probemix P060 SMA is an in vitro diagnostic (IVD)1
or research use only (RUO) assay for the detection of copy number changes of exons 7 and 8 of SMN1
for carrier testing, patient diagnosis and for the confirmation of a potential cause and clinical diagnosis of spinal muscular atrophy (SMA). This probemix can also be used for the detection of copy number changes of exons 7 and 8 of the SMN2
gene, as an interpretation aid for SMN1
copy number determination.
This assay is for use with human DNA extracted from:
This assay is not intended to be used as a standalone assay for clinical decisions. The results of this test must be interpreted by a clinical molecular geneticist or equivalent.
1 Please note that this probemix is for In Vitro Diagnostic use (IVD) in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).
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. The estimated incidence of SMA is 1:6,000-1:10,000: the second most common lethal autosomal recessive disorder in Caucasians, after cystic fibrosis (Ben-Shachar et al. 2011, Smith et al. 2007). SMA is usually divided into four clinical groups based on age of onset and maximum function obtained (type I, OMIM# 253300; type II, OMIM# 253550; type III, OMIM# 253400; and type IV, OMIM# 271150).
Two (highly-similar) genes play a pivotal role in SMA: SMN1
. Most individuals have two copies of each gene. The SMA region on 5q13.2, containing the telomeric SMN1
and the centromeric SMN2
, is a complicated inverted repeat area displaying high instability, leading to frequent deletions and gene conversions. SMN1
can only be distinguished by two single nucleotide differences: one in exon 7 and one in exon 8. The single nucleotide difference in exon 7 of SMN2
affects mRNA splicing resulting in an altered SMN protein with a limited half-life and function.
A total of 95-98% of SMA patients (this percentage is lower in SMA patients from African descent) show homozygous deletion of at least exon 7 of the telomeric SMN1
gene (Labrum et al. 2007). The remaining 3-5% present compound heterozygosity with a point mutation on one chromosome and a deletion/gene conversion on the other. Such a point mutation will not be detected by this P060 SMA Carrier MLPA assay and should be identified by sequencing. In a small number of patients, the SMN1
defect is a copy number change of SMN1
exons 1-6 which can be detected with the P021 SMA MLPA probemix (Arkblad et al. 2006).
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. Approximately 3-8% of SMA carriers (27% of African Americans) have one functional and one defective SMN1
copy, or have two SMN1
copies on one chromosome and 0 copies on the other (2+0) (Alias et al. 2014, Ben-Shachar et al. 2011, Hendrickson et al. 2009, Miskovic et al. 2011, Smith et al. 2007). Dosage analysis cannot determine the difference between '1+1' and '2+0' (silent carriers) arrangements. Both situations are simply detected as having two SMN1
copies leading to false negative results. A thorough molecular analysis should be performed in parents of SMA patients who have two SMN1
copies. Luo et al. (2014) reported that a haplotype block specific for SMN1
duplications is present in a large percentage of Ashkenazi Jews and in other ethnic groups. Identifying this haplotype will help distinguish silent carriers and can be done with the P460 SMA MLPA Probemix.
copy number is very variable with only 60-70% of individuals having two copies. Provided that at least one functional SMN1
copy is present, complete absence of the centromeric SMN2
gene seems to have no clinical consequences. More information on spinal muscular atrophy can be found in http://www.ncbi.nlm.nih.gov/books/NBK1352/
P060-B2 probemix content:
probemix P060 SMA contains 21 MLPA probes with amplification products between 154 and 342 nt (Table 2) including 2 probes each for SMN1
(Table 2) and 17 reference probes that detect sequences outside this region. The identity of the genes detected by the reference probes is available online (www.mlpa.com
- The SMN1 Exon 7 probe 14919-L17081
(183 nt) is the most important probe as it can be used to determine SMN1
which is important for deducing SMA diagnosis and carrier status. This probe is specific for SMN1
and will give no significant signal on SMN2
. The probe has its ligation site at the C-to-T transition in exon 7, which is the site that affects RNA splicing in SMN2
- The SMN1 Exon 8 probe 14881-L17082
(218 nt) is able to distinguish between SMN1
at exon 8 (G-to-A transition). The signal of this probe indicates the copy number of SMN1
exon 8. In approximately 95% of the samples, the copy number detected by the SMN1
exon 7 probe and the SMN1
exon 8 probe is identical. This SMN1
exon 8 probe cannot be used to quantify the number of SMN1
copies, as an exon 8 mutation will still result in a functional protein. Only the SMN1
exon 7 probe should be used to determine the SMN1
copy number. In the majority of the remaining 5% of samples, gene conversion between SMN1
has resulted in a chimeric gene containing the SMN1
exon 7 sequence and the SMN2
exon 8 sequence. Such a hybrid gene results in a functionally identical protein to the SMN1 protein.
- The SMN2 Exon 7 probe 14921-L17083
(282 nt) identifies the SMN2
exon 7 copy number, which aids in the detection of gene-conversion events. The SMN2
copy number has no influence on SMA carrier status.
- The SMN2 Exon 8 probe 14878-L17084
(301 nt) identifies the SMN2
exon 8 copy number, which aids in the detection of gene-conversion events. The SMN2
copy number has no influence on SMA carrier status.
The summary of these findings and what they mean for carrier/patient status can be found in Table B. Figures depicting variation as can be detected by P060 SMA Carrier can be found on page 10 (figure 1-4).
This probemix contains nine quality control fragments generating amplification products between 64 and 105 nt: four DNA Quantity Fragments (Q-fragments), two DNA Denaturation Fragments (D-fragments), one benchmark fragment, and one chromosome X and one chromosome Y-specific fragment (see table below). More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at www.mlpa.com
SALSA Reference Selection DNA SD082:
The Reference Selection DNA SD082 provided with this probemix can be used to find suitable reference DNA samples from your own sample collection for further use in MLPA experiments.
It is strongly advised to use DNA sample and reference DNA samples extracted with the same method and derived from the same source of tissue. For certain applications, the selection of suitable reference DNA samples is complicated. Inclusion of one reaction with 5 μl SD082 Reference Selection DNA facilitates the identification of suitable reference DNA samples. We recommend the use of this SD082 Reference Selection DNA (or Coriell sample HG01701) only for initial experiments on DNA samples from healthy individuals with the intention to identify suitable reference DNA samples. We do not recommend it for use in all experiments. For further instructions, consult the Reference Selection DNA SD082 product description provided.
More information regarding the selection and use of reference samples can be found in the MLPA General Protocol.