Accurate diagnosis of spinal muscular atrophy and 22q11.2 deletion syndrome using limited deoxynucleotide triphosphates and high-resolution melting

Development of a low-cost and accurate carrier screening method for spinal muscular atrophy in developing countries

Heterozygous carriers of the survival of motor neuron 1 (SMN1) gene deletion in parents account for approximately 95% of neonatal spinal muscular atrophy cases. Given the severity of the disease, professional organizations have recommended periconceptional spinal muscular atrophy carrier screening to all couples, regardless of race or ethnicity. However, the prevalence of screening activities in mainland China remains suboptimal, mainly attributed to the limitations of the existing carrier screening methods. Herein, we aimed to develop a low-cost, accessible, and accurate carrier screening method based on duplex droplet digital PCR (ddPCR), to cover a wider population in developing countries, including China. The receiver operating characteristic curve was used to determine the cut-off value of SMN1 copy numbers. Performance validation was conducted for linearity, precision, and accuracy. In total, 482 cases were considered to validate the concordance between the developed ddPCR assay and multiplex ligation-dependent probe amplification. Linear correlations were excellent between the expected concentration of the reference gene and the observed values (R2 > 0.99). Both the intra- and inter-assay precision of our ddPCR assays were less than 6.0%. The multiplex ligation-dependent probe amplification and ddPCR results were consistent in 480 of the 482 cases (99.6%). Two cases with multiplex ligation-dependent probe amplification, suggestive of two copies of SMN1 exon 7, were classified into three copies by ddPCR analysis. The overall correct classification of the samples included in our ddPCR assay was 100%. This study demonstrates that an appropriate cut-off value is an important prerequisite for establishing a semi-quantitative method to determine the SMN1 copy numbers. Compared to conventional methods, our ddPCR assay is low-cost, highly accurate, and has full potential for application in population spinal muscular atrophy carriers screening.

Detection of PTCH1 Copy-Number Variants in Mosaic Basal Cell Nevus Syndrome

Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient's father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient's blood, and the father's blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient's blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring.

Current Advances in Genetic Testing for Spinal Muscular Atrophy

Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate technique for genetic testing have become priorities for optimizing the clinical pathway for SMA. In this review, we summarize the latest technological innovations in genetic testing for SMA, including MassArray®, digital PCR (dPCR), next-generation sequencing (NGS), and third-generation sequencing (TGS). Implementation recommendations for rationally choosing different technical strategies in the tertiary prevention of SMA are also explored.

A rapid molecular diagnostic method for spinal muscular atrophy

Spinal muscular atrophy (SMA) is a common autosomal recessive disorder which has been considered as the second common cause of infant death, with an estimated prevalence of 1 in 10,000 live births. The disorder is caused by survival motor neuron 1 gene (SMN1) deficiency leading to limb weakness, difficult swallowing and abnormal breathing. Here, a fast and accurate method for SMA detection has been developed. Genomic DNA sample collected from whole blood, amniotic fluid, or dried blood spots can be analysed by using the Clarity™ Digital PCR (dPCR) System for determining the copy numbers of SMN1 and SMN2 genes. Two hundred and fourteen clinical samples determined by qPCR-based method were enrolled and used to establish the cut-off ranges for unaffected individual, SMA carrier and SMA patient categories. After setting the cut-off range for each group, 12 samples were analyzed by both dPCR-based method and MLPA (multiplex ligation-dependent probe amplification), the current testing golden standard for SMA, and 100% concordant results between the two testing methods were performed. CSB SMA Detection Kit combined with dPCR platform provides a robust and precise approach to distinguish unaffected individuals, SMA carrier and SMA patients. This rapid molecular diagnostic method can be adapted to pre-pregnancy eugenics inspection, prenatal testing as well as newborns screening and help physicians or genetic counselors to improve population SMA incidence.

Analytical validation of the droplet digital PCR assay for diagnosis of spinal muscular atrophy

BACKGROUND

Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by homozygote loss of exon 7 on the survival motor neuron 1 (SMN1) gene. The severity of the SMA phenotype is influenced by copies of SMN2, a gene that is highly homologous with SMN1.

METHODS

We validated analytical performance of droplet digital polymerase chain reaction (ddPCR) for detection of copy number variation of SMN1 and SMN2 genes for diagnosis of SMA using clinical samples. For accuracy performance evaluation, ddPCR results were compared with those of multiplex ligation-dependent probe amplification (MLPA) as a reference standard. Copy numbers of SMN1/SMN2 exon 7 from 200 clinical samples were concordant between ddPCR and MLPA.

RESULTS

For all samples, the copy number of SMN1/SMN2 exon 7 was concordant between MLPA and ddPCR. The ddPCR also showed acceptable degrees of repeatability and total imprecision.

CONCLUSION

Therefore, ddPCR is expected to be useful for SMA diagnosis and to predict phenotypic severity of SMA patients by determining the copy number of SMN2 in clinical laboratories.