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SALSA MLPA Probemix P370 BRAF-IDH1-IDH2

Gliomas

Region: BRAF 7q34; IDH1 2q33.3; IDH2 15q26.1; FGFR1 8p12; MYB 6q23.3; MYBL1 8q13.1; CDKN2A 9p21.3

MLPA | Improved
General information: The SALSA MLPA Probemix P370 BRAF-IDH1-IDH2 is a research use only (RUO) assay for detection of the BRAF p.V600E & four predominant IDH1 (p.R132H and p.R132C) and IDH2 (p.R172M and p.R172K) point mutations, for detection of genomic duplications leading to the SRGAP3-RAF1, KIAA1549-BRAF and FGFR1-TACC1 fusion genes on chromosome arms 3p, 7q and 8p respectively, and for detection of copy number aberrations in the BRAF, CDKN2A/2B, FGFR1, MYB and MYBL1 genes.

The IDH1 and IDH2 mutations represent frequent genetic abnormalities in gliomas. Their identification facilitates distinguishing the different glioma entities leading to a more accurate prognosis and treatment (Riemenschneider et al. 2010). IDH1 and IDH2 point mutations have been detected with high frequency in diffuse gliomas (Hartmann et al. 2009; Yan et al. 2009), and the presence of these mutations is associated with a longer survival (Sanson et al. 2009; van den Bent et al. 2010). IDH1/2 mutation is a marker for glioma classification since 2016, defining glioblastomas as IDH-mutant or IDH-wildtype (Wesseling and Capper 2018). 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.

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 et al. 2008). 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 et al. 2009), 2) intragenic duplications of FGFR1 and FGFR1-TACC1 microamplifications (Zhang et al. 2013; Jones et al. 2013), and 3) certain BRAF mutations, in particular the p.V600E mutation (Schiffman et al. 2010; Dougherty et al. 2010). The BRAF p.V600E activating mutation in combination with deletion of CDKN2A was found to be significantly enriched in cases of low grade glioma that are undergoing transformation to secondary high grade gliomas (Mistry et al. 2015), suggesting to define a clinical distinct subgroup of childhood glioma.

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 2a for more detailed information). Furthermore, this probemix contains 13 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.

Probemix content: The SALSA MLPA Probemix P370-C1 BRAF-IDH1-IDH2 contains 59 MLPA probes with amplification products between 124 and 500 nucleotides (nt). This includes 41 probes for the detection of genomic duplications leading to the KIAA1549-BRAF, SRGAP3-RAF1 and FGFR1-TACC1 fusion genes, and for detection of copy number aberrations in the BRAF, CDKN2A/2B, FGFR1, MYB and MYBL1 genes. Furthermore, this probemix also contains five probes specific for the detection of the BRAF p.V600E & four predominant IDH1 p.R132H and p.R132C and IDH2 p.R172M and p.R172K point mutations, which will only generate a signal when the mutation is present. In addition, 13 reference probes are included that target relatively copy number stable regions in various cancer types including brain tumours. Complete probe sequences are available online (www.mlpa.com) and the identity of the genes detected by the reference probes is available in Table 2b.

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.mlpa.com.

SALSA Binning DNA SD054: The SD054 Binning DNA provided with this probemix can be used for binning of five mutation-specific probes (BRAF p.V600E probe M08780-SP0039-L08904 at 226 nt, IDH1 p.R132H probe M19529-L16492 at 203 nt, IDH1 p.R132C probe M14787-L16493 at 220 nt, IDH2 p.R172M probe M20963-L29001 at 244 nt, and IDH2 p.R172K probe M20963-L29002 at 238 nt). SD054 Binning DNA is a mixture of genomic DNA from healthy individuals and synthetic DNA that contains the target sequence detected by the above mentioned probes. Inclusion of one reaction with 5 μl SD054 Binning DNA in initial MLPA experiments is essential as it can be used to aid in data binning of the peak pattern using Coffalyser.Net software. Furthermore, Binning DNA should be included in the experiment whenever changes have been applied to the set-up of the capillary electrophoresis device (e.g. when capillaries have been renewed). Binning DNA should never be used as a reference sample in the MLPA data analysis, neither should it be used in quantification of mutation signals. It is strongly advised that all samples tested are extracted with the same method and derived from the same source of tissue. For further details, please consult the SD054 Binning DNA product description. This product is for research use only (RUO).

Sample DNA
Sample DNA developed for this product:

Order Items

Probemix

Item no.
Description
Technology
Price
P370-025R
SALSA MLPA Probemix P370 BRAF-IDH1-IDH2 – 25 rxn
€ 243.00
P370-050R
SALSA MLPA Probemix P370 BRAF-IDH1-IDH2 – 50 rxn
€ 486.00
P370-100R
SALSA MLPA Probemix P370 BRAF-IDH1-IDH2 – 100 rxn
€ 972.00

Required Reagents

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA EK1 reagent kit – 100 rxn – FAM
€ 300.00
EK1-Cy5
SALSA MLPA EK1 reagent kit – 100 rxn – Cy5
€ 300.00
EK5-FAM
SALSA MLPA EK5 reagent kit – 500 rxn – FAM
€ 1380.00
EK5-Cy5
SALSA MLPA EK5 reagent kit – 500 rxn – Cy5
€ 1380.00
EK20-FAM
SALSA MLPA EK20 reagent kit – 2000 rxn – FAM
€ 5295.00

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