Implementation of SMA carrier testing in genetic laboratories: comparison of two methods for quantifying the SMN1 gene

The degeneration and loss of motor neurons of the anterior horn characterize children affected with spinal muscular atrophy (SMA). Mutations in the survival motor neuron gene (SMN1) are determinant for the development of the disease whereas the number of copies of SMN2, the highly homologous copy of SMN1, plays a role as a phenotypic modifier factor. The detection of SMN1 homozygous deletions is the typical test for SMA diagnosis. Owing to the limitation of this test for carrier and heterozygous deletion analysis, the demand of SMN1 quantitative tests is permanently growing. The high incidence of SMA, the notable carrier frequency, the severity of the disease, and the lack of effective treatment may justify the implementation of such an analysis in DNA diagnostic labs. The advantages and disadvantages of two reliable quantitative methods were evaluated. One of these is a competitive PCR protocol using internal standards and a genomic sequence as a reference. The other method is a real-time PCR employing an external standard as a reference. Both methods present sufficient advantages for incorporation into molecular genetic diagnostic labs. The possibility of studying samples from different labs, the versatility and reproducibility of the analysis, and cost-benefit calculations must be considered in the final choice.     

脊髓性肌萎缩症SMN基因拷贝数定量分析

目的　探讨临床诊断为脊髓性肌萎缩症 (spinal muscular atrophy,SMA)而 PCR定性无运动神经元生存 (survival motor neuron,SMN )基因 T拷贝 (SMN - T)缺失患者的遗传基础 ;并探索 SMA表型与SMN基因 C(SMN- C)拷贝数的关系及 SMA患者及其直系亲属和正常人 SMN基因拷贝数的分布。方法对临床和病理诊断为 SMA ～ 型及少见型 4 5例患者、2 5名表型正常的 SMA直系亲属进行 SMN- T和SMN- C基因拷贝数定量分析 ,并与 33名正常人进行对比 ;所有对象均已经 PCR Dra 酶切法定性检测SMN基因 ,其中 ～ 型的 7例和 型的 2例为 SMN- T纯合缺失 ,余者无缺失。建立 SMN- T和囊性纤维化跨膜调节因子 (cystic fibrosis transmembrane conductance regulator,CFTR)的内标 ,所有标本进行非放射性、非荧光标记的多重竞争性 PCR,根据产物 SMN- T/ CFTR和 SMN- C/ CFTR比值 ,计算 SMN- T和SMN - C拷贝数。结果　 7例 ～ 型 SMN - T拷贝数均为 0 ; 型 2例拷贝数为 0 ,2例为 1个拷贝数 ,系杂合缺失 ,4例为 2个拷贝 ; 型及其他型患者均为 2个拷贝 ;直系亲属中 9例为 1个拷贝 ,系杂合缺失 ,其余及正常对照组均为 2个拷贝。SMN - C拷贝数在 SMA 型为≤ 2 , ～ 型为≤ 3, 型及其它型 SMA、直系亲属和正常对照组均为 0～ 3。结     

Evaluation and characterization of a high-resolution melting analysis kit for rapid carrier-screening test of spinal muscular atrophy

Spinal muscular atrophy (SMA) is a common autosomal recessive disorder in humans, caused by the homozygous absence of the survival motor neuron gene 1 (SMN1). SMN2, a copy gene, influences the severity of SMA. Several assays have been described for molecular diagnosis or carrier screening of SMA. A newly developed tool based on a high-resolution melting analysis (HRMA) that enables high-throughput screening without sophisticated protocols but low costs reveals itself to be powerful. We evaluate the performance of an HRMA-based kit for a carrier-screening test of SMA that was designed to detect the substitution of a single nucleotide in SMN1 exon 7. Carriers were identified in 453 participants by quantifying the SMN1 gene and compared with denaturing high-performance liquid chromatography (DHPLC) assay. An HRMA-based kit had a higher sensitivity (100%) for carrier testing than the DHPLC assay (93%), with the added advantage that some homozygous sequence alterations could be identified. The HRMA kit is a new, fast, and highly reliable quantitative test for the SMA molecular carrier test.     

DYNC1H1 gene methylation correlates with severity of spinal muscular atrophy

Methylation profiles of CpG islands within the SLC23A2, CDK2AP1, and DYNC1H1 genes and their association with spinal muscular atrophy (SMA) severity were studied. High clinical heterogeneity of SMA suggests the existence of different factors modifying SMA phenotype with gene methylation as a plausible one. The genes picked up in our earlier genome‐wide methylation studies of SMA patients demonstrated obvious differences in their methylation patterns, thus suggesting the likely involvement of their protein products in SMA development. Significantly decreased methylation of CpG islands within exon 37 of the DYNC1H1 gene was observed in patients with a severe SMA manifestation (type I) compared to mildly affected SMA patients (types III–IV). This finding provides new information on peculiarities of methylation in clinically different types of SMA patients and gives a clue for identification of new SMA modifiers.     

Quantitative analysis of SMN1 and SMN2 genes based on DHPLC: a highly efficient and reliable carrier-screening test

Autosomal recessive spinal muscular atrophy (SMA) is a common, fatal neuromuscular disease caused by homozygous absence of the SMN1 gene in approximately 94% of patients. However, a highly homologous SMN2 gene exists in the same chromosome interval, centromeric to SMN1, and hampers detection of SMN1. We present a new, rapid, simple, and highly reliable method for detecting the SMN1 deletion/conversion and for determining the copy numbers of the SMN1 and SMN2 genes by DHPLC. We analyzed SMN1/SMN2 gene exon 7 deletion/conversion by DHPLC. A total of 25 patients with spinal muscular atrophy lacking the SMN1 gene as well as 309 control individuals from the general population and the family members of patients with SMA were analyzed. By DHPLC analysis, we could detect the SMA-affected cases efficiently just by recognizing an SMN2-only peak. Furthermore, after specific primer amplification and adjustment of the oven temperature, all of the SMA carriers with an SMN1/SMN2 ratio not equal to 1 could be identified unambiguously by this simple and efficient detection system. To calculate the total SMN1/SMN2 gene dosages further, we developed a specific multiplex competitive PCR protocol by simultaneously amplifying the CYBB gene (X-linked), the KRIT1 gene (on chromosome arm 7q), and the SMN1/SMN2 gene ratio by DHPLC. By applying this technique, we could successfully designate all of the genotypes with different SMN1/SMN2 gene copy numbers, including equal and unequal amounts of SMN1 and SMN2. We demonstrated that DHPLC is a fast and reliable tool for detection of carriers of SMA.     

Determination of SMN1 and SMN2 copy number using TaqMan technology

Infantile spinal muscular atrophy (SMA) is a neuromuscular disease caused by homozygous deletion of the SMN1 gene in more than 90% of patients. Identification of carriers for the SMN1 deletion is important for diagnostic purposes and for genetic counseling. The current practical implications of SMN2 copy number determination are limited but may be important, for example, for future drug trials. Here we present a new rapid and reliable approach to determine the copy numbers of the SMN1 and SMN2 genes: For differentiation of the two genes, we developed a quantitative test on the basis of TaqMan technology using minor groove binder (MGB) probes. To evaluate the approach in respect to detection of SMN1 deletion carriers, we tested 40 putative carriers as well as 100 controls. We confirmed the carrier status in all individuals; furthermore, the distribution of SMN1 and SMN2 copies in the control cohort corresponded to that published previously. In total, a clear-cut differentiation between the different copy number ranges could be observed for both genes. This distinct differentiation is based on the exact specificity of MGB probes and the parallel analysis of an external reference locus that circumvents the problem of unavoidable deviations in DNA concentrations. The simplicity and reproducibility of the TaqMan assay presented here should facilitate its establishment in molecular diagnostic laboratories. Nevertheless, the applicability of quantitative analyses of SMN copy numbers requires knowledge about its options and limitations, based on the complex nature of the SMN region and the clinical variability of SMA. Therefore, determination of SMN1 and SMN2 copy numbers should only be offered after careful consideration in each case.     

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。     

一例脊肌萎缩症患者及其家系的SMN基因突变分析

目的 对1例脊肌萎缩症(spinal muscular atrophy,SMA)患者及其家系成员的SMN基因行突变分析.方法 采用多重连接依赖性探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术、逆转录聚合酶链反应及T克隆-测序技术对患者SMN基因进行拷贝数分析和点突变的鉴定,应用MLPA和针对点突变区域的SMN基因第5外显子PCR-直接测序法对患者父母SMN基因进行拷贝数分析和点突变的证实,同时用200名正常人外周血进行相关位点对照研究.结果 患者具有1个拷贝的SMNl基因和1个拷贝的SMN2基因,在这个SMNl基因第230位密码子上存在1个未见报道的错义突变S230L(TCA→TTA);父亲具有两个SMN1和两个SMN2拷贝,其中1个SMNl基因存在S230L突变;母亲具有1个SMN1拷贝,而SMN2基因是纯合缺失的.200名对照中未发现该位点突变.结论 在1个SMA家系中发现了1个新的SMNI基因点突变,即S230L,并准确分析了此家系各成员的SMN基因型.     

PCR-RFLP法在脊髓性肌萎缩症基因检测中的局限性

目的 探讨聚合酶链反应-限制性片段长度多态性(polymerase chain reaction-restriction fragment length polymorphism,PCR-RFLP)技术在脊髓性肌萎缩症(spinal muscular atrophy,SMA)基因诊断中的应用.方法 用PCR-RFLP分析935例临床疑似SMA患儿的运动神经元存活基因1(survival motor neuron,SMN1)第7和第8外显子的缺失,同时用多重连接探针扩增技术(multiplex ligationdependent probe amplification,MLPA)分析其中339例疑似病例的SMN1基因拷贝数改变.用Pearson卡方检验分析两种方法检测SMN1纯合和杂合性缺失的一致性.结果 共发现SMN1基因第7外显子纯合缺失590例,疑似患者的SMA基因诊断率为63.1％(590/935).用PCR-RFLP和MLPA技术联合分析疑似病例339例,PCR-RFLP共发现SMN1纯合缺失194例,MLPA发现196例,二者的一致性为98.9％,差异无统计学意义(x2=0.2,P=0.88).PCR-RFLP仅发现SMN1疑似杂合性缺失4例,而MLPA证实有17例,二者的一致性为23.5％,差异有统计学意义(x2=8.29,P＜0.01).结论 PCR-RFLP尽管简便、特异、实用,但对于5％～10％ SMN1杂合缺失合并点突变的病例则存在明显的局限性.     

Detection of male 2+0 and 1+0 carriers for spinal muscular atrophy by digital PCR

Spinal muscular atrophy (SMA) is an autosomal recessive disease with a high carrier frequency. While current screening methods can identify 1+0 carriers, detecting 2+0 genotypes remains challenging, highlighting the need for additional research. Herein, we applied Digital Polymerase Chain Reaction (dPCR) to develop a novel approach for the detection of male carriers (DMC), especially for those with a 2+0 genotype. The clinical utility of DMC was evaluated in 39 semen samples. Multiple ligation-dependent probe amplification (MLPA) and pedigree analysis were performed on genomic DNA from 111 males and their family members. DMC identified 1+1, 2+1, and 1+0 genotypes in 21, 1, and 8 subjects. Importantly, seven men were identified as 2+0 carriers, while two men were excluded from the 2+0 carrier status. The results of DMC were consistent with those of MLPA and pedigree analysis. DMC provides an inexpensive and accurate method for determining the 2+0 and 1+0 genotypes.     

Carboxylic acid derivatives of histone deacetylase inhibitors induce full length SMN2 transcripts: a promising target for spinal muscular atrophy therapeutics

Introduction

Proximal spinal muscular atrophy (SMA) is a common autosomal recessively inherited neuromuscular disorder. It is caused by homozygous absence of the survival motor neuron 1 (SMN1) gene. SMN2, which modulates the severity of the disease, represents a major target for therapy. The aim of this study was to investigate whether SMN2 expression can be increased by caffeic acid, chlorogenic acid and curcumin, which are designed by modifications of the carboxylic acid class of histone deacetylase (HDAC) inhibitors.

Material and methods

Using quantitative real-time PCR, we analysed the levels of full-length SMN2 and Δ7SMN2 mRNA. We performed LDH cytotoxicity assay to analyse whether SMN2 activating concentrations of caffeic acid, chlorogenic acid and curcumin were cytotoxic to fibroblasts.

Results

We found that caffeic acid and curcumin were more efficient than chlorogenic acid and increased full-length SMN2 mRNA levels 1.5 and 1.7-fold, respectively. Δ7SMN2 mRNA levels were measured to investigate alternative splicing of exon 7. We also found that cytotoxicity was not observed at SMN2 activating concentrations.

Conclusions

Our data suggest that carboxylic acid derivatives including phenolic structure and symmetry could be a good candidate for SMA treatment.     

GARS‐related disease in infantile spinal muscular atrophy: Implications for diagnosis and treatment

The majority of patients with spinal muscular atrophy (SMA) identified to date harbor a biallelic exonic deletion of SMN1. However, there have been reports of SMA‐like disorders that are independent of SMN1, including those due to pathogenic variants in the glycyl‐tRNA synthetase gene (GARS1). We report three unrelated patients with de novo variants in GARS1 that are associated with infantile‐onset SMA (iSMA). Patients were ascertained during inpatient hospital evaluations for complications of neuropathy. Evaluations were completed as indicated for clinical care and management and informed consent for publication was obtained. One newly identified, disease‐associated GARS1 variant, identified in two out of three patients, was analyzed by functional studies in yeast complementation assays. Genomic analyses by exome and/or gene panel and SMN1 copy number analysis of three patients identified two previously undescribed de novo missense variants in GARS1 and excluded SMN1 as the causative gene. Functional studies in yeast revealed that one of the de novo GARS1 variants results in a loss‐of‐function effect, consistent with other pathogenic GARS1 alleles. In sum, the patients' clinical presentation, assessments of previously identified GARS1 variants and functional assays in yeast suggest that the GARS1 variants described here cause iSMA. GARS1 variants have been previously associated with Charcot–Marie–Tooth disease (CMT2D) and distal SMA type V (dSMAV). Our findings expand the allelic heterogeneity of GARS‐associated disease and support that severe early‐onset SMA can be caused by variants in this gene. Distinguishing the SMA phenotype caused by SMN1 variants from that due to pathogenic variants in other genes such as GARS1 significantly alters approaches to treatment.     

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.