Intended purpose
The SALSA MLPA Probemix P137 SCN1A is an in vitro diagnostic (IVD)¹ or research use only (RUO) semi-quantitative assay² for the detection of deletions or duplications in SCN1A gene in genomic DNA isolated from human peripheral whole blood specimens. P137 SCN1A is intended to confirm a potential cause for and clinical diagnosis of Dravet syndrome (DS) and other SCN1A-related seizure disorders, and for Familial hemiplegic migraine 3 (FHM3).

Copy number variations (CNVs) detected with P137 SCN1A should be confirmed with a different technique. In particular, CNVs detected by only a single probe always require confirmation by another method. Most defects in the SCN1A gene are point mutations, none of which will be detected by MLPA. It is therefore recommended to use this assay in combination with sequence analysis.

Assay results are intended to be used in conjunction with other clinical and diagnostic findings, consistent with professional standards of practice, including confirmation by alternative methods, clinical genetic evaluation, and counselling, as appropriate. The results of this test should be interpreted by a clinical molecular geneticist or equivalent.

This device is not intended to be used for standalone diagnostic purposes, pre-implantation or prenatal testing, population screening, or for the detection of, or screening for, acquired or somatic genetic aberrations.

¹ Please note that this probemix is for In Vitro Diagnostic (IVD) use in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).
² To be used in combination with a SALSA MLPA Reagent Kit and Coffalyser.Net analysis software.

Clinical background
SCN1A-related seizure disorders include at the severe end of the spectrum DS and intractable childhood epilepsy with generalized tonic-clonic seizures (ICE-GTC), and at the mild end simple febrile seizures (FS) and generalized epilepsy with febrile seizures plus (GEFS+). Myoclonic-astatic epilepsy (MAE or Doose syndrome), Lennox-Gastaut syndrome (LGS), infantile spasms, and vaccine-related encephalopathy and seizures are the less commonly observed phenotypes.

SCN1A-related seizure disorders are inherited in an autosomal dominant manner. Pathogenic variants may be inherited or de novo. The percentage of cases with de novo mutations increases as the severity of the phenotype increases. The SCN1A-related seizures phenotype varies even among family members with the same pathogenic variant.

DS (OMIM # 607208, also known as severe myoclonic epilepsy in infancy (SMEI), early infantile epileptic encephalopathy 6 (EIEE6), and polymorphic myoclonic epilepsy in infancy (PMEI)) is a rare lifelong form of epilepsy that begins in the first year of life. DS is associated with heterozygous mutations in the SCN1A gene. The frequency of SCN1A mutations in DS patients is approximately 70-80%, most of the mutations being de novo (Marini et al. 2009). Apparent de novo sporadic mutations may also be the result of germline mosaicism in apparently unaffected parents (de Lange et al. 2018). Somatic mosaic deletions of the SCN1A gene have also been identified in individuals with DS (Nakayama et al. 2018). DS is defined by prolonged and frequent seizures that do not remit, and normally evolve to include myoclonic seizures. Other symptoms of DS are behavioural and developmental delay, movement and balance problems, hyperactivity and sleep difficulties.

ICE-GTC is characterized by generalized seizures including absence seizures and generalized tonic-clonic seizures with onset in infancy or childhood. Children with frequent generalized tonic-clonic seizures often develop cognitive impairment. FS are characterized by childhood seizures that occur only in association with fever (higher than 38°C). The age of onset is 6 months, and the seizures resolve by the age of 5 years old. Generalized epilepsy with febrile seizures plus (GEFS+) refers to findings in a family instead of an individual. The seizure phenotypes tend toward the mild end of the spectrum. Affected individuals within a family with GEFS+ often have FS in early childhood, followed by occasional tonic, clonic, myoclonic, or absence seizures which respond to medication and remit by late childhood or early adolescence.

More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1318/.

Familial hemiplegic migraine (FHM) is a rare autosomal dominant subtype of migraine with aura. FHM3 is caused by mutations in the SCN1A gene. More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1388/.

Probemix content
The SALSA MLPA Probemix P137-C1 SCN1A contains 40 MLPA probes with amplification products between 142 and 454 nucleotides (nt). This includes 30 probes for the SCN1A gene, covering all 26 coding exons of SCN1A, the first non-coding exon of NM_006920.6 (exon hB), and the upstream region of SCN1A (exon hA; exon 1 of the transcript variant 4 (NM_001202435.3)). In addition, ten reference probes are included that detect autosomal chromosomal locations. Complete probe sequences and the identity of the genes detected by the reference probes are available online (www.mrcholland.com).

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. More information on how to interpret observations on these control fragments can be found in the MLPA General Protocol and online at www.mrcholland.com.