth defects can be improved, incidence of birth defects can be effectively minimized.
Collapse
Affiliation(s)
- Zhiwei Huang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China. .,Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China. .,Clinical Laboratory, The Second People's Hospital of Zhaoqing, No. 2, Jiansheer Street, 526000, Zhaoqing City, Guangdong province, The People's Republic of China.
| | - Qingchan Yang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jianxiang Ye
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jianxing Huang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jin Lin
- Obstetrical Department, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Jing Chen
- Prenatal Diagnosis Center, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Zizhao Liang
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| | - Zijie Cao
- Clinical Laboratory, The Second People's Hospital of Zhaoqing, Zhaoqing, The People's Republic of China
| |
Collapse
|
8
|
Günther R. [Gene Therapies in Motor Neuron Diseases ALS and SMA]. FORTSCHRITTE DER NEUROLOGIE-PSYCHIATRIE 2023; 91:153-163. [PMID: 36822211 DOI: 10.1055/a-2002-5215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
In the past, the diagnosis of motor neuron diseases such as amyotrophic lateral sclerosis (ALS) and 5q-associated spinal muscular atrophy (SMA) meant powerlessness in the face of seemingly untreatable diseases with severe motor-functional limitations and sometimes fatal courses. Recent advances in an understanding of the genetic causalities of these diseases, combined with success in the development of targeted gene therapy strategies, spell hope for effective, innovative therapeutic approaches, pioneering the ability to treat neurodegenerative diseases. While gene therapies have been approved for SMA since a few years, gene therapy research in ALS is still in clinical trials with encouraging results. This article provides an overview of the genetic background of ALS and SMA known to date and gene therapy approaches to them with a focus on therapy candidates that are in clinical trials or have already gained market approval.
Collapse
Affiliation(s)
- René Günther
- Klinik und Poliklinik für Neurologie, University Hospital Carl Gustav Carus at Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
9
|
Never-homozygous genetic variants in healthy populations are potential recessive disease candidates. NPJ Genom Med 2022; 7:54. [PMID: 36075934 PMCID: PMC9458638 DOI: 10.1038/s41525-022-00322-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
The rapid pace with which genetic variants are now being determined means there is a pressing need to understand how they affect biological systems. Variants from healthy individuals have previously been used to study blood groups or HLA diversity and to identify genes that can apparently be nonfunctional in healthy people. These studies and others have observed a lower than expected frequency of homozygous individuals for potentially deleterious alleles, which would suggest that several of these alleles can lead to recessive disorders. Here we exploited this principle to hunt for potential disease variants in genomes from healthy people. We identified at least 108 exclusively heterozygous variants with evidence for an impact on biological function. We discuss several examples of candidate variants/genes including CCDC8, PANK3, RHD and NLRP12. Overall, the results suggest there are many, comparatively frequent, potentially lethal or disease-causing variants lurking in healthy human populations.
Collapse
|
10
|
Rad N, Cai H, Weiss MD. Management of Spinal Muscular Atrophy in the Adult Population. Muscle Nerve 2022; 65:498-507. [PMID: 35218574 DOI: 10.1002/mus.27519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 01/30/2022] [Accepted: 02/06/2022] [Indexed: 12/14/2022]
Abstract
Spinal muscular atrophy (SMA) is a group of neurodegenerative disorders resulting from the loss of spinal motor neurons. 95% of patients share a pathogenic mechanism of loss of survival motor neuron (SMN) 1 protein expression due to homozygous deletions or other mutations of the SMN1 gene, with the different phenotypes influenced by variable copy numbers of the SMN2 gene. Advances in supportive care, disease modifying treatment and novel gene therapies have led to an increase in the prevalence of SMA, with a third of SMA patients now represented by adults. Despite the growing number of adult patients, consensus on the management of SMA has focused primarily on the pediatric population. As the disease burden is vastly different in adult SMA, an approach to treatment must be tailored to their unique needs. This review will focus on the management of the adult SMA patient as they age and will discuss proper transition of care from a pediatric to adult center, including the need for continued monitoring for osteoporosis, scoliosis, malnutrition, and declining mobility and functioning. As in the pediatric population, multidisciplinary care remains the best approach to the management of adult SMA. Novel and emerging therapies such as nusinersen and risdiplam provide hope for these patients, though these medications are of uncertain efficacy in this population and require additional study.
Collapse
Affiliation(s)
- Nassim Rad
- Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Haibi Cai
- Department of Physical Medicine and Rehabilitation, University of Washington, Seattle, Washington, USA
| | - Michael D Weiss
- Department of Neurology, University of Washington, Seattle, Washington, USA
| |
Collapse
|
11
|
Zettler B, Estrella E, Liaquat K, Lichten L. Evolving approaches to prenatal genetic counseling for Spinal Muscular Atrophy in the new treatment era. J Genet Couns 2022; 31:803-814. [PMID: 35037741 DOI: 10.1002/jgc4.1549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/31/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease characterized by muscle weakness and atrophy with usually typical cognition. The first disease-modifying therapy for SMA, nusinersen, was approved by the United States Food and Drug Administration (FDA) in 2016 and leads to improved outcomes, especially when administered presymptomatically. Population-wide carrier screening and newborn screening (NBS) are now recommended by several professional organizations to promote reproductive autonomy, early diagnosis, and treatment. Prenatal genetic counselors (GCs) are important providers of the SMA screening and diagnosis process, but the possible impact of nusinersen on their practice has not been explored. A survey of 182 prenatal GCs in the United States (US) assessed baseline knowledge of nusinersen and likelihood of discussing this option with prospective parents. The majority of GCs (94.5%) were aware of this drug, and almost all (87.3%) felt that this information would affect pregnancy management decisions. However, less than half of GCs (49.2%) felt confident discussing nusinersen, 45.1% were unaware if this treatment was available in their practice setting, and one in five (19.3%) did not know where to find information about SMA treatments. Participants were more confident and knowledgeable about NBS for SMA, and several indicated that NBS would reduce their emphasis on carrier screening and diagnostic testing, not recognizing that an early prenatal diagnosis can enable preparations for complex, time-sensitive treatment. Only 5.0% of participants felt that a prenatal GC should discuss nusinersen with prospective parents. However, encouragingly, nearly all GCs who felt confident discussing this treatment option (86.4%) reported using this information weekly in their real-world practice. These data highlight an opportunity to provide up-to-date education about SMA treatments, as well as the significant impacts of early diagnosis. Additionally, interdisciplinary communication and care may be appropriate to clarify healthcare resources available and support a variety of patient needs. Increasing awareness and confidence about available options can help prenatal GCs empower patient autonomy and shared decision-making in the new era of disease-modifying treatment for SMA.
Collapse
Affiliation(s)
- Bethany Zettler
- Genetic Counseling, Brandeis University Graduate School of Arts and Sciences, Waltham, Massachusetts, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elicia Estrella
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Khalida Liaquat
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts, USA
| | - Lauren Lichten
- Genetic Counseling, Brandeis University Graduate School of Arts and Sciences, Waltham, Massachusetts, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| |
Collapse
|
12
|
Lucas HM, Sarumi MA. Case report of pregnancy management and genetic evaluation after negative carrier screening for spinal muscular atrophy in an affected family. Case Rep Womens Health 2022; 33:e00377. [PMID: 35004188 PMCID: PMC8718837 DOI: 10.1016/j.crwh.2021.e00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
Background Screening for spinal muscular atrophy (SMA) is recommended for all pregnant women; however, interpreting the results of carrier screening in the context of family history can be challenging. Case We report the case of a 28-year-old woman (G4P3001) with two previous children affected with SMA and negative carrier screening via the Horizon 4 panel. SMN1/2 analysis was pursued to clarify risk for point mutations, carrier screening for her partner, and diagnostic testing for the fetus for SMA. Results of this testing confirmed her status as a silent carrier for SMA and the status of the fetus. Conclusion Carrier screening does not account for family history and can therefore generate results inconsistent with known inheritance patterns. In these situations, additional genetic testing and genetic counseling are indicated to clarify risk for SMA in pregnancy and guide prenatal and neonatal healthcare. A pregnant woman with two previous children with spinal muscular atrophy (SMA) presented to clinic with negative carrier screening for SMA. Additional screening and diagnostic testing of the fetus confirmed the mother's silent carrier status and the fetal status. Carrier screening for complex genetic conditions remains limited. Genetic testing and reproductive options should be discussed extensively with members of affected families.
Collapse
Affiliation(s)
- Heather M Lucas
- Department of Maternal Fetal Medicine, CHRISTUS Trinity Mother Frances, 620 S Fleishel Ave, Tyler, TX 75701, USA
| | - Mojirayo A Sarumi
- Department of Maternal Fetal Medicine, CHRISTUS Trinity Mother Frances, 620 S Fleishel Ave, Tyler, TX 75701, USA
| |
Collapse
|
13
|
Azad AK, Huang CK, Jin H, Zou H, Yanakakis L, Du J, Fiddler M, Naeem R, Goldstein Y. Enhanced Carrier Screening for Spinal Muscular Atrophy: Detection of Silent (SMN1: 2 + 0) Carriers Utilizing a Novel TaqMan Genotyping Method. Lab Med 2021; 51:408-415. [PMID: 31875889 DOI: 10.1093/labmed/lmz088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Individuals whose copies of the survival motor neuron 1 (SMN1) gene exist on the same chromosome are considered silent carriers for spinal muscular atrophy (SMA). Conventional screening for SMA only determines SMN1 copy number without any information regarding how those copies are arranged. A single nucleotide variant (SNV) rs143838139 is highly linked with the silent carrier genotype, so testing for this SNV can more accurately assess risk to a patient of having an affected child. METHODS Using a custom-designed SNV-specific Taqman genotyping assay, we determined and validated a model for silent-carrier detection in the laboratory. RESULTS An initial cohort of 21 pilot specimens demonstrated results that were 100% concordant with a reference laboratory method; this cohort was utilized to define the reportable range. An additional 177 specimens were utilized for a broader evaluation of clinical validity and reproducibility. Allelic-discrimination analysis demonstrated tight clustering of genotype groupings and excellent reproducibility, with a coefficient of variation for all genotypes ranging from 1% to 4%. CONCLUSION The custom-developed Taqman SNV genotyping assay we tested provides a rapid, accurate, and cost-effective method for routine SMA silent-carrier screening and considerably improves detection rates of residual risk for SMA carriers.
Collapse
Affiliation(s)
- Abul Kalam Azad
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| | - Chih-Kang Huang
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| | - Hong Jin
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| | | | | | - Juan Du
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| | | | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| | - Yitz Goldstein
- Department of Pathology, Montefiore Medical Center at Albert Einstein College of Medicine, Bronx, New York
| |
Collapse
|
14
|
Keinath MC, Prior DE, Prior TW. Spinal Muscular Atrophy: Mutations, Testing, and Clinical Relevance. APPLICATION OF CLINICAL GENETICS 2021; 14:11-25. [PMID: 33531827 PMCID: PMC7846873 DOI: 10.2147/tacg.s239603] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Spinal muscular atrophy (SMA) is a heritable neuromuscular disorder that causes degeneration of the alpha motor neurons from anterior horn cells in the spinal cord, which causes severe progressive hypotonia and muscular weakness. With a carrier frequency of 1 in 40–50 and an estimated incidence of 1 in 10,000 live births, SMA is the second most common autosomal recessive disorder. Affected individuals with SMA have a homozygous loss of function of the survival motor neuron gene SMN1 on 5q13 but keep the modifying SMN2 gene. The most common mutation causing SMA is a homozygous deletion of the SMN1 exon 7, which can be readily detected and used as a sensitive diagnostic test. Because SMN2 produces a reduced number of full-length transcripts, the number of SMN2 copies can modify the clinical phenotype and as such, becomes an essential predictive factor. Population-based SMA carrier screening identifies carrier couples that may pass on this genetic disorder to their offspring and allows the carriers to make informed reproductive choices or prepare for immediate treatment for an affected child. Three treatments have recently been approved by the Food and Drug Administration (FDA). Nusinersen increases the expression levels of the SMN protein using an antisense oligonucleotide to alter splicing of the SMN2 transcript. Onasemnogene abeparvovec is a gene therapy that utilizes an adeno-associated virus serotype 9 vector to increase low functional SMN protein levels. Risdiplam is a small molecule that alters SMN2 splicing in order to increase functional SMN protein. Newborn screening for SMA has been shown to be successful in allowing infants to be treated before the loss of motor neurons and has resulted in improved clinical outcomes. Several of the recommendations and guidelines in the review are based on studies performed in the United States.
Collapse
Affiliation(s)
- Melissa C Keinath
- Pathology, University Hospitals Center for Human Genetics, Cleveland, OH, USA
| | - Devin E Prior
- Neurology, Mount Auburn Hospital, Cambridge, MA, USA
| | - Thomas W Prior
- Pathology, University Hospitals Center for Human Genetics, Cleveland, OH, USA
| |
Collapse
|
15
|
Sharifi Z, Taheri M, Fallah MS, Abiri M, Golnabi F, Bagherian H, Zeinali R, Farahzadi H, Alborji M, Tehrani PG, Amini M, Asnavandi S, Hashemi M, Forouzesh F, Zeinali S. Comprehensive Mutation Analysis and Report of 12 Novel Mutations in a Cohort of Patients with Spinal Muscular Atrophy in Iran. J Mol Neurosci 2021; 71:2281-2298. [PMID: 33481221 DOI: 10.1007/s12031-020-01789-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022]
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of neuromuscular diseases characterized by loss of motor neurons, muscle weakness, hypotonia and muscle atrophy, with different modes of inheritance; however, the survival motor neuron 1 (SMN1) gene is predominantly involved. The aims of the current study were to clarify the genetic basis of SMA and determine the mutation spectrum of SMN1 and other associated genes, in order to provide molecular information for more accurate diagnosis and future prospects for treatment. We performed a comprehensive analysis of 5q SMA in 1765 individuals including 528 patients from 432 unrelated families with at least one child with suspected clinical presentation of SMA. Copy number variations of the SMN1 and SMN2 genes and linkage analysis were performed using multiplex ligation-dependent probe amplification (MLPA) and short tandem repeat (STR) markers linked to the SMN1 gene. Cases without mutation in the SMA locus on 5q were analyzed for the DNAJB2, IGHMBP2, SIGMAR1 and PLEKHG5 genes using linked STR markers. Sanger sequencing of whole genes was performed for cases with homozygous haplotypes. Whole-genome sequencing (WGS) and whole-exome analysis was conducted for some of the remaining cases. Mutations in the SMN1 gene were identified in 287 (66.43%) families including 269 patients (62.26%) with homozygous deletion of the entire SMN1 gene. Only one of the patients had a homozygous point mutation in the SMN1 gene. Among the remaining families, three families showed mutations in either the DNAJB2, SIGMAR1 or PLEKHG5 genes, which were linked using STR analysis and Sanger sequencing. From 10 families who underwent WGS, we found six homozygous point mutations in six families for either the TNNT1, TPM3, TTN, SACS or COL6A2 genes. Two mutations in the PLA2G6 gene were also found in another patient as compound heterozygous. This rather large cohort allowed us to identify genotype patterns in Iranian 5q SMA patients. The process of identifying 11 mutations (9 novel) in 9 different genes among non-5q SMA patients shows the diversity of genes involved in non-5q SMA in Iranians. Genotyping of patients with SMA is essential for prenatal and preimplantation genetic diagnosis (PGD), and may be very helpful for guiding treatment, with the advent of new, more effective, albeit very expensive, therapies. Also, combining linkage analysis was shown to be beneficial in many ways, including sample authenticity and segregation analysis, and for ruling out maternal cell contamination during prenatal diagnosis (PND).
Collapse
Affiliation(s)
- Zohreh Sharifi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad-Sadegh Fallah
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular Biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golnabi
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Hamideh Bagherian
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Razieh Zeinali
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Hossein Farahzadi
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Alborji
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | | | - Masoume Amini
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Sadaf Asnavandi
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Flora Forouzesh
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sirous Zeinali
- Dr. Zeinali's Medical Genetics Laboratory, Kawsar Human Genetics Research Center, Tehran, Iran. .,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
16
|
Wirth B. Spinal Muscular Atrophy: In the Challenge Lies a Solution. Trends Neurosci 2021; 44:306-322. [PMID: 33423791 DOI: 10.1016/j.tins.2020.11.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
The path from gene discovery to therapy in spinal muscular atrophy (SMA) has been a highly challenging endeavor, but also led to one of the most successful stories in neurogenetics. In SMA, a neuromuscular disorder with an often fatal outcome until recently, with those affected never able to sit, stand, or walk, children now achieve these motoric abilities and almost age-based development when treated presymptomatically. This review summarizes the challenges along this 30-year journey. It is also meant to inspire early-career scientists not to give up when things become difficult but to try to uncover the biological underpinnings and transform the challenge into the next big discovery. Without doubt, the improvements seen with the three therapeutic strategies in SMA are impressive; many open questions remain and are discussed in this review.
Collapse
Affiliation(s)
- Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Kerpener Str. 34, 50931 Cologne, Germany.
| |
Collapse
|
17
|
Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing: A Genetic Testing Reference Materials Coordination Program Collaborative Project. J Mol Diagn 2020; 23:103-110. [PMID: 33197628 DOI: 10.1016/j.jmoldx.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 01/21/2023] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disorder predominately caused by bi-allelic loss of the SMN1 gene. Increased copies of SMN2, a low functioning nearly identical paralog, are associated with a less severe phenotype. SMA was recently recommended for inclusion in newborn screening. Clinical laboratories must accurately measure SMN1 and SMN2 copy number to identify SMA patients and carriers, and to identify individuals likely to benefit from therapeutic interventions. Having publicly available and appropriately characterized reference materials with various combinations of SMN1 and SMN2 copy number variants is critical to assure accurate SMA clinical testing. To address this need, the CDC-based Genetic Testing Reference Materials Coordination Program, in collaboration with members of the genetic testing community and the Coriell Institute for Medical Research, has characterized 15 SMA reference materials derived from publicly available cell lines. DNA samples were distributed to four volunteer testing laboratories for genotyping using three different methods. The characterized samples had zero to four copies of SMN1 and zero to five copies SMN2. The samples also contained clinically important allele combinations (eg, zero copies SMN1, three copies SMN2), and several had markers indicative of an SMA carrier. These and other reference materials characterized by the Genetic Testing Reference Materials Coordination Program are available from the Coriell Institute and are proposed to support the quality of clinical laboratory testing.
Collapse
|
18
|
Eggermann K, Gläser D, Abicht A, Wirth B. Spinal muscular atrophy (5qSMA): best practice of diagnostics, newborn screening and therapy. MED GENET-BERLIN 2020. [DOI: 10.1515/medgen-2020-2033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Abstract
Proximal spinal muscular atrophy (SMA) is an autosomal-recessive inherited neuromuscular disorder caused by the degeneration of alpha motor neurons in the anterior horn of the spinal cord. Patients show hypotonia, muscular atrophy and weakness of voluntary proximal muscles. SMA is one of the most common genetic diseases, with a frequency of about 1 in 7,000 newborns in Germany. The vast majority of patients carry a homozygous deletion of exons 7 and 8 of the survival motor neuron (SMN) 1 gene on chromosome 5q13.2; only about 3–4 % of patients are compound heterozygous for this common mutation and an additional subtle mutation in SMN1. The severity of the disease is mainly influenced by the copy number of the highly homologous SMN2.
Since the discovery of the underlying genetic defect 25 years ago, both the diagnostics of SMA and its treatment have undergone constant and in recent times rapid improvements. SMA has become one of the first neuromuscular disorders with effective therapies based on gene targeted strategies such as splice correction of SMN2 via antisense oligonucleotides or small molecules or gene replacement therapy with a self-complementary adeno-associated virus 9 expressing the SMN1-cDNA. With the availability of treatment options, which are most effective when therapy starts at a pre-symptomatic stage, a newborn screening is indispensable and about to be introduced in Germany. New challenges for diagnostic labs as well as for genetic counsellors are inevitable.
This article aims at summarising the current state of SMA diagnostics, treatment and perspectives for this disorder and offering best practice testing guidelines to diagnostic labs.
Collapse
Affiliation(s)
- Katja Eggermann
- Institute of Human Genetics, Medical Faculty , RWTH Aachen University , Pauwelsstr. 30 , Aachen , Germany
| | - Dieter Gläser
- genetikum®, Center for Human Genetics , Wegenerstr. 15 , Neu-Ulm , Germany
| | - Angela Abicht
- Medical Genetics Center Munich , Munich , Germany
- Department of Neurology, Friedrich-Baur-Institute , Klinikum der Ludwig-Maximilians-University , Munich , Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare Diseases , University of Cologne , Kerpener Str. 34 , Cologne , Germany
| |
Collapse
|
19
|
Wadman RI, Jansen MD, Stam M, Wijngaarde CA, Curial CAD, Medic J, Sodaar P, Schouten J, Vijzelaar R, Lemmink HH, van den Berg LH, Groen EJN, van der Pol WL. Intragenic and structural variation in the SMN locus and clinical variability in spinal muscular atrophy. Brain Commun 2020; 2:fcaa075. [PMID: 32954327 PMCID: PMC7425299 DOI: 10.1093/braincomms/fcaa075] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 11/15/2022] Open
Abstract
Clinical severity and treatment response vary significantly between patients with spinal muscular atrophy. The approval of therapies and the emergence of neonatal screening programmes urgently require a more detailed understanding of the genetic variants that underlie this clinical heterogeneity. We systematically investigated genetic variation other than SMN2 copy number in the SMN locus. Data were collected through our single-centre, population-based study on spinal muscular atrophy in the Netherlands, including 286 children and adults with spinal muscular atrophy Types 1–4, including 56 patients from 25 families with multiple siblings with spinal muscular atrophy. We combined multiplex ligation-dependent probe amplification, Sanger sequencing, multiplexed targeted resequencing and digital droplet polymerase chain reaction to determine sequence and expression variation in the SMN locus. SMN1, SMN2 and NAIP gene copy number were determined by multiplex ligation-dependent probe amplification. SMN2 gene variant analysis was performed using Sanger sequencing and RNA expression analysis of SMN by droplet digital polymerase chain reaction. We identified SMN1–SMN2 hybrid genes in 10% of spinal muscular atrophy patients, including partial gene deletions, duplications or conversions within SMN1 and SMN2 genes. This indicates that SMN2 copies can vary structurally between patients, implicating an important novel level of genetic variability in spinal muscular atrophy. Sequence analysis revealed six exonic and four intronic SMN2 variants, which were associated with disease severity in individual cases. There are no indications that NAIP1 gene copy number or sequence variants add value in addition to SMN2 copies in predicting the clinical phenotype in individual patients with spinal muscular atrophy. Importantly, 95% of spinal muscular atrophy siblings in our study had equal SMN2 copy numbers and structural changes (e.g. hybrid genes), but 60% presented with a different spinal muscular atrophy type, indicating the likely presence of further inter- and intragenic variabilities inside as well as outside the SMN locus. SMN2 gene copies can be structurally different, resulting in inter- and intra-individual differences in the composition of SMN1 and SMN2 gene copies. This adds another layer of complexity to the genetics that underlie spinal muscular atrophy and should be considered in current genetic diagnosis and counselling practices.
Collapse
Affiliation(s)
- Renske I Wadman
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Marc D Jansen
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Marloes Stam
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Camiel A Wijngaarde
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Chantall A D Curial
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jelena Medic
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Peter Sodaar
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jan Schouten
- MRC Holland BV, 1057 DL Amsterdam, the Netherlands
| | | | - Henny H Lemmink
- Department of Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Leonard H van den Berg
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ewout J N Groen
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - W Ludo van der Pol
- UMC Utrecht Brain Center, Department of Neurology and Neurosurgery, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| |
Collapse
|
20
|
Zhang J, Wang Y, Ma D, Sun Y, Li Y, Yang P, Luo C, Jiang T, Hu P, Xu Z. Carrier Screening and Prenatal Diagnosis for Spinal Muscular Atrophy in 13,069 Chinese Pregnant Women. J Mol Diagn 2020; 22:817-822. [PMID: 32205292 DOI: 10.1016/j.jmoldx.2020.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/17/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a relatively common, life-shortening, autosomal recessive neuromuscular disease. The carrier frequency of SMA ranges from approximately 0.98% to 2.02%, depending on ethnicity. The American College of Medical Genetics has therefore recommended population screening for SMA carrier status, regardless of race or ethnicity. We performed the largest-scale carrier screening for SMA carriers in mainland China. Carrier screening was offered to 36,470 pregnant women between July 2017 and June 2019, of whom 13,069 women accepted the screening program [35.83%; 95% credibility interval (CI), 35.34%-36.33%]. Copy numbers of exons 7 and 8 in the SMN1 gene were detected by real-time quantitative PCR, and the results were confirmed by multiplex ligation-dependent probe amplification. A total of 231 women were identified as carriers (1.77%; 95% CI, 1.56%-2.01%), indicating a carrier prevalence of approximately 1:56 in the population. After detailed genetic counseling, 207 paternal partners were recalled and tested. Both partners were carriers in 10 couples, of whom prenatal diagnosis was implemented in seven, and one fetus was diagnosed with SMA. Carrier screening could provide couples with informed reproductive choices. Our workflow and experience of carrier screening may facilitate the popularization of SMA carrier screening in mainland China.
Collapse
Affiliation(s)
- Jingjing Zhang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuguo Wang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Dingyuan Ma
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yun Sun
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yahong Li
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Peiying Yang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Tao Jiang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Ping Hu
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| |
Collapse
|
21
|
Butcher S, Smith M, Woodcock IR, Delatycki M, Ryan MM, Forbes R. False Negative Carrier Screening in Spinal Muscular Atrophy. J Child Neurol 2020; 35:274-277. [PMID: 31858866 DOI: 10.1177/0883073819891269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe a case of spinal muscular atrophy diagnosed in an infant despite previous parental carrier testing suggesting low risk of the disease. This case report explains how this situation arose and illustrates that clinicians need to perform diagnostic testing in children where clinical suspicion for spinal muscular atrophy is high, regardless of the result of previous parental carrier testing, because of the risk of false negative results.
Collapse
Affiliation(s)
- Sophie Butcher
- Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Melanie Smith
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ian R Woodcock
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Victoria, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Victoria, Australia
| | - Monique M Ryan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Victoria, Australia
| | - Robin Forbes
- Victorian Clinical Genetics Services, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia
| |
Collapse
|
22
|
Vorster E, Essop FB, Rodda JL, Krause A. Spinal Muscular Atrophy in the Black South African Population: A Matter of Rearrangement? Front Genet 2020; 11:54. [PMID: 32117462 PMCID: PMC7033609 DOI: 10.3389/fgene.2020.00054] [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: 11/16/2018] [Accepted: 01/17/2020] [Indexed: 12/14/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder, characterized by muscle atrophy and impaired mobility. A homozygous deletion of survival motor neuron 1 (SMN1), exon 7 is the main cause of SMA in ~94% of patients worldwide, but only accounts for 51% of South African (SA) black patients. SMN1 and its highly homologous centromeric copy, survival motor neuron 2 (SMN2), are located in a complex duplicated region. Unusual copy number variations (CNVs) have been reported in black patients, suggesting the presence of complex pathogenic rearrangements. The aim of this study was to further investigate the genetic cause of SMA in the black SA population. Multiplex ligation-dependent probe amplification (MLPA) testing was performed on 197 unrelated black patients referred for SMA testing (75 with a homozygous deletion of SMN1, exon 7; 50 with a homozygous deletion of SMN2, exon 7; and 72 clinically suggestive patients with no homozygous deletions). Furthermore, 122 black negative controls were tested. For comparison, 68 white individuals (30 with a homozygous deletion of SMN1, exon 7; 8 with a homozygous deletion of SMN2, exon 7 and 30 negative controls) were tested. Multiple copies (>2) of SMN1, exon 7 were observed in 50.8% (62/122) of black negative controls which could mask heterozygous SMN1 deletions and potential pathogenic CNVs. MLPA is not a reliable technique for detecting carriers in the black SA population. Large deletions extending into the rest of SMN1 and neighboring genes were more frequently observed in black patients with homozygous SMN1, exon 7 deletions when compared to white patients. Homozygous SMN2, exon 7 deletions were commonly observed in black individuals. No clear pathogenic CNVs were identified in black patients but discordant copy numbers of exons suggest complex rearrangements, which may potentially interrupt the SMN1 gene. Only 8.3% (6/72) of clinically suggestive patients had heterozygous deletions of SMN1, exon 7 (1:0) which is lower than previous SA reports of 69.5%. This study emphasizes the lack of understanding of the architecture of the SMN region as well as the cause of SMA in the black SA population. These factors need to be taken into account when counseling and performing diagnostic testing in black populations.
Collapse
Affiliation(s)
- Elana Vorster
- National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Fahmida B Essop
- National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - John L Rodda
- Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
| | - Amanda Krause
- National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
23
|
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.
Collapse
|
24
|
Wirth B, Karakaya M, Kye MJ, Mendoza-Ferreira N. Twenty-Five Years of Spinal Muscular Atrophy Research: From Phenotype to Genotype to Therapy, and What Comes Next. Annu Rev Genomics Hum Genet 2020; 21:231-261. [PMID: 32004094 DOI: 10.1146/annurev-genom-102319-103602] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Twenty-five years ago, the underlying genetic cause for one of the most common and devastating inherited diseases in humans, spinal muscular atrophy (SMA), was identified. Homozygous deletions or, rarely, subtle mutations of SMN1 cause SMA, and the copy number of the nearly identical copy gene SMN2 inversely correlates with disease severity. SMA has become a paradigm and a prime example of a monogenic neurological disorder that can be efficiently ameliorated or nearly cured by novel therapeutic strategies, such as antisense oligonucleotide or gene replacement therapy. These therapies enable infants to survive who might otherwise have died before the age of two and allow individuals who have never been able to sit or walk to do both. The major milestones on the road to these therapies were to understand the genetic cause and splice regulation of SMN genes, the disease's phenotype-genotype variability, the function of the protein and the main affected cellular pathways and tissues, the disease's pathophysiology through research on animal models, the windows of opportunity for efficient treatment, and how and when to treat patients most effectively.This review aims to bridge our knowledge from phenotype to genotype to therapy, not only highlighting the significant advances so far but also speculating about the future of SMA screening and treatment.
Collapse
Affiliation(s)
- Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Min Jeong Kye
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Natalia Mendoza-Ferreira
- Institute of Human Genetics, Center for Molecular Medicine Cologne and Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany;
| |
Collapse
|
25
|
Vitello GA, Calì F, Vinci M, Scuderi C, L’Episcopo F, Musumeci A, Musumeci SA, Nicotera AG. Possible implication of undescribed SMN1-SMN2 genotype in chronic EMG-pattern of SMA with transitory acute denervation. JOURNAL OF MUSCULOSKELETAL & NEURONAL INTERACTIONS 2020; 20:610-613. [PMID: 33265090 PMCID: PMC7716687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Spinal muscular atrophy (SMA) refers to a group of genetic neuromuscular disorders affecting lower motor neurons causative of numerous phenotypes. To date, according to the age of onset, maximum muscular activity achieved, and life expectation four types of SMA are recognized, all caused by mutations in the SMN1 gene with SMN2 copy number influencing disease severity. Herein, we describe the case of a 31-year-old young male with normal psychomotor development who has experienced fatigue, cramps, and muscle fasciculations in the lower limbs for a period of 2 months. Based on electrophysiological and clinical findings we performed SMA genetic, clinical exome and RNA expression of candidate genes which led us to suggest SMN1-SMN2 genes [(2+0) and (0+0)] combination as possibly being implicated in the phenotype.
Collapse
Affiliation(s)
| | | | | | | | - Francesca L’Episcopo
- Oasi Research Institute – IRCCS, Troina, Italy,Corresponding author: Dr. Francesco Calì, Oasi Research Institute – IRCCS, Via Conte Ruggero 73, 94018Troina, Italy E-mail:
| | | | | | - Antonio G. Nicotera
- Oasi Research Institute – IRCCS, Troina, Italy,Child Neuropsychiatry Unit, Department of Human Pathology of the Adult and Developmental Age University Hospital “G. Martino” Messina, Italy
| |
Collapse
|
26
|
Wei X, Lv W, Tan H, Liang D, Wu L. Development and validation of a haplotype-free technique for non-invasive prenatal diagnosis of spinal muscular atrophy. J Clin Lab Anal 2019; 34:e23046. [PMID: 31556165 PMCID: PMC7031576 DOI: 10.1002/jcla.23046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/31/2019] [Accepted: 09/09/2019] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE To develop a technique for non-invasive prenatal diagnosis of spinal muscular atrophy and validate its performance. STUDY DESIGN Pregnant women with 1 copy of SMN1 and male fetuses were enrolled. Seventeen women were included in test set A, and 10 of them were selected into test set B randomly and blinded. The two sets were tested independently by two different researchers blinded to fetal genotypes. Fetal DNA fractions were calculated based on the relative proportion of mapped chromosome Y sequencing reads. An algorithm was developed to decide fetal SMN1 copy numbers. RESULTS The concordance rate with the results of MLPA testing of amniocyte DNA was 94.12% in test set A and 90% in set B. For all tests with a classifiable result, the percent of agreement with the results of MLPA testing of amniocyte DNA was up to 100% (25/25). CONCLUSION We have developed a direct, rapid, and low-cost technique, which has a potential to be utilized for first-trimester non-invasive prenatal diagnosis and screening for spinal muscular atrophy with considerable reliability and feasibility.
Collapse
Affiliation(s)
- Xianda Wei
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Weigang Lv
- Hunan Jiahui Genetics Hospital, Changsha, China
| | - Hu Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lingqian Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| |
Collapse
|
27
|
High-throughput genetic newborn screening for spinal muscular atrophy by rapid nucleic acid extraction from dried blood spots and 384-well qPCR. Eur J Hum Genet 2019; 28:23-30. [PMID: 31363188 DOI: 10.1038/s41431-019-0476-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/27/2019] [Accepted: 07/03/2019] [Indexed: 12/17/2022] Open
Abstract
Establishing nucleic acid-based assays for genetic newborn screening (NBS) provides the possibility to screen for genetically encoded diseases like spinal muscular atrophy (SMA), best before the onset of symptoms. Such assays should be easily scalable to 384-well reactions that make the screening of up to 2000 samples per day possible. We developed a test procedure based on a cleanup protocol for dried blood spots and a quantitative (q)PCR to screen for a homozygous deletion of exon 7 of the survival of motor neuron 1 gene (SMN1) that is responsible for >95% of SMA patients. Performance of this setup is evaluated in detail and tested on routine samples. Our cleanup method for nucleic acids from dried blood spots yields enough DNA for diverse subsequent qPCR applications. To date, we have applied this approach to test 213,279 samples within 18 months. Thirty patients were identified and confirmed, implying an incidence of 1:7109 for the homozygous deletion. Using our cleanup method, a rapid workflow could be established to prepare nucleic acids from dried blood spot cards. Targeting the exon 7 deletion, no invalid, false-positive, or false-negative results were reported to date. This allows timely identification of the disease and grants access to the recently introduced treatment options, in most cases before the onset of symptoms. Carriers are not identified, thus, there are no concerns of whether to report them.
Collapse
|
28
|
Vijzelaar R, Snetselaar R, Clausen M, Mason AG, Rinsma M, Zegers M, Molleman N, Boschloo R, Yilmaz R, Kuilboer R, Lens S, Sulchan S, Schouten J. The frequency of SMN gene variants lacking exon 7 and 8 is highly population dependent. PLoS One 2019; 14:e0220211. [PMID: 31339938 PMCID: PMC6655720 DOI: 10.1371/journal.pone.0220211] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/10/2019] [Indexed: 01/30/2023] Open
Abstract
Spinal Muscular Atrophy (SMA) is a disorder characterized by the degeneration of motor neurons in the spinal cord, leading to muscular atrophy. In the majority of cases, SMA is caused by the homozygous absence of the SMN1 gene. The disease severity of SMA is strongly influenced by the copy number of the closely related SMN2 gene. In addition, an SMN variant lacking exons 7 and 8 has been reported in 8% and 23% of healthy Swedish and Spanish individuals respectively. We tested 1255 samples from the 1000 Genomes Project using a new version of the multiplex ligation-dependent probe amplification (MLPA) P021 probemix that covers each SMN exon. The SMN variant lacking exons 7 and 8 was present in up to 20% of individuals in several Caucasian populations, while being almost completely absent in various Asian and African populations. This SMN1/2Δ7-8 variant appears to be derived from an ancient deletion event as the deletion size is identical in 99% of samples tested. The average total copy number of SMN1, SMN2 and the SMN1/2Δ7-8 variant combined was remarkably comparable in all populations tested, ranging from 3.64 in Asian to 3.75 in African samples.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Sylvia Lens
- MRC Holland B.V., Amsterdam, The Netherlands
| | | | | |
Collapse
|
29
|
Ruhno C, McGovern VL, Avenarius MR, Snyder PJ, Prior TW, Nery FC, Muhtaseb A, Roggenbuck JS, Kissel JT, Sansone VA, Siranosian JJ, Johnstone AJ, Nwe PH, Zhang RZ, Swoboda KJ, Burghes AHM. Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype. Hum Genet 2019; 138:241-256. [PMID: 30788592 PMCID: PMC6503527 DOI: 10.1007/s00439-019-01983-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by loss or mutation of the survival motor neuron 1 (SMN1) gene and retention of SMN2. We performed targeted capture and sequencing of the SMN2, CFTR, and PLS3 genes in 217 SMA patients. We identified a 6.3 kilobase deletion that occurred in both SMN1 and SMN2 (SMN1/2) and removed exons 7 and 8. The deletion junction was flanked by a 21 bp repeat that occurred 15 times in the SMN1/2 gene. We screened for its presence in 466 individuals with the known SMN1 and SMN2 copy numbers. In individuals with 1 SMN1 and 0 SMN2 copies, the deletion occurred in 63% of cases. We modeled the deletion junction frequency and determined that the deletion occurred in both SMN1 and SMN2. We have identified the first deletion junction where the deletion removes exons 7 and 8 of SMN1/2. As it occurred in SMN1, it is a pathogenic mutation. We called variants in the PLS3 and SMN2 genes, and tested for association with mild or severe exception patients. The variants A-44G, A-549G, and C-1897T in intron 6 of SMN2 were significantly associated with mild exception patients, but no PLS3 variants correlated with severity. The variants occurred in 14 out of 58 of our mild exception patients, indicating that mild exception patients with an intact SMN2 gene and without modifying variants occur. This sample set can be used in the association analysis of candidate genes outside of SMN2 that modify the SMA phenotype.
Collapse
Affiliation(s)
- Corey Ruhno
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Vicki L McGovern
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | | | - Pamela J Snyder
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Thomas W Prior
- Department of Pathology, Case Western Reserve Medical Center, Cleveland, OH, USA
| | - Flavia C Nery
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Abdurrahman Muhtaseb
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - John T Kissel
- Department of Neurology, The Ohio State University, Columbus, OH, USA
| | | | - Jennifer J Siranosian
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alec J Johnstone
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Pann H Nwe
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ren Z Zhang
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn J Swoboda
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
30
|
Boemer F, Caberg JH, Dideberg V, Dardenne D, Bours V, Hiligsmann M, Dangouloff T, Servais L. Newborn screening for SMA in Southern Belgium. Neuromuscul Disord 2019; 29:343-349. [PMID: 31030938 DOI: 10.1016/j.nmd.2019.02.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 11/29/2022]
Abstract
Approval was recently granted for a new treatment for spinal muscular atrophy (SMA). Given that the treatment is effective when administered early and the societal burden of SMA-related disability, the implementation of a newborn screening program is warranted. We describe the stepwise process that led us to launch a newborn screening program for SMA in Southern Belgium. Different political, ethical, and clinical partners were informed about this project and were involved in its governance, as were genetic and screening labs. We developed and validated a newborn screening method to specifically recognize homozygous deletions of exon 7 in the SMN1 gene. Subsequently, a 3-year pilot study has been recently initiated in one Belgian neonatal screening laboratory to cover 17.000 neonates per year. Coverage extension to all of Southern Belgium to screen 55.000 babies each year is underway.
Collapse
Affiliation(s)
- François Boemer
- Biochemical Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege 4000, Belgium.
| | - Jean-Hubert Caberg
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Vinciane Dideberg
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Domien Dardenne
- Molecular Genetics Lab, Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Vincent Bours
- Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium
| | - Mickaël Hiligsmann
- Department of Health Services Research, CAPHRI Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Tamara Dangouloff
- I-Motion, Platform for Pediatric Clinical Trials, Arnold Trousseau Hospital, Paris, France; Neuromuscular Center, CHR Citadelle, University of Liege, Liege, Belgium
| | - Laurent Servais
- I-Motion, Platform for Pediatric Clinical Trials, Arnold Trousseau Hospital, Paris, France; Neuromuscular Center, CHR Citadelle, University of Liege, Liege, Belgium
| |
Collapse
|
31
|
Maretina MA, Zheleznyakova GY, Lanko KM, Egorova AA, Baranov VS, Kiselev AV. Molecular Factors Involved in Spinal Muscular Atrophy Pathways as Possible Disease-modifying Candidates. Curr Genomics 2018; 19:339-355. [PMID: 30065610 PMCID: PMC6030859 DOI: 10.2174/1389202919666180101154916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by mutations in the SMN1 gene. Being a monogenic disease, it is characterized by high clinical heterogeneity. Variations in penetrance and severity of symptoms, as well as clinical discrepancies between affected family members can result from modifier genes influence on disease manifestation. SMN2 gene copy number is known to be the main phenotype modifier and there is growing evidence of additional factors contributing to SMA severity. Potential modifiers of spinal muscular atrophy can be found among the wide variety of different factors, such as multiple proteins interacting with SMN or promoting motor neuron survival, epigenetic modifications, transcriptional or splicing factors influencing SMN2 expression. Study of these factors enables to reveal mechanisms underlying SMA pathology and can have pronounced clinical application.
Collapse
Affiliation(s)
- Marianna A. Maretina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Galina Y. Zheleznyakova
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska Universitetssjukhuset, 171 76 Stockholm, Sweden
| | - Kristina M. Lanko
- Saint Petersburg State Institute of Technology, Moskovsky prospect, 26, Saint Petersburg190013, Russia
| | - Anna A. Egorova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
| | - Vladislav S. Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Anton V. Kiselev
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
| |
Collapse
|
32
|
Alves I, Houle AA, Hussin JG, Awadalla P. The impact of recombination on human mutation load and disease. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160465. [PMID: 29109227 PMCID: PMC5698626 DOI: 10.1098/rstb.2016.0465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Recombination promotes genomic integrity among cells and tissues through double-strand break repair, and is critical for gamete formation and fertility through a strict regulation of the molecular mechanisms associated with proper chromosomal disjunction. In humans, congenital defects and recurrent structural abnormalities can be attributed to aberrant meiotic recombination. Moreover, mutations affecting genes involved in recombination pathways are directly linked to pathologies including infertility and cancer. Recombination is among the most prominent mechanism shaping genome variation, and is associated with not only the structuring of genomic variability, but is also tightly linked with the purging of deleterious mutations from populations. Together, these observations highlight the multiple roles of recombination in human genetics: its ability to act as a major force of evolution, its molecular potential to maintain genome repair and integrity in cell division and its mutagenic cost impacting disease evolution.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
Collapse
Affiliation(s)
- Isabel Alves
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Armande Ang Houle
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Molecular Genetics, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Julie G Hussin
- Montreal Heart Institute, Department of Medicine, University of Montreal, 5000 Rue Bélanger, Montréal, Quebec, Canada H1T 1C8
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Philip Awadalla
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Molecular Genetics, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| |
Collapse
|
33
|
Mercuri E, Finkel RS, Muntoni F, Wirth B, Montes J, Main M, Mazzone ES, Vitale M, Snyder B, Quijano-Roy S, Bertini E, Davis RH, Meyer OH, Simonds AK, Schroth MK, Graham RJ, Kirschner J, Iannaccone ST, Crawford TO, Woods S, Qian Y, Sejersen T. Diagnosis and management of spinal muscular atrophy: Part 1: Recommendations for diagnosis, rehabilitation, orthopedic and nutritional care. Neuromuscul Disord 2017; 28:103-115. [PMID: 29290580 DOI: 10.1016/j.nmd.2017.11.005] [Citation(s) in RCA: 503] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/06/2017] [Accepted: 11/13/2017] [Indexed: 01/02/2023]
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder due to a defect in the survival motor neuron 1 (SMN1) gene. Its incidence is approximately 1 in 11,000 live births. In 2007, an International Conference on the Standard of Care for SMA published a consensus statement on SMA standard of care that has been widely used throughout the world. Here we report a two-part update of the topics covered in the previous recommendations. In part 1 we present the methods used to achieve these recommendations, and an update on diagnosis, rehabilitation, orthopedic and spinal management; and nutritional, swallowing and gastrointestinal management. Pulmonary management, acute care, other organ involvement, ethical issues, medications, and the impact of new treatments for SMA are discussed in part 2.
Collapse
Affiliation(s)
- Eugenio Mercuri
- Paediatric Neurology Unit, Catholic University, Rome, Italy; Centro Clinico Nemo, Policlinico Gemelli, Rome, Italy.
| | - Richard S Finkel
- Nemours Children's Hospital, University of Central Florida College of Medicine, Orlando, FL, USA
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Diseases and Institute for Genetics, University of Cologne, Germany
| | - Jacqueline Montes
- Departments of Rehabilitation and Regenerative Medicine and Neurology, Columbia University Medical Center, New York, NY, USA
| | - Marion Main
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Elena S Mazzone
- Paediatric Neurology Unit, Catholic University, Rome, Italy; Centro Clinico Nemo, Policlinico Gemelli, Rome, Italy
| | - Michael Vitale
- Department of Orthopaedic Surgery, Columbia University Medical Center, New York, NY, USA
| | - Brian Snyder
- Department of Orthopaedic Surgery, Children's Hospital, Harvard Medical School, Boston, USA
| | - Susana Quijano-Roy
- Assistance Publique des Hôpitaux de Paris (AP-HP), Unit of Neuromuscular Disorders, Department of Pediatric Intensive Care, Neurology and Rehabilitation, Hôpital Raymond Poincaré, Garches, France; Hôpitaux Universitaires Paris-Ile-de-France Ouest, INSERM U 1179, University of Versailles Saint-Quentin-en-Yvelines (UVSQ), Paris, France
| | - Enrico Bertini
- Unit of Neuromuscular & Neurodegenerative Disorders, Dept of Neurosciences & Neurorehabilitation, Bambino Gesù Children's Research Hospital, Rome, Italy
| | | | - Oscar H Meyer
- Division of Pulmonology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Anita K Simonds
- NIHR Respiratory Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust, London, UK
| | - Mary K Schroth
- Division of Pediatric Pulmonary, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, American Family Children's Hospital, Madison, WI, USA
| | - Robert J Graham
- Division of Critical Care, Dept of Anesthesiology, Perioperative & Pain Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susan T Iannaccone
- Departments of Pediatrics and Neurology and Neurotherapeutics, Division of Pediatric Neurology, University of Texas Southwestern Medical Center and Children's Medical Center Dallas, USA
| | - Thomas O Crawford
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Simon Woods
- Policy Ethics and Life Sciences Research Centre, Newcastle University, Newcastle, UK
| | | | - Thomas Sejersen
- Department of Women's and Children's Health, Paediatric Neurology, Karolinska Institute, Stockholm, Sweden
| | | |
Collapse
|
34
|
Ottesen EW, Seo J, Singh NN, Singh RN. A Multilayered Control of the Human Survival Motor Neuron Gene Expression by Alu Elements. Front Microbiol 2017; 8:2252. [PMID: 29187847 PMCID: PMC5694776 DOI: 10.3389/fmicb.2017.02252] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
Humans carry two nearly identical copies of Survival Motor Neuron gene: SMN1 and SMN2. Mutations or deletions of SMN1, which codes for SMN, cause spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Aberrant expression or localization of SMN has been also implicated in other pathological conditions, including male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. SMN2 fails to compensate for the loss of SMN1 due to skipping of exon 7, leading to the production of SMNΔ7, an unstable protein. In addition, SMNΔ7 is less functional due to the lack of a critical C-terminus of the full-length SMN, a multifunctional protein. Alu elements are specific to primates and are generally found within protein coding genes. About 41% of the human SMN gene including promoter region is occupied by more than 60 Alu-like sequences. Here we discuss how such an abundance of Alu-like sequences may contribute toward SMA pathogenesis. We describe the likely impact of Alu elements on expression of SMN. We have recently identified a novel exon 6B, created by exonization of an Alu-element located within SMN intron 6. Irrespective of the exon 7 inclusion or skipping, transcripts harboring exon 6B code for the same SMN6B protein that has altered C-terminus compared to the full-length SMN. We have demonstrated that SMN6B is more stable than SMNΔ7 and likely functions similarly to the full-length SMN. We discuss the possible mechanism(s) of regulation of SMN exon 6B splicing and potential consequences of the generation of exon 6B-containing transcripts.
Collapse
Affiliation(s)
- Eric W Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| |
Collapse
|
35
|
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.
Collapse
|
36
|
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: 343] [Impact Index Per Article: 49.0] [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.
Collapse
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
| |
Collapse
|
37
|
Verhaart IEC, Robertson A, Leary R, McMacken G, König K, Kirschner J, Jones CC, Cook SF, Lochmüller H. A multi-source approach to determine SMA incidence and research ready population. J Neurol 2017; 264:1465-1473. [PMID: 28634652 PMCID: PMC5502065 DOI: 10.1007/s00415-017-8549-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 12/02/2022]
Abstract
In spinal muscular atrophy (SMA), degeneration of motor neurons causes progressive muscular weakness, which is caused by homozygous deletion of the SMN1 gene. Available epidemiological data on SMA are scarce, often outdated, and limited to relatively small regions or populations. Combining data from different sources including genetic laboratories and patient registries may provide better insight of the disease epidemiology. To investigate the incidence of genetically confirmed SMA, and the number of patients who are able and approachable to participate in new clinical trials and observational research, we used both genetic laboratories, the TREAT-NMD Global SMA Patient Registry and the Care and Trial Sites Registry (CTSR). In Europe, 4653 patients were genetically diagnosed by the genetic laboratories in the 5-year period 2011 to 2015, with 992 diagnosed in 2015 alone. The data provide an estimated incidence of SMA in Europe of 1 in 3900-16,000 live births. Patient numbers in the national patient registries and CTSR were considerably lower. By far, most patients registered in the national patient registries and the CTSR live in Europe and are reported to have SMA type II. Considerable differences between countries in patient participation in the registries were observed. Our findings indicate that not all patients with SMA are accessed by specialist healthcare services and these patients may not have access to research opportunities and optimal care.
Collapse
Affiliation(s)
- Ingrid E. C. Verhaart
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - Agata Robertson
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - Rebecca Leary
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - Grace McMacken
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| | - Kirsten König
- Clinical Trials Unit, Medical Center, University of Freiburg, Freiburg, Germany
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Medical Center, University of Freiburg, Freiburg, Germany
| | | | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
| |
Collapse
|
38
|
Rietz A, Li H, Quist KM, Cherry JJ, Lorson CL, Burnett BG, Kern NL, Calder AN, Fritsche M, Lusic H, Boaler PJ, Choi S, Xing X, Glicksman MA, Cuny GD, Androphy EJ, Hodgetts KJ. Discovery of a Small Molecule Probe That Post-Translationally Stabilizes the Survival Motor Neuron Protein for the Treatment of Spinal Muscular Atrophy. J Med Chem 2017; 60:4594-4610. [PMID: 28481536 DOI: 10.1021/acs.jmedchem.6b01885] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Spinal muscular atrophy (SMA) is the leading genetic cause of infant death. We previously developed a high-throughput assay that employs an SMN2-luciferase reporter allowing identification of compounds that act transcriptionally, enhance exon recognition, or stabilize the SMN protein. We describe optimization and characterization of an analog suitable for in vivo testing. Initially, we identified analog 4m that had good in vitro properties but low plasma and brain exposure in a mouse PK experiment due to short plasma stability; this was overcome by reversing the amide bond and changing the heterocycle. Thiazole 27 showed excellent in vitro properties and a promising mouse PK profile, making it suitable for in vivo testing. This series post-translationally stabilizes the SMN protein, unrelated to global proteasome or autophagy inhibition, revealing a novel therapeutic mechanism that should complement other modalities for treatment of SMA.
Collapse
Affiliation(s)
- Anne Rietz
- Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Hongxia Li
- Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Kevin M Quist
- Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Jonathan J Cherry
- Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Christian L Lorson
- Department of Veterinary Pathobiology, Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65201, United States
| | - Barrington G Burnett
- Department of Anatomy, Physiology and Genetics, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
| | - Nicholas L Kern
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Alyssa N Calder
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Melanie Fritsche
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Hrvoje Lusic
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Patrick J Boaler
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Sungwoon Choi
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Xuechao Xing
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Marcie A Glicksman
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Gregory D Cuny
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| | - Elliot J Androphy
- Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
| | - Kevin J Hodgetts
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women's Hospital and Harvard Medical School , 65 Landsdowne Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
39
|
Calder AN, Androphy EJ, Hodgetts KJ. Small Molecules in Development for the Treatment of Spinal Muscular Atrophy. J Med Chem 2016; 59:10067-10083. [PMID: 27490705 PMCID: PMC5744254 DOI: 10.1021/acs.jmedchem.6b00670] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease resulting from pathologically low levels of survival motor neuron (SMN) protein. The majority of mRNA from the SMN2 allele undergoes alternative splicing and excludes critical codons, causing an SMN protein deficiency. While there is currently no FDA-approved treatment for SMA, early therapeutic efforts have focused on testing repurposed drugs such as phenylbutyrate (2), valproic acid (3), riluzole (6), hydroxyurea (7), and albuterol (9), none of which has demonstrated clinical effectiveness. More recently, clinical trials have focused on novel small-molecule compounds identified from high-throughput screening and medicinal chemistry optimization such as olesoxime (11), CK-2127107, RG7800, LMI070, and RG3039 (17). In this paper, we review both repurposed drugs and small-molecule compounds discovered following medicinal chemistry optimization for the potential treatment of SMA.
Collapse
Affiliation(s)
- Alyssa N. Calder
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women’s Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| | - Elliot J. Androphy
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kevin J. Hodgetts
- Laboratory for Drug Discovery in Neurodegeneration, Brigham & Women’s Hospital and Harvard Medical School, 65 Landsdowne Street, Cambridge, MA 02139, USA
| |
Collapse
|
40
|
Dimitriadi M, Derdowski A, Kalloo G, Maginnis MS, O'Hern P, Bliska B, Sorkaç A, Nguyen KCQ, Cook SJ, Poulogiannis G, Atwood WJ, Hall DH, Hart AC. Decreased function of survival motor neuron protein impairs endocytic pathways. Proc Natl Acad Sci U S A 2016; 113:E4377-86. [PMID: 27402754 PMCID: PMC4968725 DOI: 10.1073/pnas.1600015113] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by depletion of the ubiquitously expressed survival motor neuron (SMN) protein, with 1 in 40 Caucasians being heterozygous for a disease allele. SMN is critical for the assembly of numerous ribonucleoprotein complexes, yet it is still unclear how reduced SMN levels affect motor neuron function. Here, we examined the impact of SMN depletion in Caenorhabditis elegans and found that decreased function of the SMN ortholog SMN-1 perturbed endocytic pathways at motor neuron synapses and in other tissues. Diminished SMN-1 levels caused defects in C. elegans neuromuscular function, and smn-1 genetic interactions were consistent with an endocytic defect. Changes were observed in synaptic endocytic proteins when SMN-1 levels decreased. At the ultrastructural level, defects were observed in endosomal compartments, including significantly fewer docked synaptic vesicles. Finally, endocytosis-dependent infection by JC polyomavirus (JCPyV) was reduced in human cells with decreased SMN levels. Collectively, these results demonstrate for the first time, to our knowledge, that SMN depletion causes defects in endosomal trafficking that impair synaptic function, even in the absence of motor neuron cell death.
Collapse
Affiliation(s)
- Maria Dimitriadi
- Department of Neuroscience, Brown University, Providence, RI 02912; Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, United Kingdom
| | - Aaron Derdowski
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912
| | - Geetika Kalloo
- Department of Neuroscience, Brown University, Providence, RI 02912
| | - Melissa S Maginnis
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912; Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469
| | - Patrick O'Hern
- Department of Neuroscience, Brown University, Providence, RI 02912
| | - Bryn Bliska
- Department of Neuroscience, Brown University, Providence, RI 02912
| | - Altar Sorkaç
- Department of Neuroscience, Brown University, Providence, RI 02912
| | - Ken C Q Nguyen
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Steven J Cook
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - George Poulogiannis
- Chester Beatty Labs, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Walter J Atwood
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912
| | - David H Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Anne C Hart
- Department of Neuroscience, Brown University, Providence, RI 02912;
| |
Collapse
|
41
|
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]
|
42
|
Prior TW, Nagan N. Spinal Muscular Atrophy: Overview of Molecular Diagnostic Approaches. ACTA ACUST UNITED AC 2016; 88:9.27.1-9.27.13. [PMID: 26724723 DOI: 10.1002/0471142905.hg0927s88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease and the most common genetic cause of infant mortality, affecting ∼1 in 10,000 live births. The disease is characterized by progressive symmetrical muscle weakness resulting from the degeneration and loss of anterior horn cells in the spinal cord and brain stem nuclei. The disease is classified on the basis of age of onset and clinical course. SMA is caused by mutations in the telomeric copy of the survival motor neuron 1 (SMN1) gene, but all patients retain a centromeric copy of the gene, SMN2. The homozygous absence of the SMN1 exon 7 has been observed in the majority of patients and is being utilized as a reliable and sensitive SMA diagnostic test. In the majority of cases, the disease severity correlates inversely with an increased SMN2 gene copy number. Carrier detection, in the deletion cases, relies on the accurate determination of the SMN1 gene copies. Since SMA is one of the most common lethal genetic disorders, with a carrier frequency of 1 in 40 to 1 in 60, direct carrier dosage testing has been beneficial to many families. This unit attempts to highlight the molecular genetics of SMA with a focus on the advantages and limitations of the current molecular technologies.
Collapse
Affiliation(s)
- Thomas W Prior
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Narasimhan Nagan
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
| |
Collapse
|
43
|
Larson JL, Silver AJ, Chan D, Borroto C, Spurrier B, Silver LM. Validation of a high resolution NGS method for detecting spinal muscular atrophy carriers among phase 3 participants in the 1000 Genomes Project. BMC MEDICAL GENETICS 2015; 16:100. [PMID: 26510457 PMCID: PMC4625734 DOI: 10.1186/s12881-015-0246-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022]
Abstract
Background Spinal muscular atrophy (SMA) is the most common pan-ethnic cause of early childhood death due to mutations in a single gene, SMN1. Most chromosome 5 homologs have a functional gene and dysfunctional copy, SMN2, with a single synonymous base substitution that results in faulty RNA splicing. However, the copy number of SMN1 and SMN2 is highly variable, and one in 60 adults worldwide are SMA carriers. Although population-wide screening is recommended, current SMA carrier tests have not been incorporated into targeted gene panels. Methods Here we describe a novel computational protocol for determining SMA carrier status based solely on individual exome data. Our method utilizes a Bayesian hierarchical model to quantify an individual’s carrier probability given only his or her SMN1 and SMN2 reads at six loci of interest. Results We find complete concordance with results obtained with the current qPCR-based testing standard in known SMA carriers and affecteds. We applied our protocol to the phase 3 cohort of the 1,000 Genomes Project and found carrier frequencies in multiple populations consistent with the present literature. Conclusion Our process is a convenient, robust alternative to qPCR, which can easily be integrated into the analysis of large multi-gene NGS carrier screens. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0246-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Ari J Silver
- GenePeeks, Inc., Cambridge, MA, USA. .,GenePeeks, Inc., New York, NY, USA.
| | | | | | | | - Lee M Silver
- GenePeeks, Inc., Cambridge, MA, USA. .,GenePeeks, Inc., New York, NY, USA. .,Department of Molecular Biology and the Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
44
|
Brkušanin M, Kosać A, Jovanović V, Pešović J, Brajušković G, Dimitrijević N, Todorović S, Romac S, Milić Rašić V, Savić-Pavićević D. Joint effect of the SMN2 and SERF1A genes on childhood-onset types of spinal muscular atrophy in Serbian patients. J Hum Genet 2015; 60:723-8. [PMID: 26311540 DOI: 10.1038/jhg.2015.104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/08/2015] [Accepted: 07/30/2015] [Indexed: 11/09/2022]
Abstract
Spinal muscular atrophy (SMA) is caused by functional loss of the survival of motor neuron 1 (SMN1) gene. Despite genetic homogeneity, phenotypic variability indicates the involvement of disease modifiers. SMN1 is located in 5q13.2 segmental duplication, enriched in genes and prone to unequal rearrangements, which results in copy number polymorphism (CNP). We examined the influence of CNP of 5q13.2 genes and their joint effect on childhood-onset SMA phenotype. Multiplex ligation-dependent probe amplification (MLPA) was used to construct 5q13.2 alleles and assess copy number of the SMN2, small EDRK-rich factor 1A (SERF1A) and NLR family apoptosis inhibitory protein (NAIP) genes in 99 Serbian patients with SMN1 homozygous absence (23-type I, 37-type II and 39-mild type III) and 122 patients' parents. Spearman rank test was performed to test correlation of individual genes and SMA type. Generalized linear models and backward selection were performed to obtain a model explaining phenotypic variation with the smallest set of variables. 5q13.2 alleles most commonly associated with type I harbored large-scale deletions, while those detected in types II and III originated from conversion of SMN1 to SMN2. Inverse correlation was observed between SMN2, SERF1A and NAIP CNP and SMA type (P=2.2e-16, P=4.264e-10, P=2.722e-8, respectively). The best minimal model describing phenotypic variability included SMN2 (P<2e-16), SERF1A (P<2e-16) and their interaction (P=0.02628). SMN2 and SERF1A have a joint modifying effect on childhood-onset SMA phenotype.
Collapse
Affiliation(s)
- Miloš Brkušanin
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Ana Kosać
- Clinic for Neurology and Psychiatry for Children and Youth, Belgrade, Serbia
| | - Vladimir Jovanović
- Department of Genetic Research, Institute for Biological Research 'Siniša Stanković', University of Belgrade, Belgrade, Serbia
| | - Jovan Pešović
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Goran Brajušković
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Nikola Dimitrijević
- Department of Neurology, University Children's Hospital, Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Slobodanka Todorović
- Clinic for Neurology and Psychiatry for Children and Youth, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Stanka Romac
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Vedrana Milić Rašić
- Clinic for Neurology and Psychiatry for Children and Youth, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| |
Collapse
|
45
|
Genetic findings of Cypriot spinal muscular atrophy patients. Neurol Sci 2015; 36:1829-34. [PMID: 26017350 DOI: 10.1007/s10072-015-2263-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive, neurodegenerative disorder characterised commonly by proximal muscle weakness and wasting in the absence of sensory signs. Deletion or disruption of the SMN1 gene causes the disease. The SMN1 gene is located within an inverted duplication on chromosome 5q13 with the genes SMN2, NAIP and GTF2H2. MLPA analysis of 13 Cypriot SMA patients revealed that, 12 patients carried a homozygous SMN1 gene deletion and one patient carried two copies of the SMN1 gene. Two of 13 cases were a consequence of a paternally originating de novo mutation. Five genotypes were identified within the population, with the most frequent being a homozygous SMN1 and NAIP genes deletion. In conclusion, genotype-phenotype correlation revealed that SMN2 is inversely related to disease severity and that NAIP and GTF2H2 act as negative modifiers. This study provided, for the first time, a comprehensive overview of gene copy numbers and inheritance patterns within Cypriot SMA families.
Collapse
|
46
|
Clinical utility gene card for: Proximal spinal muscular atrophy (SMA) - update 2015. Eur J Hum Genet 2015; 23:ejhg201590. [PMID: 25990799 DOI: 10.1038/ejhg.2015.90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 03/03/2015] [Accepted: 03/19/2015] [Indexed: 11/08/2022] Open
|
47
|
Phan HC, Taylor JL, Hannon H, Howell R. Newborn screening for spinal muscular atrophy: Anticipating an imminent need. Semin Perinatol 2015; 39:217-29. [PMID: 25979781 DOI: 10.1053/j.semperi.2015.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality. Children with type I SMA typically die by the age of 2 years. Recent progress in gene modification and other innovative therapies suggest that improved outcomes may soon be forthcoming. In animal models, therapeutic intervention initiated before the loss of motor neurons alters SMA phenotype and increases lifespan. Presently, supportive care including respiratory, nutritional, physiatry, and orthopedic management can ameliorate clinical symptoms and improve survival rates if SMA is diagnosed early in life. Newborn screening could help optimize these potential benefits. A recent report demonstrated that SMA detection can be multiplexed at minimal additional cost with the assay for severe combined immunodeficiency, already implemented by many newborn screening programs. The public health community should remain alert to the rapidly changing developments in early detection and treatment of SMA.
Collapse
Affiliation(s)
- Han C Phan
- Department of Pediatrics, Emory University, Atlanta, GA.
| | | | - Harry Hannon
- Newborn Screening Consensus Committee, Clinical and Laboratory Standards Institute (CLSI), Wayne, PA
| | - Rodney Howell
- Miller School of Medicine, University of Miami, Miami, FL
| |
Collapse
|
48
|
Miskovic M, Lalic T, Radivojevic D, Cirkovic S, Ostojic S, Guc-Scekic M. Ten years of experience in molecular prenatal diagnosis and carrier testing for spinal muscular atrophy among families from Serbia. Int J Gynaecol Obstet 2013; 124:55-8. [DOI: 10.1016/j.ijgo.2013.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/04/2013] [Accepted: 09/26/2013] [Indexed: 12/12/2022]
|
49
|
Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, Eversley C, Kornreich R, Desnick RJ, Edelmann L. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genet Med 2013; 16:149-56. [PMID: 23788250 DOI: 10.1038/gim.2013.84] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 05/02/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Spinal muscular atrophy is a common autosomal-recessive disorder caused by mutations of the SMN1 gene. Spinal muscular atrophy carrier screening uses dosage-sensitive methods that determine SMN1 copy number, and the frequency of carriers varies by ethnicity, with detection rates ranging from 71 to 94% due to the inability to identify silent (2 + 0) carriers with two copies of SMN1 on one chromosome 5 and deletion on the other. We hypothesized that identification of deletion and/or duplication founder alleles might provide an approach to identify silent carriers in various ethnic groups. METHODS SMN1 founder alleles were investigated in the Ashkenazi Jewish population by microsatellite analysis and next-generation sequencing. RESULTS An extended haplotype block, specific to Ashkenazi Jewish SMN1 duplications, was identified by microsatellite analysis, and next-generation sequencing of SMN1 further defined a more localized haplotype. Of note, six novel SMN1 sequence variants were identified that were specific to duplications and not present on single-copy alleles. The haplotype was also identified on SMN1 duplication alleles in additional ethnic groups. CONCLUSION Identification of these novel variants in an individual with two copies of SMN1 significantly improves the accuracy of residual risk estimates and has important implications for spinal muscular atrophy carrier screening.
Collapse
Affiliation(s)
- Minjie Luo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Liu Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Geping Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | | | - Ruth Kornreich
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| |
Collapse
|
50
|
Anazi S, Al-Sabban E, Alkuraya FS. Gonadal mosaicism as a rare cause of autosomal recessive inheritance. Clin Genet 2013; 85:278-81. [PMID: 23551117 DOI: 10.1111/cge.12156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/27/2013] [Accepted: 03/27/2013] [Indexed: 11/26/2022]
Abstract
Autosomal recessive diseases are typically caused by the biparental inheritance of familial mutant alleles. Unusual mechanisms by which the recessiveness of a mutant allele is unmasked include uniparental isodisomy and the occurrence of a de novo chromosomal rearrangement that disrupts the other allele. Gonadal mosaicism is a condition in which a postfertilization mutation is confined to the gamete precursors and is not detected in somatic tissues. Gonadal mosaicism is known to give the impression of autosomal recessive inheritance when recurrence of an autosomal-dominant condition among offspring of phenotypically normal parents is observed. Here, we report an extremely rare event in which maternal gonadal mosaicism for a recessive mutation in COL4A4 caused the recurrence of Alport syndrome within a consanguineous family. Such rare occurrence should be taken into account when analyzing pedigrees both for clinical and research purposes.
Collapse
|