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SALSA® MLPA® Probemix P460 SMA (Silent) Carrier detects copy number variations in the SMN1 and SMN2 genes. P460 SMA has been specifically designed for SMA carrier detection and risk factors for silent carriers.
Contents: 23 MLPA probes, including 2 probes for SMN1, 1 probe for SMN1 polymorphisms g.27134T>G and g.27706-27707delAT each, and 1 probe for SMN2.
Tissue: genomic DNA isolated from human peripheral whole blood.
Application: spinal muscular atrophy (SMA).
CE-marked for in vitro diagnostic (IVD) use.
MRC Holland offers four different assays for SMA that fit the complete range of genetic testing needs. Compare our SMA products.
The SALSA MLPA Probemix P460 SMA (Silent) Carrier is an in vitro diagnostic (IVD) or research use only (RUO) semi-quantitative assay for the detection of 1. copy number changes of exons 7 and 8 of the SMN1 gene for carrier testing, patient diagnosis and for the confirmation of a potential cause and clinical diagnosis of spinal muscular atrophy (SMA), and 2. the presence of the g.27134T>G and g.27706-27707delAT polymorphisms in SMN1 that are a risk factor for silent carriership of SMA in genomic DNA isolated from human peripheral whole blood specimens. P460 SMA (Silent) Carrier is also intended for molecular genetic testing of at-risk family members.
For the full intended purpose, see the product description.
The SALSA MLPA Probemix P460 SMA (Silent) Carrier is an assay for the detection of deletions or duplications in the SMN1 gene, which are associated with Spinal Muscular Atrophy (SMA). This probemix can also be used to detect the presence of two SMN1 polymorphisms, g.27134T>G and g.27706-27707delAT, for haplotype identification.
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder characterised by degeneration of the anterior horn cells of the spinal cord, leading to symmetrical muscle weakness and atrophy. SMA is the second most common lethal autosomal recessive disorder in Caucasians, after cystic fibrosis. SMA is usually divided into three clinical groups. Patients with type I SMA (OMIM# 253300) show onset at birth or before six months, and usually die of respiratory insufficiency within two years. Type I SMA patients are never able to sit or walk. Patients with type II SMA (OMIM# 253550) show onset after six months. They can sit but are never able to walk unaided, and their life expectancy is significantly reduced. Type III SMA (OMIM# 253400) patients show the first symptoms after 18 months and are able to stand and walk, but often become wheelchair-bound during youth or adulthood.
There are two (highly similar) genes playing a pivotal role in SMA: SMN1 and SMN2. The telomeric SMN1 and the centromeric SMN2 genes are located in a complicated inverted repeat area spanning ~500 kb on chromosome 5q13.2. This area displays high instability, leading to frequent deletions and gene conversions. Most individuals have two copies each of SMN1 and SMN2, both consisting of nine exons (exons 1, 2a, 2b, and 3-8). The SMN1 and SMN2 genes can only be distinguished by two single nucleotide differences: one in exon 7 and one in exon 8. The exon 8 difference has no effect on the transcript; however, the exon 7 difference disrupts splicing in SMN2 most of the time leading to loss of functionality. Only 10-15% of the SMN2 transcripts are functional. This SALSA MLPA Probemix P460 SMA (Silent) Carrier detects the copy number of exons 7 and 8 of the SMN1 gene.
Absence of any functional SMN1 copy results in insufficient amounts of full-length transcripts. More than 95% of SMA patients show homozygous deletion of at least exon 7 of the telomeric SMN1 gene. Individuals with only one functional SMN1 copy are carriers of the disease. The great majority of SMA carriers can be identified by the presence of only a single SMN1 exon 7 copy. The one copy frequency in the US is estimated to be 1:37 for Caucasians, 1:46 for Ashkenazi Jews, 1:56 for Asians, 1:91 for African-Americans and 1:125 for Hispanics (Hendrickson et al. 2009).
Although the great majority of SMA carriers can be detected by copy number analysis of the SMN1 exon 7 sequence, some carriers remain undetected. These include carriers with (1) a defective SMN1 allele due to a point mutation in the SMN1 gene or a copy number change of exons 1-6 or 8, and (2) individuals that have two SMN1 copies on one allele and none on the other allele, the so-called “Silent Carriers” (2+0 genotype). The P460 probemix increases the detection rate of the latter group.
In most populations, approximately 6.3-15.5% of the individuals have two SMN1 copies on a single chromosome 5 strand, of which 0.07-0.19% are a silent carrier. In the African-American population this percentage is even as high as 47.2%, of which 0.41% is a silent carrier (Hendrickson et al 2009). Luo et al. (2014) has reported that a specific SMN1 haplotype block is present in a large percentage of Ashkenazi Jews who carry an SMN1 duplication. This haplotype was also identified on SMN1 duplication alleles in other ethnic groups, but in lower percentages. Detection of the SMN1 polymorphisms g.27134T>G and g.27706-27707delAT can aid in identifying this haplotype and thereby silent carriers.
More information on Spinal Muscular Atrophy is available at http://www.ncbi.nlm.nih.gov/books/NBK1352/.
SALSA MLPA Probemix P460 SMA (Silent) Carrier is CE-marked for in vitro diagnostic (IVD) use.
This assay is for research use only (RUO) in all other territories.
SALSA Reference Selection & Binning DNA SD084 is an artificial DNA sample with a signal for all probes in the P460 SMA (Silent) Carrier probemix. It has two distinct functions:
SD084 cannot be used as a reference sample after the initial selection of suitable reference samples from your own sample collection, and cannot be used to quantify the signals of mutation-specific probes.
A vial of SD084 is included with every order of the P460 SMA (Silent) Carrier probemix, but it is possible to order additional vials separately.
For more information, see the product description.
A general SALSA MLPA Reagent Kit is required for MLPA experiments (to be ordered separately).
A vial is included with every order of this probemix, but additional vials can also be purchased separately.
Inclusion of a positive sample is usually not required, but can be useful for the analysis of your experiments. MRC Holland has very limited access to positive samples and cannot supply such samples. We recommend using positive samples from your own collection. Alternatively, you can use positive samples from an online biorepository, such as the Coriell Institute.
The commercially available positive samples below have been tested with the current (A1) version of this product and have been shown to produce useful results.
Coriell Sample ID | Copy Number | ||||
---|---|---|---|---|---|
SMN1 exon 7 | SMN1 exon 8 | SMN2 exon 7 | SMN1 g.27134T>G | SMN1 g.27706-27707delAT | |
NA00232 | 0 | 0 | 2 | 0 | 0 |
NA03815 | 1 | 1 | 1 | 0 | 0 |
HG01773 | 1 | 1 | 4* | 0 | 0 |
NA19984 | 2 | 2 | 1 | 1 | 1 |
NA20294 | 3 | 3 | 1 | 1 | 1 |
HG02882 | 3 | 3 | 1 | 2 | 2 |
NA19235 | 4 | 4 | 0 | 3 | 3 |
* SMN2 probes in this probemix cannot reliably distinguish between 4 or more copies. The indicated copy numbers have been validated using SALSA MLPA Probemix P021 SMA.
A large set of additional potentially useful positive control samples can be found on the product page of SALSA MLPA Probemix P021 SMA or in Prior et al. (2021).