Gliomas are the most common primary brain tumours and account for one third of central nervous system (CNS) tumours. Gliomas comprise a very heterogeneous group of CNS neoplasms derived from glial cells. There are several oncogenes and tumour suppressor genes, which have been shown to undergo copy number changes in these tumours. Somatic mutations, disruptions, or copy number aberrations in three critical signalling pathways, a) the RTK/PI3K pathway (involving e.g. EGFR, PDGFRA and PTEN genes), b) the p53 pathway (involving e.g. CDKN2A, MDM2 and TP53 genes) and c) the RB pathway (involving e.g. CDKN2A and CDK4 genes), are suggested to contribute to the development of gliomas (TCGA, 2008. Nature. 455:1061-8).
Epidermal growth factor receptor (EGFR) and its ligands are cell signalling molecules involved in diverse cellular functions. These include cell proliferation, differentiation, motility and survival, and tissue development. Glioblastomas often express EGFRvIII, a constitutively active genomic deletion variant of EGFR which is characterised by deletions of exons 2-7 of the EGFR gene (Humphrey PA et al. 1990. PNAS. 87:4207-11; Sugawa N et al. 1990. PNAS. 87:8602-6).
This P105-D2 Glioma-2 probemix can be used to determine aberrant copy numbers of the PDGFRA (4q12), EGFR (7p11.2), CDKN2A (9p21.3), PTEN (10q23.31), TP53 (17p13.1), CDK4-MIR26A2-MDM2 (12q14-q15) and NFKBIA (14q13.2) genes. This probemix also allows detection of deletions of EGFR that result in EGFRvIII. In addition, 12 reference probes have been included in this probemix, detecting several different autosomal chromosomal locations, which are relatively stable in copy number in gliomas.
This SALSA® MLPA® probemix is designed to detect deletions/duplications of one or more sequences in the aforementioned genes in a DNA sample. Heterozygous deletions of recognition sequences should give a 35-50% reduced relative peak height of the amplification product of that probe. Note that a mutation or polymorphism in the sequence detected by a probe can also cause a reduction in relative peak height, even when not located exactly on the ligation site! In addition, some probe signals are more sensitive to sample purity and small changes in experimental conditions. Therefore, deletions and duplications detected by MLPA should always be confirmed by other methods. Not all deletions and duplications detected by MLPA will be pathogenic; users should always verify the latest scientific literature when interpreting their findings. We have no information on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Finally, note that most defects in this gene are expected to be small (point) mutations which will not be detected by this SALSA® MLPA® test.