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ME042 CIMP

SALSA MS-MLPA Probemix ME042 CIMP detects copy number variations and methylation status of the promoter regions of the CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 genes.

Specifications

Contents: 49 MLPA probes, including 3 probes for CACNA1G, 4 probes for CDKN2A, 4 probes for CRABP1, 3 probes for IGF2, 4 probes for MLH1, 6 probes for NEUROG1, 3 probes for RUNX3, and 4 probes for SOCS1, which all provide information on the methylation status. In addition, a probe for BRAF p.V600E (c.1799T>A) is included.

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

Application: research on CpG island methylator phenotype (CIMP) tumours.

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

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Key related products

ME001 Tumour suppressor mix

Detects methylation status of promoter regions of various tumour suppressor genes.

ME011 Mismatch Repair Genes

Contains MS-MLPA probes for promoter regions of MLH1, MSH2, MSH6 and PMS2 genes.

ME024 9p21 CDKN2A/2B region

Contains copy number and MS-MLPA probes for CDKN2A/2B gene region, as well as copy number probes for MIR31, MTAP and PAX5 genes.

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This product is for basic research and intended for experienced users only! Interpretation of results may be complicated, and MRC Holland may only be able to provide basic support.

General information

The SALSA MS-MLPA Probemix ME042 CIMP is a research use only (RUO) assay for the detection of aberrant methylation of one or more sequences in the promoter regions of the CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 genes. This probemix can also be used to detect deletions/duplications in the promoter regions aforementioned genes, and the presence of the BRAF p.V600E (c.1799T>A) point mutation in a DNA sample.

CpG-islands are located in or near the promoter region or other regulatory regions of approximately 50% of human genes. Aberrant methylation of CpG-islands has been shown to be associated with transcriptional inactivation of genes in a wide spectrum of human cancers. The CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 genes are frequently silenced by methylation in CpG Island Methylator Phenotype (CIMP) tumours, but are unmethylated in blood-derived DNA, with the exception of constitutional epimutations. In addition, DNA methylation analysis can indicate in some cases from which type of tissue the tumour was derived.

CIMP tumours are characterized by the hypermethylation of promoters mainly in tumour suppressor genes and DNA repair genes, which leads to genetic silencing and a loss of protein expression. CIMP is a typical feature for a subset of colorectal cancers, where also BRAF mutations are commonly found (Weisenberger et al. 2006). CIMP status was also identified in glioblastoma, gastric cancer, endometrial and breast cancers (reviewed in Weisenberger (2014)).

Regulatory status

SALSA MLPA Probemix ME042 CIMP is for research use only (RUO) in all territories.

SALSA Sample DNA for this product

SALSA Binning DNA SD029 is an artificial DNA sample with a signal for all probes in the ME042 CIMP probemix. Inclusion of a reaction with SD029 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 SD029 is included with every order of the ME042 CIMP probemix, but it is possible to order additional vials separately.

For more information, see the product description.

Product documentation

Version C2

Other versions

Contact us for earlier versions.

List prices

Product

Item no.
Description
Technology
Price
ME042-025R
SALSA MLPA Probemix ME042 CIMP – 25 rxn
MS-MLPA
€ 296.00
ME042-050R
SALSA MLPA Probemix ME042 CIMP – 50 rxn
MS-MLPA
€ 580.00
ME042-100R
SALSA MLPA Probemix ME042 CIMP – 100 rxn
MS-MLPA
€ 1135.00

Required reagents

A general SALSA MLPA Reagent Kit and SALSA HhaI are required for MS-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
€ 361.00
EK1-CY5
SALSA MLPA Reagent Kit – 100 rxn – Cy5 (6 vials)
MLPA MS-MLPA
€ 361.00
EK5-FAM
SALSA MLPA Reagent Kit – 500 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 1658.00
EK5-CY5
SALSA MLPA Reagent Kit – 500 rxn – Cy5 (5×6 vials)
MLPA MS-MLPA
€ 1658.00
EK20-FAM
SALSA MLPA Reagent Kit – 2000 rxn – FAM (5×6 vials)
MLPA MS-MLPA
€ 6373.00
SMR50
SALSA HhaI – 115 μl
MS-MLPA
€ 48.00

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
SD029
SALSA Binning DNA SD029 – 6 rxn
MLPA MS-MLPA
€ 25.00

Other products

These optional accessories can be ordered separately.

Item no.
Description
Technology
Price
SMR05
SALSA FFPE Solution (SFS) – 50 rxn (10 ml)
MLPA MS-MLPA
€ 47.00

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 can be used with the current (C2) version of this product.

“Methylated” refers to cases where half or more probes for the specific gene promoter have ratios higher than baseline methylation, the rest is not methylated.

Germline samples

  • Coriell NA02819: Gain affecting the probes for CDKN2A on chromosome 9. IGF2 on chromosome 11 is methylated.
  • Coriell NA04127: Gain affecting the probes for MLH1 on chromosome 3.
  • Coriell NA05067: Gain affecting the probes for CDKN2A on chromosome 9.
  • Coriell NA06226: Gain affecting the probes for SOCS1 on chromosome 16.
  • Coriell NA08039: Gain affecting the probes for SOCS1 on chromosome 16. IGF2 on chromosome 11 is methylated.
  • Coriell NA13031: Heterozygous deletion affecting the probes for CACNA1G1 on chromosome 17. CRABP1 on chromosome 15 is methylated.

Cancer cell line samples

  • DSMZ ACC-22 (REH): Heterozygous deletion affecting the probes for MLH1 on chromosome 3, homozygous deletion affecting the probes for CDKN2A on chromosome 9, and gain affecting the probes for SOCS1 on chromosome 16. RUNX3 on chromosome 1, NEUROG1 on chromosome 5, IGF2 on chromosome 11 and CRABP1 on chromosome 15 are methylated.
  • DSMZ ACC-42 (697): RUNX3 on chromosome 1, NEUROG1 on chromosome 5, CDKN2A on chromosome 9, IGF2 on chromosome 11, CRABP1 on chromosome 15 and CACNA1G1 on chromosome 17 are methylated.
  • DSMZ ACC-255 (CADO-ES1): Homozygous deletion affecting the probes of CDKN2A on chromosome 9, and gain affecting the probes for CACNA1G1 on chromosome 17. NEUROG1 on chromosome 5, IGF2 on chromosome 11 and CRABP1 on chromosome 15 are methylated.
  • DSMZ ACC-427 (DU-4475): RUNX3 on chromosome 1, MLH1 on chromosome 3, NEUROG1 on chromosome 5, CDKN2A on chromosome 9, IGF2 on chromosome 11, CRABP1 on chromosome 15 and CACNA1G1 on chromosome 17 are methylated. Positive for the BRAF p.V600E mutation.
  • DSMZ ACC-573 (SU-DHL-8): RUNX3 on chromosome 1, NEUROG1 on chromosome 5, CDKN2A on chromosome 9, IGF2 on chromosome 11, CRABP1 on chromosome 15 and CACNA1G1 on chromosome 17 are methylated.
  • DSMZ ACC-581 (HCT-116): Gain affecting the probes for CACNA1G1 on chromosome 17. NEUROG1 on chromosome 5, CDKN2A on chromosome 9, IGF2 on chromosome 11, CRABP1 on chromosome 15 and CACNA1G1 on chromosome 17 are methylated.

Resources

General MLPA resources

MLPA education

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