Determination of SMN1/SMN2 Gene Dosage by a Quantitative Genotyping Platform Combining Capillary Electrophoresis and MALDI-TOF Mass Spectrometry

Newborn screening facilitates early theranostics and improved spinal muscular atrophy outcome: five-year real-world evidence from Taiwan

BACKGROUND

Recent findings indicate that infants with spinal muscular atrophy (SMA) treated early through newborn screening (NBS) have better outcomes. This study aimed to investigate the long-term outcomes of a 5-year SMA NBS program in Taiwan.

RESULTS

From September 2017 to August 2022, two NBS centers screened patients for SMN1 homozygous deletion using quantitative real-time polymerase chain reaction (RT-PCR) or the Sequenom MassARRAY platform and subsequently confirmed the findings using multiplex ligation-dependent probe amplification (MLPA). Implementation of SMA NBS using RT-PCR or MassARRAY platform efficiently led to the detection of neonates with homozygous survival motor neuron 1 (SMN1) deletions at a median age of 9 (range 4-14) days. Among the 446,966 newborns screened, 22 were detected to have a homozygous deletion of SMN1, followed by MLPA confirmation. One patient initially showed negative screening results but was later confirmed to have a compound heterozygous mutation. Among the 23 confirmed cases, 8 patients had two SMN2 copies (all classified as SMA type 1), 11 patients had three SMN2 copies (including 4 with SMA type 1, 2 with SMA type 2, 3 with SMA type 3, and 2 asymptomatic cases), and 4 patients had four SMN2 copies (all asymptomatic). The mean (median) follow-up duration for 19 survivors was 4.2 (5.0) years. All patients with two SMN2 copies developed symptoms within 62 days; those with three SMN2 copies experienced disease onset within 1 year. After diagnosis, most patients were on a watch and wait to receive disease-modifying therapy (DMT) due to initial lack of insurance coverage and limitations on indications after coverage was granted. Of the 19 children who received DMT, the outcomes included 12 walkers, 1 walker requiring support, 3 sitters, 1 non-sitter, and 2 patients with SMA type 1b with two SMN2 copies who succumbed to acute respiratory failure.

CONCLUSIONS

This 5-year SMA NBS study using RT-PCR or the MassARRAY platform, along with an extended follow-up, demonstrates that early diagnosis and prompt treatment can enhance SMA clinical outcomes and change its natural progression in the therapeutic era. Infants with NBS who received presymptomatic DMT had better clinical outcomes than those who received symptomatic DMT.

Development and validation of a one-step SMN assay for genetic testing in spinal muscular atrophy via MALDI-TOF MS

Spinal muscular atrophy (SMA) is a fatal neuromuscular disorder primarily attributed to the homozygous deletion of the survival motor neuron 1 (SMN1) gene, with disease severity closely correlated to the copy number variations (CNV) of SMN2. Conventional methodologies, however, fail to provide a comprehensive gene overview of SMN and are often both time-intensive and costly. In this study, we present a novel one-step MALDI-TOF MS assay for SMA gene testing. To accurately quantify CNV, we incorporated RPPH1 as an internal control alongside normal samples and competing templates targeting SMN1, SMN2, and RPPH1 for multiple corrections. The CNV assay enables precise quantification of exons 7/8 in both SMN1 and SMN2 genes, achieving a kappa value of 0.935 (P < 0.001) when compared with multiple ligation-dependent probe amplification (MLPA) during its development phase. This accuracy was further corroborated in a cohort comprising 78 individuals. To identify patients harboring compound heterozygous mutations or silent carriers, prevalent pathogenic variants along with sequence variants of SMN1 were integrated into our analysis framework; plasmids were constructed for methodological validation purposes. Utilizing these combinatorial assays for SMN detection, we identified one patient exhibiting a compound heterozygous mutation characterized by genotype [0 + 1d] and another subject presenting genotype [2 + 1], who harbored simultaneous variants of g.27134T > G and g.27706_27707delAT. The CNV assessment combined with pathogenic variants analysis developed through MALDI-TOF MS provides a comprehensive gene profile of SMN within a single analytical run. Given its unparalleled cost-effectiveness and time efficiency, this approach holds significant promise for further application in clinical diagnosis as well as newborn screening for SMA.

Molecular inversion probe-rolling circle amplification with single-strand poly-T luminescent copper nanoclusters for fluorescent detection of single-nucleotide variant of SMN gene in diagnosis of spinal muscular atrophy

In this study, a simple fluorescent detection of survival motor neuron gene (SMN) in diagnosis of spinal muscular atrophy (SMA) based on nucleic acid amplification test and the poly-T luminescent copper nanoclusters (CuNCs) was established. SMA is a severely genetic diseases to cause infant death in clinical, and detection of SMN gene is a powerful tool for pre- and postnatal diagnosis of this disease. This study utilized the molecular inversion probe for recognition of nucleotide variant between SMN1 (c.840 C) and SMN2 (c.840 C  >  T) genes, and rolling circle amplification with a universal primer for production of poly-T single-strand DNA. Finally, the fluorescent CuNCs were formed on the poly-T single-strand DNA template with addition of CuSO₄ and sodium ascorbate. The fluorescence of CuNCs was only detected in the samples with the presence of SMN1 gene controlling the disease of SMA. After optimization of experimental conditions, this highly efficient method was performed under 50 °C for DNA ligation temperature by using 2U Ampligase, 3 h for rolling circle amplification, and the formation of the CuNCs by mixing 500 μM Cu²⁺ and 4 mM sodium ascorbate. Additionally, this highly efficient method was successfully applied for 65 clinical DNA samples, including 4 SMA patients, 4 carriers and 57 wild individuals. This label-free detection strategy has the own potential to not only be a general method for detection of SMN1 gene in diagnosis of SMA disease, but also served as a tool for detection of other single nucleotide polymorphisms or nucleotide variants in genetic analysis through designing the different sensing probes.

Specific Gene Capture Combined with Restriction-Fragment Release for Directly Fluorescent Genotyping of Single-Nucleotide Polymorphisms in Diagnosing Spinal Muscular Atrophy

In this study, a fast and simple fluorescent genotyping strategy, streptavidin magnetic beads combined with biotin-coupled PCR and restriction-fragment release, was developed for determination of nucleotide variants. This method was further applied for analyzing SMN1 gene in diagnosis of spinal muscular atrophy (SMA). After biotin-coupled PCR, the streptavidin magnetic beads would capture the biotin-labeled SMN genetic fragments, and then the restriction enzyme of HPY188I could only digest and release the fluorescent end of SMN1 genetic fragment into the supernatant. Therefore, the SMN1 gene could be easily fluorescently quantified, and SMN2 would not, for diagnosis of SMA. The copy number of the SMN1 gene could be regressed using the relative fluorescent unit versus the known copy number, and the coefficient of correlation is equal to 0.9617 ( r = 0.9617). In this research, a total of 16 blind DNA samples were analyzed, including 6 wild types, 5 carriers, and 5 SMA patients. Importantly, this fast, simple, and highly efficient method is universal for detection of all nucleotides variants by replacing the specific restriction enzyme. This technique has the potency to be served as a tool for fast and accurate diagnosis of genotypes in clinical medicine.

Molecular inversion probes equipped with discontinuous rolling cycle amplification for targeting nucleotide variants: Determining SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy

The novel techniques of molecular inversion probes (MIPs) combined with discontinuous rolling cycle amplification (DRCA) was developed for determination of the multi-nucleotide variants at single base. The different-length MIPs, a padlock-probe based technology, are designed to simultaneously recognize the identical nucleotide variants. After ligation and DRCA, the different-length genetic products representing the certain genotypes could be simply determined by the short-end capillary electrophoresis (CE) method. By using MIPs-DRCA method, the various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects were successfully quantified for diagnosis of spinal muscular atrophy (SMA). The length of the MIP for SMN1 gene was 106 bp, and for SMN2 gene was 86 bp. After method optimization, the MIP products of SMN1 and SMN2 were well separated with the resolution of 1.13 ± 0.17 (n = 3) within 10 min. There were total of 56 DNA blind samples analyzed by this strategy, including 38 wild types, 12 carriers and 6 SMA patients, and the data of gene dosages was corresponding to those analyzed by conformation sensitive CE and denatured high performance liquid chromatography (DHPLC) methods. This MIPs-DRCA method which could be applied to simultaneously genotype multi nucleotide variants at single base, such as K-ras gene, was very feasible for determination of genetic diseases in clinical.

Evaluation and comparison of three assays for molecular detection of spinal muscular atrophy

BACKGROUND

Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA.

METHODS

A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays. A total of 317 samples were used to assess the specificity of the two assays.

RESULTS

The multiplex quantitative PCR (qPCR) assay had higher reproducibility. Intra-assay CVs were 3.01%-8.52% and inter-assay CVs were 4.12%-6.24%. The CNVplex assay had ratios that were closer to expected (0.49-0.5 for one copy, 1.03-1.0 for two copies, and 1.50-1.50 for three copies). Diagnostic accuracy rates for the two assays were 100%.

CONCLUSIONS

The multiplex qPCR assay was a simple, rapid, and cost-effective method for routine SMA diagnosis and carrier screening. The CNVplex assay could be used to detect SMAs with complicated gene structures. The assays were reliable and could be used as alternative methods for clinical diagnosis of SMA.

Copy Number Assessment by Competitive PCR with Limiting Deoxynucleotide Triphosphates and High-Resolution Melting

BACKGROUND

DNA copy number variation is associated with genetic disorders and cancer. Available methods to discern variation in copy number are typically costly, slow, require specialized equipment, and/or lack precision.

METHODS

Multiplex PCR with different primer pairs and limiting deoxynucleotide triphosphates (dNTPs) (3–12 μmol/L) were used for relative quantification and copy number assessment. Small PCR products (50–121 bp) were designed with 1 melting domain, well-separated Tms, minimal internal sequence variation, and no common homologs. PCR products were displayed as melting curves on derivative plots and normalized to the reference peak. Different copy numbers of each target clustered together and were grouped by unbiased hierarchical clustering.

RESULTS

Duplex PCR of a reference gene and a target gene was used to detect copy number variation in chromosomes X, Y, 13, 18, 21, epidermal growth factor receptor (EGFR), survival of motor neuron 1, telomeric (SMN1), and survival of motor neuron 2, centromeric (SMN2). Triplex PCR was used for X and Y and CFTR exons 2 and 3. Blinded studies of 50 potential trisomic samples (13, 18, 21, or normal) and 50 samples with potential sex chromosome abnormalities were concordant to karyotyping, except for 2 samples that were originally mosaics that displayed a single karyotype after growth. Large cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) (CFTR) deletions, EGFR amplifications, and SMN1 and SMN2 copy number assessments were also demonstrated. Under ideal conditions, copy number changes of 1.11-fold or lower could be discerned with CVs of about 1%.

CONCLUSIONS

Relative quantification by restricting the dNTP concentration with melting curve display is a simple and precise way to assess targeted copy number variation.

Universal fluorescent tri-probe ligation equipped with capillary electrophoresis for targeting SMN1 and SMN2 genes in diagnosis of spinal muscular atrophy

This is the first ligase chain reaction used for diagnosis of spinal muscular atrophy (SMA). Universal fluorescent tri-probe ligation (UFTPL), a novel strategy used for distinguishing the multi-nucleotide alternations at single base, is developed to quantitatively analyze the SMN1/SMN2 genes in diagnosis of SMA. Ligase chain reaction was performed by adding three probes including universal fluorescent probe, connecting probe and recognizing probe to differentiate single nucleotide polymorphisms in UFTPL. Our approach was based on the two UFTPL products of survival motor neuron 1 (SMN1) and SMN2 genes (the difference of 9 mer) and analyzed by capillary electrophoresis (CE). We successfully determined various gene dosages of SMN1 and SMN2 genes in homologous or heterologous subjects. By using the UFTPL-CE method, the SMN1 and SMN2 genes were fully resolved with the resolution of 2.16±0.37 (n=3). The r values of SMN1 and SMN2 regression curves over a range of 1-4 copies were above 0.9944. Of the 48 DNA samples, the data of gene dosages were corresponding to that analyzed by conformation sensitive CE and denatured high-performance liquid chromatography (DHPLC). This technique was found to be a good methodology for quantification or determination of the relative genes having multi-nucleotide variants at single base.

Colorimetric Assay for Exon 7 SMN1/SMN2 Single Nucleotide Polymorphism Using Gold Nanoprobes

INTRODUCTION

Proximal spinal muscular atrophy (SMA) is one of the most significant neurodegenerative diseases amongst the autosomal-recessive genetic disorders which is caused by the absence of protein survival of motor neuron (SMN). A critical nucleotide difference in SMN2 compared to SMN1 gene leads to an inefficient protein. Hence, homozygous lack of SMN1 provides a progressive disease. Due to the high prevalence, up to now, several molecular diagnostic methods have been used which most of them are lengthy, expensive, and laborious.

METHODS

In the present study, we exploited a gold nanoprobe-based method for semi-quantitative SMN1 gene dosage analysis compared to SMN2. The assay was done under hybridization process between Au nanoprobes and different ratios of SMN1/SMN2 amplicons.

RESULTS

UV-vis spectra indicated that after the salt addition, nanoprobes aggregated gradually and their peak shifted to longer wavelengths except in the stable target-nanoprobes hybridization. The results revealed that the homozygous genotype of SMN2 gene is distinguished from the heterozygous genotypes of SMN genes by the naked eye, whereas different ratio of heterozygous genotypes (SMN1/SMN2) are differentiated better from each other using peak analysis ratios.

CONCLUSION

The presented strategy is an alternative simple method for discrimination of homozygous deletion of SMN1 in less than 30 min. However, further evaluation of the assay using clinical samples is recommended prior to real-world use.

CYP2D6, SULT1A1 and UGT2B17 copy number variation: quantitative detection by multiplex PCR

Aim: Among the genes of drug-metabolizing enzymes, CYP2D6 is notoriously difficult to characterize owing to the complexity of gene deletions, duplications, multiplications and the presence of hybrid genes composed of CYP2D6 and CYP2D7. For SULT1A1 up to five gene copies have been reported, while UGT2B17 is known for gene deletions only. Different platforms exist for copy number variation (CNV) detection; however, there are no gold standards. Robust methods are required that address specific challenges to accurately determine gene CNVs in complex gene loci. Materials & methods: Quantitative multiplex PCR amplification (MPA) was performed on a diverse set of genomic DNA samples. Resulting PCR fragments were separated on an ABI 3730 instrument and analyzed with GeneMapper. CYP2D6 was targeted at four different gene regions and either normalized against CYP2D8 or UGT2B15 and SULT1A2. Inconsistent observations and CNVs contrasting genotype data were further characterized by long-range PCR and/or DNA sequence analysis. UGT2B17 and SULT1A1 were normalized against UGT2B15 and SULT1A2, respectively. Results: MPA detected 0–5, 1–5 and 0–2 copies for CYP2D6, SULT1A1 and UGT2B17, respectively. The interrogation of four CYP2D6 regions resulted in robust copy number assignments that were in agreement with genotype, sequencing and extra long PCR-based data. Gene deletions, duplication, and multiplications among known and novel hybrid genes were reliably identified. Novel findings regarding allelic variation include nonfunctional CYP2D6/2D7 hybrids such as CYP2D6*4N and *68, which were consistently identified on a subset of CYP2D6*4 alleles. In addition, a novel variant, designated CYP2D6*83, was discovered. For SULT1A1, we report the first six-copy case and for UGT2B15 and UGT2B17 we have evidence for rare deletion and duplication events, respectively. Conclusion: This MPA-based copy number platform not only allowed us to determine CNVs, but also served as a tool for allele discovery and characterization in a diverse panel of samples in a fast and reliable manner.

Original submitted 6 July 2011; Revision submitted 24 August 2011

Multi-exon genotyping of SMN gene in spinal muscular atrophy by universal fluorescent PCR and capillary electrophoresis

In this study, we established the first method for simultaneous evaluation of nine exons in the survival motor neuron (SMN) genes for full-scale genotyping. This method was used not only to quantify the copy numbers of highly homogenous telomeric SMN (SMN1)/centromeric SMN genes in exons 7 and 8 but also to determine intragenic mutations in all nine exons for complete diagnosis of spinal muscular atrophy (SMA). Additionally, we utilized the "universal fluorescent PCR" for simultaneously fluorescent labeling of eleven gene fragments (nine exons in SMN and two internal standards). Such technique is very beneficial for multi-exon analysis due to only requirement of one universal fluorescent primer which could fluorescently amplify all gene fragments. Of all 262 detected individuals, three subjects possessing different ratios of SMN1/centromeric SMN in the two exons were determined as gene conversion, and we also detected three interesting intragenic mutations (c.1 -39A>G, c.22_23insA in exon 1, c.84C>T in exon 2a) which were associated with the SMA patients owning one copy of SMN1 including two mutations never reported previously. This high-resolved method provided better potential technique for genotyping and identifying SMA, carrier and normal controls in large population.

Quick MLPA test for quantification of SMN1 and SMN2 copy numbers

Spinal muscular atrophy (SMA) is an autosomal recessive disease caused in about 95% of SMA patients by homozygous deletion of the survival motor neuron 1 (SMN1) gene or its conversion to the highly homologous SMN2 gene. In the majority of cases, disease severity correlates inversely with increased SMN2 copy number. Because of the comparatively high incidence of healthy carriers and severity of the disease, detection of sequence alterations and quantification of SMN1 and SMN2 copy numbers are essential for exact diagnosis and genetic counselling. Several assays have been developed for this purpose. Multiplex ligation-dependent probe amplification (MLPA) is a versatile technique for relative quantification of different nucleic acid sequences in a single reaction. Here, we establish a quick MLPA-based assay for the detection of SMN1 and SMN2 copy numbers with high specificity and low complexity.

Universal fluorescent multiplex PCR and capillary electrophoresis for evaluation of gene conversion between SMN1 and SMN2 in spinal muscular atrophy

We have developed a capillary electrophoresis (CE) method with universal fluorescent multiplex PCR to simultaneously detect the SMN1 and SMN2 genes in exons 7 and 8. Spinal muscular atrophy (SMA) is a very frequent inherited disease caused by the absence of the SMN1 gene in approximately 94% of patients. Those patients have deletion of the SMN1 gene or gene conversion between SMN1 and SMN2. However, most methods only focus on the analysis of whole gene deletion, and ignore gene conversion. Simultaneous quantification of SMN1 and SMN2 in exons 7 and 8 is a good strategy for estimating SMN1 deletion or SMN1 to SMN2 gene conversion. This study established a CE separation allowing differentiation of all copy ratios of SMN1 to SMN2 in exons 7 and 8. Among 212 detected individuals, there were 23 SMA patients, 45 carriers, and 144 normal subjects. Three individuals had different ratios of SMN1 to SMN2 in two exons, including an SMA patient having two SMN2 copies in exon 7 but one SMN1 copy in exon 8. This method could provide more information about SMN1 deletion or SMN1 to SMN2 gene conversion for SMA genotyping and diagnosis.

Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: simultaneous detection of SMN1 and SMN2 deletion

Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.