Deletion analysis of Bulgarian SMA families

All three types of autosomal recessive spinal muscular atrophy map to chromosome region 5q13. Recent reports suggest that they are associated with deletions of two adjacent genes: SMN and NAIP. Here we report the first deletion analysis of Bulgarian SMA families. Homozygous deletion of exons 7 and 8 of the SMN gene were found in 85% of our patients, but the NAIP gene (exons 5 and 6) was deleted in only 26% of patients. To our knowledge, these frequencies are some of the lowest reported so far. The NAIP gene was deleted predominantly in severely affected patients (type I), while in the group with milder types SMA only deletions of the SMN gene were detected. Our phenotype–genotype correlation study confirmed that larger deletions are associated with more severe clinical course. The Bulgarian data support the thesis that the telomeric SMN gene could play a major role in determining SMA, while the NAIP or the centromeric SMN copy have a modifying effect on the phenotype. Hum Mutat 12:33–38, 1998. © 1998 Wiley-Liss, Inc.     

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.      

Molecular analysis of candidate genes on chromosome 5q13 in autosomal recessive spinal muscular atrophy: evidence of homozygous deletions of the SMN gene in unaffected individuals

Proximal spinal muscular atrophy (SMA) is a common autosomalrecessive neuromuscular disorder characterized by degenerationof anterior horn cells in the spinal cord leading to weaknessand wasting of voluntary muscles. Here we present the molecularanalysis of both SMA candidate genes, the survival motor neurongene (SMN; exons 7 and 8) and the neuronal apoptosis inhibitoryprotein gene (NAIP; exons 5, 6 and 13), in 195 patients and348 parents of SMA families mainly of German origin. The SMNgene is homozygously deleted for both exons 7 and 8 or exon7 only in 96% of type I SMA, 94% of type II SMA and 82% of typeIII SMA as well as in 0.3% of SMA parents. The NAIP gene ishomozygously deleted in 46% of type I SMA, 17% of type II SMA,7% of type III SMA and 2% of SMA parents. The frequencies ofdeletions in patients for both genes, SMN and NAIP, correspondto those for the NAIP gene only. SMA patients of this serieswho did not show deletions were clinically Indistinguishablefrom deleted patients. In addition to one unaffected motherof a type II SMA patient, we found homozygous deletions of theSMN gene exons 7 and 8 in six further unaffected individuais,all sibs of type II and III patients. These belonged to fourfamilies with affected and unaffected sibs who showed identicalhaplotypes for all SMA flanking markers; therefore, we had regardedthese families as chromosome 5 unlinked. All seven unaffectedindividuals in whom we detected SMA deletions do not show anysigns of muscle weakness and are physically inconspicuous. Thelargest divergence between age at onset of an affected subjectand the present age of unaffected deleted sibs is four decadesnow. The occurrence of SMN deletions in unaffected individualssuggests that other genes or mechanisms may be necessary toproduce the SMA phenotype.     

Large scale deletions of the 5q13 region are specific to Werdnig-Hoffmann disease.

Spinal muscular atrophy (SMA) is characterised by degeneration of anterior horn cells of the spinal cord and represents the second most common, lethal, autosomal recessive disorder after cystic fibrosis. Based on the criteria of the Internatinal SMA Consortium, childhood SMAs are classified into type I (Werdnig-Hoffmann disease), type II (intermediate form), and type III (Kugelberg-Welander disease). Recently, two genes have been found to be associated with SMA. The survival motor neurone gene (SMN) is an SMA determining gene as it is absent in 98.6% of patients. A second gene, XS2G3, or the highly homologous neuronal apoptosis inhibitory protein gene (NAIP) have been found to be more frequently deleted in type I than in the milder forms (types II and III). We investigated the correlation between the clinical phenotype and the genotype at this loci. A total of 106 patients were classified into type I (44), type II (31), and type III (31) and analysed using SMN, markers C212 and C272, and NAIP mapping upstream and downstream from SMN respectively. The combined analysis of all markers showed a large proportion of type I patients (43%) carried deletions of both SMN and its flanking markers (C212/272) and NAIP exon 5), as compared with none of the patients with type II or III SMA. The presence of large scale deletions involving these loci is specific to Werdnig-Hoffman disease (type I) and allows one to predict the severity of the disease in our series.     

Different molecular basis for spinal muscular atrophy in South African black patients.

Spinal muscular atrophy (SMA) is an autosomal recessive disorder occurring at a rate of between 1/5,000 and 1/10,000 births in most European countries. The phenotype results from the degeneration of the anterior horn cells of the spinal cord, resulting in symmetrical muscle weakness and wasting. The disorder can be classified according to the severity of the disease and the age of onset into three major types. Two candidate SMA genes, NAIP and SMN, isolated from the 5q13 region, have been reported to be homozygously deleted in approximately 30% and >95% of SMA patients, respectively. Black SMA patients have been reported to have facial muscle weakness more commonly. This study aimed to determine the molecular basis of SMA in South African black SMA patients. The SMN gene was found to be homozygously deleted in 65.5% (19/29) of patients, significantly less frequently than in previous studies. Similarly, the NAIP gene was homozygously deleted in a smaller number, 14% (4/29) of patients; 47% (9/19) of SMN deletion patients appeared to have deletions of telomeric exon 7, but not exon 8. In at least six of these patients a gene conversion event has occurred. No detectable deletions were found in 35% (10/29) of patients. Haplotype analysis in the nondeletion patients, using six closely linked markers, provided no evidence for a founder mutation. No mutations were found in exons 3 and intron 6 through exon 8 by sequence analysis of these nondeletion patients. It is proposed that the differences in the SMA phenotype observed in black patients may in part be explained by a different molecular basis.     

Evidence for compound heterozygosity causing mild and severe forms of autosomal recessive spinal muscular atrophy.

Spinal muscular atrophy is an autosomal recessive disease of motor neurone degeneration which shows a variable phenotype. Two candidate genes show deletions in affected subjects but with no distinction between different forms of the disease. We report an unusual family in which mild and severe SMA coexists and patients are deleted for the SMN gene. The father is affected with late onset SMA; therefore this family shows pseudodominant inheritance. When typed using closely linked flanking markers the severely affected son does not share the same haplotype as his sib, who is deleted for SMN but shows no signs yet of SMA. This supports the hypothesis that differences in SMA phenotype can be explained by a multiple allele model.     

Different molecular basis for spinal muscular atrophy in South African black patients

Spinal muscular atrophy (SMA) is an autosomal recessive disorder occurring at a rate of between 1/5,000 and 1/10,000 births in most European countries. The phenotype results from the degeneration of the anterior horn cells of the spinal cord, resulting in symmetrical muscle weakness and wasting. The disorder can be classified according to the severity of the disease and the age of onset into three major types. Two candidate SMA genes, NAIP and SMN, isolated from the 5q13 region, have been reported to be homozygously deleted in ∼30% and >95% of SMA patients, respectively. Black SMA patients have been reported to have facial muscle weakness more commonly. This study aimed to determine the molecular basis of SMA in South African black SMA patients. The SMN gene was found to be homozygously deleted in 65.5% (19/29) of patients, significantly less frequently than in previous studies. Similarly, the NAIP gene was homozygously deleted in a smaller number, 14% (4/29) of patients; 47% (9/19) of SMN deletion patients appeared to have deletions of telomeric exon 7, but not exon 8. In at least six of these patients a gene conversion event has occurred. No detectable deletions were found in 35% (10/29) of patients. Haplotype analysis in the nondeletion patients, using six closely linked markers, provided no evidence for a founder mutation. No mutations were found in exons 3 and intron 6 through exon 8 by sequence analysis of these nondeletion patients. It is proposed that the differences in the SMA phenotype observed in black patients may in part be explained by a different molecular basis. Am. J. Med. Genet. 86:420–426, 1999. © 1999 Wiley-Liss, Inc.     

Characterization of survival motor neuron (SMNT) gene deletions in asymptomatic carriers of spinal muscular atrophy

Previous reports have established that the telomeric copy of the survival motor neuron (SMNT) gene and the intact copy of the neuronal apoptosis inhibitory protein (NAIP) gene are preferentially deleted in patients with spinal muscular atrophy (SMA). Although deletions or mutations in the SMNT gene are most highly correlated with SMA, it is not clear to what extent NAIP or other genes influence the SMA phenotype, or whether a small fraction of SMA patients actually have functional copies of both SMNT and NAIP. To evaluate further the part of SMNT in the development of SMA, we analyzed 280 asymptomatic SMA family members for the presence or absence of SMNT exons 7 and 8. We report the following observations: (i) 4% of the sample harbored a polymorphic variant of SMNT exon 7 that looks like a homozygous deletion; (ii) approximately 1% of the parents are homozygously deleted for both exons 7 and 8; (iii) one asymptomatic parent lacking both copies of SMNT exons 7 and 8 displays a 'subclinical phenotype' characterized by mild neurogenic pathology; (iv) another asymptomatic parent lacking both SMNT exons showed no signs of motor neuron disorder by clinical and neurodiagnostic analyses. The demonstration of polymorphic variants of exon 7 that masquerade as homozygous nulls, and the identification of SMA parents who harbor two disease alleles, serve as a caution to those conducting prenatal tests with these markers.      

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.     

Frameshift mutation in the survival motor neuron gene in a severe case of SMA type I

Recently, a spinal muscular atrophy (SMA) determining gene, termed survival motor neuron (SMN) gene, has been isolated from the 5q13 region and found deleted in most patients. A highly homologous copy of this gene has also been isolated and located in a centromeric position. We have analyzed 158 patients (SMA types I-IV) and found deletions of SMN exon 7 in 96.8%. Mutations other than gross deletions seem to be extremely rare. In one of the undeleted SMA type I patients, a newborn who survived for only 42 days, we detected a maternally inherited 5 bp microdeletion in exon 3, resulting in a premature stop codon. By RT-PCR and long range PCR amplification we were able to show that the deletion belongs to the SMN gene, rather than to the centromeric copy, and that the proposita had no paternal SMN gene. Analysis of the neuronal apoptosis inhibitor protein (NAIP) gene, which maps close to SMN and has been proposed as a SMA modifying gene, suggests the presence of at least one full-length copy. Haplotype analysis of closely linked polymorphic markers suggests that the proposita also lacks the maternally derived copy of the centromeric homologue of SMN supporting the hypothesis that the severity of the phenotype might depend on the reduced number of centromeric genes in addition to the frameshift mutation.      

Allelic association and deletions in autosomal recessive proximal spinal muscular atrophy: association of marker genotype with disease severity and candidate cDNAs

The candidate region for spinal muscular atrophy (SMA) has beendefined as a 750 kb interval on 5q13. In this study, we performedallelic association studies in 154 German SMA families withthe multicopy markers Ag1-CA (D5S1556); C212 (D5F149S1/S2) andcorrelated genotype data with deletion of candidate genes. Bothmulticopy markers recognize 0–3 alleles pro chromosome.Deletions were detected for all copies of the markers Ag1-CA(C272) and C212 in 13 of 88 (15%) type I SMA patients and threeof 48 (6%) type II patients. In all informative cases, the deletionwas inherited from one parent. In two further cases (one typeI and one type III SMA), de novo deletions of only one copyof Ag1-CA and C212 were found. In both cases the patients werehomozygously deleted for the survival motor neuron (SMN) gene(exons 7 and 8) but only the type I SMA patient was deletedfor the neuronal apoptosis inhibitory protein (NAIP) gene (exons5 and 6). A third case (type II SMA) showed de novo deletionof SMN, but not of Ag1-CA, C212 and NAIP. Specific alleles ofAg1-CA and C212 showed significant association with SMA, particularlyin type I SMA. When the number of marker copies defines genotypes,1,1 (one allele on each chromosome) is found to be increasedin type I SMA (50%) and 1, 2 (one allele on one chromosome andtwo alleles on the other one) in type II SMA (60%). The 2,2genotype (two alleles on each chromosome) was found in 4% oftype I and II patients. By comparison, pooled normal genotypefrequencies were 20, 44 and 36%, respectively. These resultssuggest a strong correlation between genotype and severity ofdisease. Based on these data we propose a model which indicatesthat type I SMA patients are composed of two severe alleles,type II of a mild and a severe, and type III of two mild alleles.Correlation of Ag1-CA genotype with deletion of the XS2G3/NAIPgenes indicates that most patients with a deletion have a 1,1genotype. Owing to the physical proximity of these markers,we propose that a large deletion occurs on type I SMA chromosomesthat removes DNA between C212 and XS2G3/NAIP and that type IISMA results from compound heterozygosity for mild (small deletion)and severe mutations.     

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     

脊髓性肌萎缩患儿的NAIP基因分析

目的探讨脊髓性肌萎缩的基因型与临床表型（ｓｕｒｖｉｖａｌｍｏｔｏｒｎｅｕｒｏｎｅ,ＳＭＮ）的关系。方法应用ＰＣＲ技术对１３例运动神经元型基因缺失的脊髓性肌萎缩患儿进一步进行神经原性细胞凋亡抑制蛋白（ｎｅｕｒｏｎａｌａｐｏｐｔｏｓｉｓｉｎｈｉｂｉｔｏｒｙｐｒｏｔｅｉｎＮＡＩＰ）基因分析（Ⅰ型５例,Ⅱ型４例,Ⅲ型４例）。结果２例Ⅰ型患儿携有ＮＡＩＰ基因缺失（２／５,４０％）。结论ＮＡＩＰ基因缺失可能与脊髓性肌萎缩的临床表型严重程度有关     

Quantification, by solid-phase minisequencing, of the telomeric and centromeric copies of the survival motor neuron gene in families with spinal muscular atrophy

In an analysis of 30 families affected by spinal muscular atrophy (SMA) we have used the solid-phase minisequencing method to determine the ratio between the number of telomeric and centromeric copies of the survival motor neuron gene (SMN and cBCD541 respectively) on normal and SMA chromosomes. This has enabled us to establish haplotypes with regard to SMN and cBCD541, and estimate their frequencies, on both types of chromosomes. Six predominant haplotypes were identified, three for normal chromosomes and three for SMA chromosomes, characterized by having 0, 1, or 2 copies, respectively, of cBCD541. We found evidence for the presence of patients homozygous for a deletion of SMN and with only one copy of cBCD541, but found none deleted for all copies of this gene. Several asymptomatic carriers of SMA with only a single copy of SMN and no copy of cBCD541 were identified. We could not confirm the hypothesis that the presence of more copies of cBCD541 is correlated to a less severe course of the disease. The frequencies of haplotypes characterized by having 0, 1, or 2 copies, respectively, of cBCD541 were found to differ significantly between normal and SMA chromosomes. This distribution can be explained by an underrepresentation of the haplotype completely lacking SMN genes, which is expected to cause early embryonic death in homozygotes. This first report of a direct haplotype analysis of SMN and cBCD541 should help clarify the role of cBCD541 in the pathogenesis of SMA.      

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.     

Unusual molecular findings in autosomal recessive spinal muscular atrophy.

All three types of autosomal recessive spinal muscular atrophy map to chromosome 5q11.2-q13.3 and are associated with deletions or mutations of the SMN (survival motor neurone) gene. The availability of a test to distinguish between the SMN gene and its nearly identical centromeric copy cBCD541 allows molecular diagnosis. We have analysed patients from 24 Belgian and 34 Turkish families for the presence or absence of a deletion in the SMN gene. A homozygous deletion in the SMN gene was seen in 90% of unrelated SMA patients. A non-radioactive SSCP assay allows for a semiquantitative analysis of the copy number of the centromeric and SMN genes. Hence, direct carrier detection has become feasible under certain conditions. We observed a phenotypically normal male, father of an SMA type I patient, presenting with only a single copy of the SMN gene and lacking both copies of the cBCD541 gene. This illustrates that a reduction of the total number of SMN and cBCD541 genes to a single SMN copy is compatible with normal life. In another SMA type I family, there is evidence for a de novo deletion of the centromeric gene in a normal sib. This observation illustrates the susceptibility of the SMA locus to de novo deletions and rearrangements.     

Population screening and cascade testing for carriers of SMA

Spinal muscular atrophy (SMA) is one of the most common autosomal-recessive diseases, caused by absence of both copies of the survival motor neuron 1 (SMN1) gene. Identification of SMA carriers has important implications for individuals with a family history and the general population. SMA carriers are completely healthy and most are unaware of their carrier status until they have an affected child. A total of 422 individuals have been studied to identify SMA carriers. This cohort included 117 parents of children homozygously deleted for SMN1 (94% were carriers and 6% had two copies of SMN1; of these individuals, two in seven had the '2+0' genotype, two in seven were normal but had children carrying a de novo deletion and three in seven were unresolved), 158 individuals with a significant family history of SMA (47% had one copy, 49% had two copies and 4% had three copies of SMN1) and 146 individuals with no family history of SMA (90% had two copies, 2% had one copy and 8% had three copies of SMN1). The SMA carrier frequency in the Australian population appears to be 1/49 and the frequency of two-copy SMN1 alleles and de novo deletion mutations are both at least 1.7%. A multimodal approach involving quantitative analysis, linkage analysis and genetic risk assessment (GRA), facilitates the resolution of SMA carrier status in individuals with a family history as well as individuals of the general population, providing couples with better choices in their family planning.     

Deletion of SMN and NAIP genes in Korean patients with spinal muscular atrophy

Childhood-onset proximal spinal muscular atrophies (SMAs) are an autosomal recessive, clinically heterogeneous group of neuronopathies characterized by selective degeneration of anterior horn cells. The causative genes to be reported are survival motor neuron (SMN) and neuronal apoptosis inhibitory protein (NAIP) genes. The deletion of telomeric copy of SMN (SMN(T)) gene was observed in over 95% of SMAs. The deletion rate of NAIP gene is 20-50% according to disease severity. The objective of this article is to genetically characterize the childhood-onset spinal muscular atrophy in Koreans. Five Korean families (14 constituents containing 5 probands) with SMA were included in this study. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were used for the deletion analysis of SMN(T). Multiplex PCR method was used for NAIP analysis. Four probands showed deletion of SMNT gene. Deletion of SMN(C) (centromeric SMN) gene was found in one proband who did not show the deletion of SMN(T) gene and in the father of one proband who showed the deletion of SMN(T) gene. The deletion of NAIP gene was not found among all the studied individuals. The extent of deletion in Koreans was smaller than that in other studied population. PCR-RFLP deletion analysis can be applied to diagnose SMA and make a prenatal diagnosis.