General information
The SALSA MLPA Probemix P339 SHANK3 is a research use only (RUO) assay for the detection of deletions or duplications in the SHANK3 gene, which is associated with Phelan-McDermid syndrome and autism spectrum disorder (ASD).

SHANK3 is a synaptic scaffolding protein enriched in the postsynaptic density of excitatory synapses, and plays important roles in the formation, maturation, and maintenance of synapses. Haploinsufficiency of the SHANK3 gene causes a developmental disorder, 22q13.3 deletion syndrome (known as Phelan-McDermid syndrome), which is characterized by severe expressive language and speech delay, hypotonia, global developmental delay, and autistic behaviour. Since several SHANK3 mutations have been identified in a particular phenotypic group in patients with ASD, SHANK3 is strongly suspected of being involved in the pathogenesis and neuropathology of ASD.

Warning: All SHANK3 probes are located in an extremely GC-rich chromosomal area. Such CpG islands are more difficult to denature than the rest of the human genome. The presence of salt in DNA samples can result in incomplete denaturation of these CpG islands, which may result in false positive results: apparent deletions of several consecutive SHANK3 probes, while reference probes are normal. Such false positive results are even more likely when DNA has been extracted by the Qiagen EZ1, M48 or M96 systems, as these leave a higher salt concentration in the sample. High salt concentrations can also be due to evaporation (dried out samples; SpeedVac concentration). Most severely affected will be probes for exons 11-17; see figure 1 on page 4 of the Product Description. In particular, any deletions that include exons 11-13 should be treated with caution (be aware that the exon numbering has been adjusted in this Product description version B2-02).

More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1198/.

This SALSA MLPA probemix is not CE/FDA registered for use in diagnostic procedures. Purchase of this product includes a limited license for research purposes.

Probemix content
The SALSA MLPA Probemix P339-B2 SHANK3 contains 44 MLPA probes with amplification products between 133 and 481 nucleotides (nt). This includes 30 probes for the SHANK3 gene. Furthermore, four probes are added as flanking probes for the 22q13.33 region. 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.