Detection of SMN1 to SMN2 gene conversion events and partial SMN1 gene deletions using array digital PCR

Neurogenetics ◽  
2021 ◽  
Author(s):  
Deborah L. Stabley ◽  
Jennifer Holbrook ◽  
Mena Scavina ◽  
Thomas O. Crawford ◽  
Kathryn J. Swoboda ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Digital Pcr ◽  
Gene Deletions ◽  
Smn1 Gene ◽  
Smn2 Gene

Spinal Muscular Atrophy

2017 ◽  
Author(s):  
Arthur H. M. Burghes ◽  
Vicki L. McGovern
Keyword(s):  
Motor Neuron ◽  
Gene Locus ◽  
Autosomal Recessive ◽  
Muscular Atrophy ◽  
Autosomal Recessive Disorder ◽  
Clinical Testing ◽  
Smn1 Gene ◽  
Smn2 Gene ◽  
Spinal Muscular Atrophies ◽  
Smn Gene

Spinal muscular atrophies affect the lower motor neuron. The most common SMA maps to 5q is an autosomal recessive disorder. SMA is caused by loss or mutation of the SMN1 gene and retention of the SMN2 gene, and these genes lie in a complex area of the genome. Mild missense alleles of SMN1 work to complement SMN2 to give function and therapeutics that restore SMN levels are in clinical testing. Modifiers that lie outside the SMN gene locus and influence severity clearly exist, but what they are remains unknown as do the critical genes affected by SMN deficiency.

scholarly journals SAM68 is a physiological regulator of SMN2 splicing in spinal muscular atrophy

2015 ◽  
Vol 211 (1) ◽  
pp. 77-90 ◽  
Author(s):  
Vittoria Pagliarini ◽  
Laura Pelosi ◽  
Maria Blaire Bustamante ◽  
Annalisa Nobili ◽  
Maria Grazia Berardinelli ◽  
...  
Keyword(s):  
Spinal Muscular Atrophy ◽  
Motor Neurons ◽  
Messenger Rna ◽  
Muscular Atrophy ◽  
Splicing Factors ◽  
Hnrnp A1 ◽  
Smn1 Gene ◽  
Smn2 Gene ◽  
Physiological Regulator

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by loss of motor neurons in patients with null mutations in the SMN1 gene. The almost identical SMN2 gene is unable to compensate for this deficiency because of the skipping of exon 7 during pre–messenger RNA (mRNA) processing. Although several splicing factors can modulate SMN2 splicing in vitro, the physiological regulators of this disease-causing event are unknown. We found that knockout of the splicing factor SAM68 partially rescued body weight and viability of SMAΔ7 mice. Ablation of SAM68 function promoted SMN2 splicing and expression in SMAΔ7 mice, correlating with amelioration of SMA-related defects in motor neurons and skeletal muscles. Mechanistically, SAM68 binds to SMN2 pre-mRNA, favoring recruitment of the splicing repressor hnRNP A1 and interfering with that of U2AF65 at the 3′ splice site of exon 7. These findings identify SAM68 as the first physiological regulator of SMN2 splicing in an SMA mouse model.

scholarly journals Null alleles of human complement C4. Evidence for pseudogenes at the C4A locus and for gene conversion at the C4B locus.

1990 ◽  
Vol 171 (1) ◽  
pp. 129-140 ◽  
Author(s):  
L Braun ◽  
P M Schneider ◽  
C M Giles ◽  
J Bertrams ◽  
C Rittner
Keyword(s):  
Gene Conversion ◽  
Null Alleles ◽  
Human Complement ◽  
Class Iii ◽  
Fragment Analysis ◽  
Gene Deletions ◽  
Oligonucleotide Hybridization ◽  
Mhc Class Iii ◽  
Fourth Component ◽  
Specific Sequences

The two genes for the C4A and C4B isotypes of the fourth component of human complement are located in the MHC class III region. Previous studies have demonstrated the unusual expression of C4 genes in the form of aberrant or duplicated haplotypes. Null alleles of C4A or C4B (AQ0 or BQ0) have been defined by the absence of gene products and occur at frequencies of 0.1-0.3. However, only some C4 null alleles are due to gene deletions, the remainder were thought to be nonexpressed genes. We have analyzed the C4 gene structure of 26 individuals lacking either C4A or C4B protein. The DNA of individuals with apparently nonexpressed C4 genes was tested for the presence of C4A- and C4B-specific sequences using restriction fragment analysis and isotype-specific oligonucleotide hybridization of DNA amplified by polymerase chain reaction. All nondeleted AQ0 allels had C4A-specific sequences and may thus be described as pseudogenes, whereas the nondeleted BQ0 alleles had C4A-instead of C4B-specific sequences. Gene conversion is the probable mechanism by which a C4A gene is found at the second C4 locus normally occupied by C4B genes.

scholarly journals Phenotype modifiers of spinal muscular atrophy: the number of SMN2 gene copies, deletion in the NAIP gene and probably gender influence the course of the disease.

2009 ◽  
Vol 56 (1) ◽  
Author(s):  
Maria Jedrzejowska ◽  
Michał Milewski ◽  
Janusz Zimowski ◽  
Janina Borkowska ◽  
Anna Kostera-Pruszczyk ◽  
...  
Keyword(s):  
Spinal Muscular Atrophy ◽  
Autosomal Recessive ◽  
Clinical Symptoms ◽  
Muscular Atrophy ◽  
Neuromuscular Disorder ◽  
Smn1 Gene ◽  
Gender Influence ◽  
Gene Copies ◽  
Smn2 Gene ◽  
Naip Gene

Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by mutations of the SMN1 gene. It is characterized by significant phenotype variability. In this study, we analyzed possible phenotype modifiers of the disease - the size of the deletion in the SMA region, the number of SMN2 gene copies, as well as the effect of gender. Among the factors analyzed, two seem to influence the SMA phenotype: the number of SMN2 gene copies and a deletion in the NAIP gene. A higher number of SMN2 copies makes the clinical symptoms more benign, and the NAIP gene deletion is associated with a more severe phenotype. The influence of gender remains unclear. In a group of 1039 patients, 55% of whom were male, the greatest disproportion was in the SMA1 (F/M = 0.78) and SMA3b (F/M = 0.45) forms. In SMA1 a deletion in the NAIP gene was seen twice as frequently in girls compared to boys. In three patients, we observed genotypes atypical for the chronic forms of SMA: two patients with SMA3a and 3b had a deletion of the NAIP gene, and a third patient with SMA2 had one copy of the SMN2 gene.

scholarly journals Detection of pseudorabies virus by duplex droplet digital PCR assay

2017 ◽  
Vol 30 (1) ◽  
pp. 105-112 ◽  
Author(s):  
Meishen Ren ◽  
Hua Lin ◽  
Shijie Chen ◽  
Miao Yang ◽  
Wei An ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Wild Type ◽  
Serum Samples ◽  
Swine Industry ◽  
Gene Deletions ◽  
Glycoprotein E ◽  
Low Concentrations ◽  
Nonspecific Amplification

Aujeszky’s disease, caused by pseudorabies virus (PRV), has damaged the economy of the Chinese swine industry. A large number of PRV gene-deleted vaccines have been constructed based on deletion of the glycoprotein E ( gE) gene combined with other virulence-related gene deletions, such as thymidine kinase ( TK), whereas PRV wild-type strains contain an intact gE gene. We developed a sensitive duplex droplet digital PCR (ddPCR) assay to rapidly detect PRV wild-type isolates and gE gene–deleted viral vaccines. We compared this assay with a TaqMan real-time PCR (qPCR) using the same primers and probes. Both assays exhibited good linearity and repeatability; however, ddPCR maintained linearity at extremely low concentrations, whereas qPCR did not. Based on positive results for both gE and gB, the detection limit of ddPCR was found to be 4.75 copies/µL in contrast of 76 copies/µL for qPCR, showing that ddPCR provided a 16-fold improvement in sensitivity. In addition, no nonspecific amplification was shown in specificity testing, and the PRV wild-type was distinguished from a gE-deleted strain. The ddPCR was more sensitive when analyzing clinical serum samples. Thus, ddPCR may become an appropriate detection platform for PRV.

scholarly journals Onasemnogene Abeparvovec (Zolgensma)

2021 ◽  
Vol 1 (9) ◽  
Author(s):  
Reimbursement Team
Keyword(s):  
Single Dose ◽  
Cost Effectiveness ◽  
Pediatric Patients ◽  
Drug Class ◽  
Clinical Effectiveness ◽  
Survival Motor Neuron ◽  
Smn1 Gene ◽  
Smn2 Gene ◽  
Clinician Perspectives ◽  
Biallelic Mutations

CADTH reimbursement reviews are comprehensive assessments of the clinical effectiveness and cost-effectiveness, as well as patient and clinician perspectives, of a drug or drug class. The assessments inform non-binding recommendations that help guide the reimbursement decisions of Canada's federal, provincial, and territorial governments, with the exception of Quebec. This review assesses onasemnogene abeparvovec (Zolgensma), given as a single-dose IV infusion of 1.1 × 1014 vector genomes/kg Indication: For the treatment of pediatric patients with 5q SMA with biallelic mutations in the survival motor neuron 1 (SMN1) gene and: 3 or fewer copies of the SMN2 gene or infantile-onset SMA  

scholarly journals Association between the SMN2 gene copy number and clinical characteristics of patients with spinal muscular atrophy with homozygous deletion of exon 7 of the SMN1 gene

2015 ◽  
Vol 72 (10) ◽  
pp. 859-863 ◽  
Author(s):  
Marija Zarkov ◽  
Aleksandra Stojadinovic ◽  
Slobodan Sekulic ◽  
Iva Barjaktarovic ◽  
Olivera Stojiljkovic ◽  
...  
Keyword(s):  
Copy Number ◽  
Muscular Atrophy ◽  
Gene Copy Number ◽  
Homozygous Deletion ◽  
Gene Copy ◽  
Type Ii ◽  
Disease Phenotype ◽  
Smn1 Gene ◽  
Type Iv ◽  
Smn2 Gene

Background/Aim. Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by degeneration of alpha motor neurons in the spinal cord and the medulla oblongata, causing progressive muscle weakness and atrophy. The aim of this study was to determine association between the SMN2 gene copy number and disease phenotype in Serbian patients with SMA with homozygous deletion of exon 7 of the SMN1 gene. Methods. The patients were identified using regional Serbian hospital databases. Investigated clinical characteristics of the disease were: patients? gender, age at disease onset, achieved and current developmental milestones, disease duration, current age, and the presence of the spinal deformities and joint contractures. The number of SMN1 and SMN2 gene copies was determined using real-time polymerase chain reaction (PCR). Results. Among 43 identified patients, 37 (86.0%) showed homozygous deletion of SMN1 exon 7. One (2.7%) of 37 patients had SMA type I with 3 SMN2 copies, 11 (29.7%) patients had SMA type II with 3.1 ? 0.7 copies, 17 (45.9%) patients had SMA type III with 3.7 ? 0.9 copies, while 8 (21.6%) patients had SMA type IV with 4.2 ? 0.9 copies. There was a progressive increase in the SMN2 gene copy number from type II towards type IV (p < 0.05). A higher SMN2 gene copy number was associated with better current motor performance (p < 0.05). Conclusion. In the Serbian patients with SMA, a higher SMN2 gene copy number correlated with less severe disease phenotype. A possible effect of other phenotype modifiers should not be neglected.

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