Implementation of population-based newborn screening reveals low incidence of spinal muscular atrophy

PurposeSpinal muscular atrophy (SMA) was added to the Recommended Uniform Screening Panel (RUSP) in July 2018, following FDA approval of the first effective SMA treatment, and demonstration of feasibility of high-throughput newborn screening using a primary molecular assay. SMA newborn screening was implemented in New York State (NYS) on 1 October 2018.MethodsScreening was conducted using DNA extracted from dried blood spots with a multiplex real-time quantitative polymerase chain reaction (qPCR) assay targeting the recurrent SMN1 exon 7 gene deletion.ResultsDuring the first year, 225,093 infants were tested. Eight screened positive, were referred for follow-up, and confirmed to be homozygous for the deletion. Infants with two or three copies of the SMN2 gene, predicting more severe, earlier-onset SMA, were treated with antisense oligonucleotide and/or gene therapy. One infant with ≥4 copies SMN2 also received gene therapy.ConclusionNewborn screening permits presymptomatic SMA diagnosis, when treatment initiation is most beneficial. At 1 in 28,137 (95% confidence interval [CI]: 1 in 14,259 to 55,525), the NYS SMA incidence is 2.6- to 4.7-fold lower than expected. The low SMA incidence is likely attributable to imprecise and biased estimates, coupled with increased awareness, access to and uptake of carrier screening, genetic counseling, cascade testing, prenatal diagnosis, and advanced reproductive technologies.     

Improving detection and genetic counseling in carriers of spinal muscular atrophy with two copies of the SMN1 gene

Spinal muscular atrophy (SMA) is an autosomal recessive disease caused by mutations in the survival motor neuron1 gene (SMN1). Global carrier frequency is around 1 in 50 and carrier detection is crucial to define couples at risk to have SMA offspring. Most SMA carriers have one SMN1 copy and are currently detected using quantitative methods. A few, however, have two SMN1 genes in cis (2/0 carriers), complicating carrier diagnosis in SMA. We analyzed our experience in detecting 2/0 carriers from a cohort of 1562 individuals, including SMA parents, SMA relatives, and unrelated individuals of the general population. Interestingly, in three couples who had an SMA child, both the parents had two SMN1 copies. Families of this type have not been previously reported. Our results emphasize the importance of performing a detailed carrier study in SMA parents with two SMN1 copies. Expanding the analysis to other key family members might confirm potential 2/0 carriers. Finally, when a partner of a known carrier presents two SMN1 copies, the study of both parents will provide a more accurate diagnosis, thus optimizing genetic counseling.     

云南地区3049名育龄人群脊髓性肌萎缩症携带者筛查结果分析

目的对云南地区3049名育龄人群进行脊髓性肌萎缩症(spinal muscular atrophy,SMA)的携带者筛查,探讨本地区人群运动神经元存活基因(survival motor neuron,SMN)的拷贝数情况及携带频率。方法应用多重连接探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)对SMN1及SMN2基因第7外显子的拷贝数进行检测,筛查出SMN1基因第7外显子拷贝数为1的SMA携带者。对双方均为携带者的夫妇提供产前诊断。结果在3049名育龄人群中,共检测出SMA携带者62例,携带率为1/49(2.03%)。男性携带率为1.91%(40/2094),女性携带率为2.30%(22/955),二者的差异无统计学意义(P>0.05)。SMN1杂合缺失占1.30%(41/3049),由SMN1转换为SMN2者占0.69%(21/3049)。SMN1等位基因的平均拷贝数为1.99。检出双方均为SMA携带者的夫妇2对,通过产前诊断避免了1例患病胎儿的出生。结论云南地区SMA男女携带者的频率无显著差异,符合常染色体隐性遗传模式。阐明SMA携带者的频率和SMN基因的拷贝数情况,可为遗传咨询和产前预防提供依据。     

Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data

PurposeSpinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics.MethodsWe developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2.ResultsWe characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers.ConclusionThis SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.     

Clinical application of the molecular diagnosis of spinal muscular atrophy: Deletions of neuronal apoptosis inhibitor protein and survival motor neuron genes

The molecular genetic diagnosis of spinal muscular atrophy (SMA) has recently been complicated by the identification of two candidate genes, which are often deleted in affected individuals but are also occasionally deleted in apparently unaffected carriers. We present a compilation of genotypes, from our laboratory and recent reports, for the survival motor neuron (SMN) and neuronal apoptosis inhibitor protein (NAIP) genes. Bayesian analyses were used to generate probabilities for SMA when deletions are present or absent in SMN. We found that when the SMN^T exon 7 is deleted, the probability of SMA can reach greater than 98% in some populations, and when SMN^T is present, the probability of SMA is approximately 17 times less than the prior population risk. Deletion of NAIP exon 5, as well as SMN^T exon 7, is associated with a 5-fold increased risk of type I SMA. Case studies are used to illustrate differing disease risks for pre- and postnatal testing, depending on the presence of information about clinical status or molecular results. These analyses demonstrate that deletion screening of candidate genes can be a powerful tool in the diagnosis of SMA. Am. J. Med. Genet. 69:159–165, 1997. © 1997 Wiley-Liss, Inc.     

Screening for spinal muscular atrophy mutation carriers among 4931 pregnant women from Liuzhou region of GuangxiCSCD

Objective: To screen for carriers of SMN1 gene mutation, which underlies spinal muscular atrophy (SMA), in 4931 pregnant women from Liuzhou region of Guangxi, and to determine the carrier rate. Methods: Combined denaturing high-performance liquid chromatography (DHPLC) and multiple PCR techniques were used to detect the copy number of SMN1 gene. The carrier frequency was calculated. The spouse of the carrier was also screened, and prenatal diagnosis was provided to the couples who were both positive. Results: Among the 4931 pregnant women, 61 were found to harbor only one copy of the SMN1 gene, which yielded a carrier rate of 1. 2%. Subsequent testing has identified 1 fetus carrying homozygous deletions of the SMN1 gene. Conclusion: The carrier rate of SMA mutation in Liuzhou region is slightly lower than that of other regions of southern China. DHPLC can effectively screen the carriers of SMA mutation and provide a basis for genetic counseling and prenatal diagnosis. © 2018 MeDitorial Ltd. All rights reserved.     

Single-sperm analysis for recurrence risk assessment of spinal muscular atrophy

With the detection of a homozygous deletion of the survival motor neuron 1 gene (SMN1), prenatal and preimplantation genetic diagnosis (PGD) for spinal muscular atrophy has become feasible and widely applied. The finding of a de novo rearrangement, resulting in the loss of the SMN1 gene, reduces the recurrence risk from 25% to a lower percentage, the residual risk arising from recurrent de novo mutation or germline mosaicism. In a couple referred to our PGD center because their first child was affected with SMA, the male partner was shown to carry two SMN1 copies. An analysis of the SMN1 gene and two flanking markers was performed on 12 single spermatozoa, to determine whether the father carried a CIS duplication of the SMN1 gene on one chromosome and was a carrier, or if the deletion has occurred de novo. We showed that all spermatozoa that were carriers of the ‘at-risk haplotype'' were deleted for the SMN1 gene, confirming the carrier status of the father. We provide an original application of single germ cell studies to recessive disorders using coamplification of the gene and its linked markers. This efficient and easy procedure might be useful to elucidate complex genetic situations when samples from other family members are not available.     

Pilot study of population-based newborn screening for spinal muscular atrophy in New York state

PurposeTo determine feasibility and utility of newborn screening for spinal muscular atrophy (SMA) in New York State.MethodsWe validated a multiplex TaqMan real-time quantitative polymerase chain reaction assay using dried blood spots for SMA. From January 2016 to January 2017, we offered, consented, and screened 3,826 newborns at three hospitals in New York City and tested newborns for the deletion in exon 7 of SMN1.ResultsNinety-three percent of parents opted in for SMA screening. Overall the SMA carrier frequency was 1.5%. We identified one newborn with a homozygous SMN1 deletion and two copies of SMN2, which strongly suggests the severe type 1 SMA phenotype. The infant was enrolled in the NURTURE clinical trial and was first treated with Spinraza at age 15 days. She is now age 12 months, meeting all developmental milestones, and free of any respiratory issues.ConclusionOur pilot study demonstrates the feasibility of population-based screening, the acceptance by families, and the benefit of newborn screening for SMA. We suggest that SMA be considered for addition to the national recommended uniform screening panel.     

Spinal Muscular Atrophy Carrier Screening by Multiplex Polymerase Chain Reaction using Dried Blood Spot on Filter Paper

Spinal muscular atrophy (SMA) is a common, often fetal, autosomal recessively inherited disease leading to progressive muscle wasting and paralysis as a result of degeneration of anterior horn cells of the spinal cord. The SMA‐determining gene, called the survival of motor neuron gene (SMN), is present on 5q13 in two nearly identical copies, telomeric SMN (SMN1) and centromeric SMN (SMN2). It has been established that SMA is caused by mutations in SMN1 whereas homozygous deletion of SMN2 has apparently no pathological consequences. The aim of this study is to develop an easy and inexpensive method for the isolation of high‐quality template DNA from blood samples for SMA carrier screening by multiplex polymerase chain reaction. We have developed a protocol that optimizes detection of the SMN1 copy number in the human genome, producing a specific and sensitive assay using DNA extracted from a dried blood spot on IsoCode? paper.     

<Emphasis Type="Italic">SMN1</Emphasis>dosage analysis in spinal muscular atrophy from India

Background  

Spinal muscular atrophy (SMA) represents the second most common fatal autosomal recessive disorder after cystic fibrosis. Due to the high carrier frequency, the burden of this genetic disorder is very heavy in developing countries like India. As there is no cure or effective treatment, genetic counseling becomes very important in disease management. SMN1 dosage analysis results can be utilized for identifying carriers before offering prenatal diagnosis in the context of genetic counseling.     

Genetic risk assessment in carrier testing for spinal muscular atrophy

As evidenced by the complete absence of a functionally critical sequence in exon 7, approximately 94% of individuals with clinically typical spinal muscular atrophy (SMA) lack both copies of the SMN1 gene at 5q13. Hence most carriers have only one copy of SMN1. Combining linkage and dosage analyses for SMN1, we observed unaffected individuals who have two copies of SMN1 on one chromosome 5 and zero copies of SMN1 on the other chromosome 5. By dosage analysis alone, such individuals, as well as carriers of non-deletion disease alleles, are indistinguishable from non-carrier individuals. We report that approximately 7% of unaffected individuals without a family history of SMA have three or four copies of SMN1, implying a higher frequency of chromosomes with two copies of SMN1 than previously reported. We present updated calculations for disease and non-disease allele frequencies and we describe how these frequencies can be used for genetic risk assessment in carrier testing for SMA.     

脊髓性肌萎缩症SMN1基因定量研究及基因携带者的筛查

目的进行脊髓性肌萎缩症（spinal muscular atrophy，SMA）基因携带者的筛查，为遗传咨询提供理论依据。方法应用实时荧光定量PCR特异性扩增264名健康人、88例经基因诊断确诊SMA患者的双亲、32名SMA家系其它成员的SMN1基因第7外显子及其邻近区域，以已确定只有2拷贝SMN1的样品作为标准对照。结果88例确诊SMA患者双亲除4名SMN1拷贝数为2外，其余均只有1拷贝SMN1。264名正常人中5人仅有1拷贝SMN1，为基因携带者，该组中含2、3、4拷贝SMN1的人数分别为232、25、2。32名SMA家系成员中有2名SMN1拷贝数为1，为基因携带者，25名SMN1拷贝数为2，另5名拷贝数为3。结论实时荧光定量PCR技术可进行单拷贝差异SMN1基因的定量检测，结果准确、重复性好，基因携带者的筛查为本病遗传咨询提供了重要依据。     

Identification of two novel SMN1 point mutations associated with a very severe SMA-I phenotype

Spinal muscular atrophy (SMA) is a common autosomal recessive genetic disorder characterized by degeneration of motor neurons and weakness and muscle atrophy. Approximately 95% of SMA patients are caused by homozygous deletions of the SMN1 gene, whereas the remaining 5% of patients harbor compound heterozygous mutations such as an SMN1 deletion allele and an intragenic mutation (insertions, deletions, or point mutations) in the other SMN1 allele. Although analysis for the SMN1/SMN2 copy number is relatively easy, molecular genetic testing for patients with subtle mutations is still compromised due to the presence of a highly homologous SMN2 gene. Herein, we analyzed the SMN1/SMN2 copy number by multiplex ligation-dependent probe amplification (MLPA) and subtle mutations by long-range PCR (LR-PCR) for two “nondeletion” SMA patients. We identified a missense mutation (c.280G > T, p. (Val94Phe)) and a splicing mutation c.*3+3A > T in SMN1 gene not previously described in the scientific literature. Giving the severe phenotype of the two patients, we speculated that these two point mutations could significantly affect the function of SMN proteins. Our results provide important information for genetic counseling and prenatal diagnosis in these families and enrich the SMN1 mutation database.     

Six unaffected livebirths following preimplantation diagnosis for spinal muscular atrophy

Spinal muscular atrophy (SMA) is a severe neurodegenerativeautosomal recessive disorder, second only in frequency to cysticfibrosis. In its most severe form, SMA type I (Werdnig–Hoffman),death invariably ensues before age 2 years from respiratoryfailure or infection. Around 98% of clinical cases of SMA arecaused by the homozygous absence of a region of exons 7 and8 of the telomeric copy of the SMN gene (SMN1) on chromosome5. We have developed a novel means of preimplantation diagnosisof SMA using a nested polymerase chain reaction (PCR) amplificationof exon 7 of SMN, followed by a HinfI restriction digest ofthe PCR product enabling the important SMN1 gene to be distinguishedfrom the centromeric SMN2 gene which has no clinical phenotype.This method was designed to reduce the likelihood of misdiagnosis.Five couples were treated using this method. Four proceededto embryo transfer which resulted in six liveborns (one singleton,one twin and one triplet), all free of SMA. Embryo transferwas not performed in one cycle because of PCR contamination. preimplantation genetic diagnosis/SMN1/spinal muscular atrophy     

Molecular analysis of the SMN and NAIP genes in Spanish spinal muscular atrophy (SMA) families and correlation between number of copies of cBCD541 and SMA phenotype [published erratum appears in Hum Mol Genet 1996 May;5(5):710]

Spinal muscular atrophy is an autosomal recessive disorder which affects about 1 in 10,000 individuals. The three clinical forms of SMA were mapped to the 5q13 region. Three candidate genes have been isolated and shown to be deleted in SMA patients: the Survival Motor Neuron gene (SMN), the Neuronal Apoptosis Inhibitory Protein gene (NAIP) and the XS2G3 cDNA. In this report we present the molecular analysis of the SMN exons 7 and 8 and NAIP exon 5 in 65 Spanish SMA families. NAIP was mostly deleted in type I patients (67.9%) and SMN was deleted in 92.3% of patients with severe and milder forms. Most patients who lacked the NAIP gene also lacked the SMN gene, but we identified one type II patient deleted for NAIP exon 5 but not for SMN exons 7 and 8. Two other patients carried deletions of NAIP exon 5 and SMN exon 7 but retained the SMN exon 8. Three polymorphic variants from the SMN gene, showing changes on the sequence of the centromeric (cBCD541) and telomeric copies of the SMN gene, were found. In addition, we show several genetic rearrangements of the telomeric SMN gene, which include duplication of this gene in one normal chromosome, and putative gene conversion events in affected and normal chromosomes. Altogether these results corroborate the high genetic variability of the SMA region. Finally, we have determined the ratio between the number of centromeric and telomeric copies of the SMN gene in parents of SMA patients, showing that the majority of parents of types II and III patients carried three or more copies of the cBCD541 gene; we suggest a relationship between the number of copies of cBCD541 and the disease phenotype.      

Spinal Muscular Atrophy: From Gene Discovery to Clinical Trials

Spinal muscular atrophy (SMA) is a common neuromuscular disorder with autosomal recessive inheritance, resulting in the degeneration of motor neurons. The incidence of the disease has been estimated at 1 in 6000–10,000 newborns with a carrier frequency of 1 in 40–60. SMA is caused by mutations of the SMN1 gene, located on chromosome 5q13. The gene product, survival motor neuron (SMN) plays critical roles in a variety of cellular activities. SMN2, a homologue of SMN1, is retained in all SMA patients and generates low levels of SMN, but does not compensate for the mutated SMN1. Genetic analysis demonstrates the presence of homozygous deletion of SMN1 in most patients, and allows screening of heterozygous carriers in affected families. Considering high incidence of carrier frequency in SMA, population‐wide newborn and carrier screening has been proposed. Although no effective treatment is currently available, some treatment strategies have already been developed based on the molecular pathophysiology of this disease. Current treatment strategies can be classified into three major groups: SMN2‐targeting, SMN1‐introduction, and non‐SMN targeting. Here, we provide a comprehensive and up‐to‐date review integrating advances in molecular pathophysiology and diagnostic testing with therapeutic developments for this disease including promising candidates from recent clinical trials.     

Spinal muscular atrophies: recent insights and impact on molecular diagnosis

 Spinal muscular atrophies (SMA) are a group of motor neuron diseases characterized by degeneration of anterior horn cells of the spinal cord and by muscular atrophy. Childhood-onset SMA is one of the most frequent autosomal recessive diseases and a leading cause of infant mortality. The underlying biochemical defect of SMA is unknown. Recently two genes have been isolated from the critical region at 5q13, the survival motor neuron (SMN) gene and the neuronal apoptosis inhibitor protein (NAIP) gene. Both genes are frequently deleted in SMA patients. NAIP is deleted in at least 45% of severely affected patients but less frequently in the milder forms. Homozygous deletions of exon 7 of SMN are found in approximately 95% of patients independently of clinical severity. A few point mutations and microdeletions in SMN have also been reported. This high frequency of deletions makes SMN analysis an important molecular diagnostic tool for childhood-onset SMA and greatly facilitates prenatal diagnosis. SMN analysis has also proven useful for the diagnosis of adult-onset SMA and variant forms. Although questions such as phenotype-genotype correlation must still be solved, the isolation of SMN and adjacent genes constitutes an important step towards the understanding of the molecular basis of the disease. Received: 5 February 1995 / Accepted: 13 June 1996     

Inverse correlation between SMN1 and SMN2 copy numbers: evidence for gene conversion from SMN2 to SMN1

Most carriers of autosomal recessive spinal muscular atrophy (SMA) have only one copy of SMN1 because of SMN1 gene deletions or gene conversions from SMN1 to SMN2, which has only one base difference in coding sequence from SMN1. Using SMN gene dosage analysis, we determined the copy numbers of SMN1 and SMN2 in the general population as well as in SMA patients and carriers. Increased SMN1 copy number is associated with decreased SMN2 copy number in the general population; that is, SMN2 copy number was decreased to one or zero copies in 11 of 13 individuals with three or four copies of SMN1, whereas only 71 of 164 individuals with two copies of SMN1 had one or zero copies of SMN2 (P<0.01). SMN2 copy number was increased to three or four in a subset of SMN1 deletion/conversion carriers, and in most SMA patients with a milder phenotype. In conclusion, our data provide evidence that gene conversion from SMN2 to SMN1 occurs, and that SMN1 converted from SMN2 is present in the general population.