Intended purpose
The SALSA MLPA Probemix P138 SLC2A1-STXBP1 is an in vitro diagnostic (IVD)¹ or research use only (RUO) semi-quantitative assay² for (1) the detection of deletions or duplications in the SLC2A1 gene in order to confirm a potential cause for and clinical diagnosis of Glucose transporter type 1 deficiency syndrome (GLUT1 DS), and (2) the detection of deletions or duplications in the human STXBP1 gene in order to confirm a potential cause for and clinical diagnosis of STXBP1 Encephalopathy with epilepsy (STXBP1-E) including Ohtahara syndrome (OS). This assay is for use with genomic DNA isolated from human peripheral whole blood specimens.

Copy number variations (CNVs) detected with P138 SLC2A1-STXBP1 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 SLC2A1 and STXBP1 genes 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
Glucose transporter type 1 deficiency syndrome (GLUT1 DS; OMIM #606777) is a neurologic disorder with broad phenotypic variability. GLUT1 DS is usually inherited in an autosomal dominant manner, and in very rare cases, it can occur as an autosomal recessive disease. About 10% of the autosomal dominant cases have a clinically affected parent, the remaining 90% results from a de novo heterozygous pathogenic variant. The de novo sporadic mutations may also be the result of germline mosaicism in apparently unaffected parents (Takahashi et al. 2017).

The GLUT1 DS phenotype has been reported as classic (~90%) and non-classic (~10%). The classic phenotype is characterised by infantile-onset seizures (usually between 1-6 months), delayed neurologic development, dysarthria, acquired microcephaly, and movement disorders (ataxia, dystonia, chorea). The non-classic phenotype is milder and is characterised by absence of clinical seizures and frequent paroxysmal dyskinesias (intermittent ataxia, choreoathetosis, dystonia, alternating hemiplegia). More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1430/.

STXBP1 Encephalopathy with epilepsy (STXBP1-E), also known as STXBP1 Encephalopathy or Early infantile epileptic encephalopathy-4 (EIEE4; OMIM #612164), belongs to the genetically heterogeneous group of early infantile epileptic encephalopathy (EIEE) disorders. STXBP1-E is inherited in an autosomal dominant pattern, with most of the cases being the result of a de novo mutation in the STXBP1 gene and with no history of the disorder in their family. However, these de novo sporadic mutations may also be the result of germline mosaicism in apparently unaffected parents (Saitsu et al. 2011).

STXBP1-E is characterised by recurrent seizures with early-onset (from day 1 to 13 years of age in 94% of the cases), global development delay (90% of the cases), abnormal brain function and intellectual disability. Electroencephalography (EEG) abnormalities such as burst suppression pattern and hypsarrhythmia were reported in affected individuals. The most common type of seizures is infantile spasms that consist of involuntary muscles spasms. Several epileptic syndromes have been linked to the STXBP1 gene, such as Ohtahara syndrome (OS; the most common syndrome, with STXBP1 defects being reported in ~20% of OS patients), West syndrome (WS), Lennox-Gastaut syndrome (LGS), Dravet syndrome (not SCN1A-related), classic Rett syndrome (not MECP2-related) and atypical Rett syndrome (not CDKL5-related). OS can develop into WS, this transition is accompanied by changes in the EEG, from suppression burst (OS) to hypsarrhythmia (WS). When progression continues to LGS, a generalized slow spike-wave pattern develops. More information is available at https://www.ncbi.nlm.nih.gov/books/NBK396561/.

Probemix content
The SALSA MLPA Probemix P138-D1 SLC2A1-STXBP1 contains 43 MLPA probes with amplification products between 130 and 472 nucleotides (nt). This includes 12 probes for the SLC2A1 gene and 22 probes for the STXBP1 gene covering each exon of these genes. In addition, nine 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.