Gliomas, which include astrocytomas, oligodendrogliomas, mixed oligoastrocytomas and ependymomas, are the most common malignant CNS tumours with often a poor survival. This probemix can be used to detect genomic duplications leading to the KIAA1549-BRAF, SRGAP3-RAF1 and FGFR1-TACC1 fusion genes, to identify the BRAF V600E & four predominant IDH1 and IDH2 point mutations, and to detect copy number aberrations in the BRAF, CDKN2A/B, FGFR1, MYB and MYBL1 genes.
Activation of the MAPK pathway has been detected with high frequency in pilocytic astrocytomas, in particular via a 2 Mb tandem duplication leading to an oncogenic KIAA1549-BRAF fusion gene at 7q34 (Jones DTW et al. 2008, Cancer Res. 68:8673-7). Detection of this duplication is of help in differentiating these tumours from diffuse astrocytomas. Alternative MAPK pathway activation mechanisms include: 1) the formation of a similar SRGAP3-RAF1 fusion gene at 3p25, through a 3.6 Mb tandem duplication (Jones DTW et al. 2009, Oncogene 28:2119-23), 2) intragenic duplications of FGFR1 and FGFR1-TACC1 microamplifications (Zhang J et al. 2013, Nat Genet. 45:602-12; Jones DTW et al. 2013, Nat Genet. 45:927-32), and 3) certain BRAF mutations, in particular the V600E mutation (Schiffman JD et al. 2010, Cancer Res. 70:512-9; Dougherty MJ et al. 2010, Neuro Oncol. 12:621-30). The BRAF V600E activating mutation in combination with deletion of CDKN2A is suggested to define a clinical distinct subgroup of childhood glioma: the presence of these genetic alterations was found to be significantly enriched in cases of low grade glioma that are undergoing transformation to secondary high grade gliomas (Mistry M et al. 2015, J Clin Oncol. 33:1015-22).
The IDH1/2 mutations represent frequent genetic abnormalities in gliomas. Their identification facilitates distinguishing the different glioma entities leading to a more accurate prognosis and treatment (Riemenschneider MJ et al. 2010, Acta Neuropathol. 120:567-84). IDH1 and IDH2 point mutations have been detected with high frequency in diffuse gliomas (Hartmann C et al. 2009, Acta Neuropathol. 118:469-74; Yan H et al. 2009, N Engl J Med. 360:765-73), and the presence of these mutations is associated with a longer survival (Sanson M et al. 2009, J Clin Oncol. 27:4150-4; van den Bent MJ et al. 2010, Clin Cancer Res. 16:1597-604). This MLPA probemix contains probes that are specific for the two most frequent IDH1 (p.R132H and p.R132C) and the two most frequent IDH2 (p.R172M and p.R172K) mutations.
This probemix also includes probes for the FGFR1, MYB and MYBL1 genes and for the 9p21.3 region (CDKN2A/2B, MIR31). All these genes and regions are suggested to help in differentiating molecular subtypes of gliomas (see Table 2 for more detailed information). Furthermore, this probemix contains 12 reference probes detecting autosomal chromosomal locations that are regarded as relatively stable in gliomas and brain tumours. However, it should be noticed that glioma karyotypes can harbour multiple numerical and structural aberrations, which can complicate interpretation of these reference probes.
SALSA Binning DNA SD043
Please note that the mutation-specific probes have only been tested on artificial sample DNA and not on positive human DNA samples with the BRAF (p.V600E=c.1799T>A), IDH1 (p.R132H=c.395G>A and p.R132C=c.394C>T) or IDH2 (p.R172M=c.515G>T and p.R172K=c.515G>A) point mutations! The SD043 Binning DNA is provided with each probemix vial and can be used in data binning in the fragment analysis and as an artificial positive control for the mutation-specific probes.
This SALSA® MLPA® probemix is designed to detect copy number changes of one or more sequences in the above mentioned genes and chromosomal regions and to detect the presence of the aforementioned point mutations 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 majority of defects in these genes are expected to be small (point) mutations which will not be detected by this SALSA® MLPA® test.
sample DNA
Sample DNA developed for this product: