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P105 Glioma

SALSA® MLPA® Probemix P105 Glioma detects copy number alterations in 9 genes commonly affected in gliomas, as well as chr. 7 gains and chr. 10 losses and the C228T and C250T TERT promoter mutations.

Specifications

Contents: 60 MLPA probes, including 43 probes for the PDGFRA, EGFR, CDKN2A, PTEN, CDK4, MIR26A2, MDM2, NFKBIA and TP53 genes, 2 flanking probes for the 7q and 10p arms, and 2 mutation-specific probes for TERT C228T and C250T.

Tissue: human genomic DNA, including DNA from FFPE tissue.

Application: research on gliomas.

For research use only (RUO). Not for use in diagnostics.

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Key related products

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P056 TP53

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General information

SALSA® MLPA® Probemix P105 Glioma is a research use only (RUO) assay for the detection of deletions or gains in the following genes PDGFRA (4q12), EGFR (7p11.2), CDKN2A (9p21.3), PTEN (10q23.31), CDK4-MIR26A2-MDM2 (12q14-q15), NFKBIA (14q13.2) and TP53 (17p13.1). Moreover, this probemix can be used to detect the chr. 7 gains and chr. 10 losses and to detect the presence of TERT promoter mutations C228T and C250T.

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 gliomas. 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 (Cancer Genome Atlas Research Network 2008). Please see Table 2 in the product description for more details.

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 EGFR variant III (EGFRvIII), a constitutively active genomic deletion variant of EGFR which is characterised by deletions of exons 2-7 of the EGFR gene (Sugawa et al. 1990). This probemix allows detection of deletions of EGFR that result in EGFRvIII. Please see Table 2 in the product description for more details.

Point mutations in TERT promoter region generate novel transcription factor binding sites and thus increase the expression of telomerase enzyme encoded by TERT. Common TERT promoter mutations are known as C228T and C250T, referring to C>T transitions at hg19/GCRh37 chr5:1295228 and chr5:1295250 positions, respectively. These mutations are predominantly present in oligodendroglioma and are associated with poor prognosis and reduced survival in the absence of IDH-mutation (Labussière et al. 2014). TERT promoter mutation, in combination with IDH-mutation and 1p/19q codeletion, is characteristic of oligodendroglioma. Absence of TERT promoter mutation, coupled with the presence of IDH-mutation, designates astrocytoma (Cahill et al. 2015; Eckel-Passow et al. 2015).

Regulatory status

SALSA MLPA Probemix P105 Glioma is for research use only (RUO) in all territories.

SALSA Sample DNA for this product

SALSA Binning DNA SD097 is an artificial DNA sample with a signal for all probes in the P105 Glioma probemix. Inclusion of a reaction with SD097 in initial experiments and in experiments following a change in electrophoresis conditions is recommended to aid in the creation of a bin set that links peaks to the probes that produce them. Binning DNA cannot be used as a reference sample in the MLPA data analysis, and cannot be used to quantify the signals of mutation-specific probes.

A vial of SALSA Binning DNA SD097 is included with every order of the P105 Glioma probemix, but it is possible to order additional vials separately.

For more information, see the product description.

Product documentation

Version E1

Version D3

Other versions

Contact us for earlier versions.

List prices

Product

Item no.
Description
Technology
Price
P105-025R
SALSA MLPA Probemix P105 Glioma – 25 rxn
MLPA
€ 286.00
P105-050R
SALSA MLPA Probemix P105 Glioma – 50 rxn
MLPA
€ 560.00
P105-100R
SALSA MLPA Probemix P105 Glioma – 100 rxn
MLPA
€ 1096.00

Required reagents

A general SALSA MLPA Reagent Kit is required for MLPA experiments (to be ordered separately).

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA Reagent Kit – 100 rxn – FAM (6 vials)
MLPA MS-MLPA
€ 348.00
EK1-Cy5
SALSA MLPA Reagent Kit – 100 rxn – Cy5 (6 vials)
MLPA MS-MLPA
€ 348.00
EK5-FAM
SALSA MLPA Reagent Kit – 500 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 1600.00
EK5-Cy5
SALSA MLPA Reagent Kit – 500 rxn – Cy5 (5×6 vials)
MLPA MS-MLPA
€ 1600.00
EK20-FAM
SALSA MLPA Reagent Kit – 2000 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 6152.00

Sample DNAs (included)

A vial is included with every order of this probemix, but additional vials can also be purchased separately.

Item no.
Description
Technology
Price
SD097
SALSA Binning DNA SD097 – 6 rxn
MLPA
€ 24.15

Price details & ordering

The prices above are list prices for direct orders from MRC Holland. Contact us for a quote that takes discounts and additional costs (such as shipping costs) into account. Different prices apply for orders through one of our sales partners; contact your local supplier for a quote.

More information about ordering & prices

Positive samples

Inclusion of a positive sample is usually not required, but can be useful for the analysis of your experiments. MRC Holland has very limited access to positive samples and cannot supply such samples. We recommend using positive samples from your own collection. Alternatively, you can use positive samples from an online biorepository, such as the Coriell Institute.

The commercially available positive samples below have been tested with the current (E1) version of this product and have been shown to produce useful results.

  • Coriell NA07081: Heterozygous duplication affecting the probes for EGFR.
  • Coriell NA02819, Coriell NA03226, Coriell NA05067, Coriell NA01750: Heterozygous duplication affecting the probes for CDKN2A.
  • Coriell NA20125: Heterozygous duplication affecting the probes for PTEN.
  • Coriell NA06801: Heterozygous duplication affecting the probes for NFKBIA.
  • DSMZ ACC-203 (SK-N-MC): Heterozygous deletion affecting the probes for PARD3, PTEN and TP53 (homozygous deletion affecting the TP53 exon 2a probe).†
  • DSMZ ACC-237 (IGR-37): Heterozygous deletion affecting the probes for PDGFRA, CDKN2A (homozygous deletion affecting the CDKN2A exon 3-4 probes), PARD3, PTEN, CDK4, MIR26A2, MDM2, NFKBIA and TP53.†
  • DSMZ ACC-277 (DK-MG): Gives a signal for the TERT promoter C250T mutation-specific probe. Amplification affecting the probes for EGFR exons 1 and 8-23 and MDM2. Gain affecting the probes for CDK6. Homozygous deletion affecting the probes for CDKN2A. Heterozygous deletion affecting the probes for PARD2, PTEN and NFKBIA.†
  • DSMZ ACC-360 (CGTH-W-1): Gives a signal for the TERT promoter C228T mutation-specific probe. Amplification affecting the probes for PDGFRA. Homozygous deletion affecting the probes for CDKN2A. Heterozygous deletion affecting the probes for PARD3. Potential subclonal gain^ affecting the probes for EGFR. Potential subclonal deletion# affecting the probes for CDK4, MIR26A2 and MDM2.†
  • DSMZ ACC-180 (HEP-G2): Gives a signal for the TERT promoter C228T mutation-specific probe. Amplification affecting the probes for NFKBIA.†

† Some of the reference probes are also affected by copy number alterations.
^ Ratios between 1.20 and 1.30 found for all probes for EGFR.
# Ratios between 0.65 and 0.80 found for all probes for CDK4, MIR26A2 and MDM2.

Resources

General MLPA resources

MLPA education

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