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SALSA MLPA Probemix ME042 CIMP

CpG Island methylator phenotype (CIMP)

Region: Various

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 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 region of the 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 promoter regions of the CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 genes are unmethylated in blood-derived DNA of healthy individuals, but have been reported to be frequently methylated in CpG Island Methylator Phenotype (CIMP) tumours. The CIMP status of a tumour may be useful for prediction of treatment response and prognosis in colorectal cancer (Walther et al. 2009). In addition, recent studies have shown that a BRAF V600E activating mutation is tightly associated with CIMP positivity (Weisenberg et al. 2006).

Probemix content: The SALSA MLPA Probemix ME042-C1 CIMP contains 48 (MS-)MLPA probes with amplification products between 124 and 492 nt. In total, 31 MS-MLPA probes contain a HhaI recognition site and provide information on the methylation status of promoter regions of the CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 genes. All probes present will also give information on copy number changes of the promoter region in the analysed sample. In addition, 15 reference probes are included which are not affected by HhaI digestion and target relatively quiet regions in colorectal tumours. Also, one digestion control probe is included in this probemix indicating whether or not restriction endonuclease digestion in the MS-MLPA reaction was complete. Complete probe sequences and the identity of the genes detected by the reference probes is available online (www.mlpa.com) and in Table 2b of the Product Description.

This probemix contains nine quality control fragments generating amplification products between 64 and 121 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 SD029: The SD029 Binning DNA provided with this probemix can be used as Binning DNA sample for binning of one mutation-specific probe (BRAF probe 08780-SP0039-L08904 p.V600E (c.1799T>A)). SD029 Binning DNA is a mixture of genomic DNA from healthy individuals and plasmid DNA that contains the target sequence detected by the above mentioned probe. Inclusion of one reaction with 5 μl of SD029 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 signal, as for this purpose true mutation/SNP positive patient samples or cell lines should be used. It is strongly advised to use DNA sample and reference DNA samples extracted with the same method and derived from the same source of tissue. For further details, please consult the SD029 Binning DNA product description provided. This product is for research use only (RUO).

Sample DNA
Sample DNA developed for this product:

Order Items

Probemix

Item no.
Description
Technology
Price
ME042-025R
SALSA MLPA Probemix ME042 CIMP – 25 rxn
€ 243.00
ME042-050R
SALSA MLPA Probemix ME042 CIMP – 50 rxn
€ 486.00
ME042-100R
SALSA MLPA Probemix ME042 CIMP – 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
SMR50
SALSA HhaI – 200 rxn
€ 40.00

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Improved Nov 03, 2020

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Improvements

One HhaI digestion control probe replaced,four reference probes removed,one SNP-specific probe added