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SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region

Tumours, Cutaneous melanoma

Region: 9p21: CDKN2A, CDKN2B, and flanking genes

General information: The SALSA MS-MLPA Probemix ME024 9p21 CDKN2A/2B region is a research use only (RUO) assay for the detection of aberrant methylation of one or more sequences of the CDKN2A and CDKN2B genes on chromosome band 9p21. This probemix can also be used to detect deletions/duplications in the aforementioned chromosomal region including MIR31, MTAP, CDKN2A and CDKN2B genes, and PAX5 gene on 9p13.

Genomic losses of the 9p21.3 region, encompassing the CDKN2A/2B genes, are frequent events in many human cancers. This locus encodes three cyclin-dependent kinase inhibitors p14ARF, p16INK4A, and p15INK4B (see schematic presentation on page 2 of the product description). Genomic deletion of one or both copies of these important cell cycle regulator genes is the main inactivation mechanism. CDKN2A deletion can extend to the MTAP gene, located 110 kb away. The MTAP gene encodes methylthioadenosine phosphorylase, an important enzyme for the salvage of both adenine and methionine. It is known that many tumour cells require addition of methionine to their growth medium, because their MTAP gene is co-deleted with CDKN2A. Cells lacking MTAP are expected to be sensitive to purine synthesis inhibitors and/or methionine starvation, and therefore homozygous co-deletion of the CDKN2A and MTAP genes might open possibilities for alternative treatment for cancer patients. Other genes that are frequently co-deleted with CDKN2A/2B are CDKN2B-AS1, PAX5, and microRNA 31 (MIR31). Loss of MIR31 has been shown to have pro-tumorigenic effects on e.g. breast and ovarian cancer (Creighton et al. 2010). CDKN2B-AS1 (non-protein coding CDKN2B antisense RNA 1) is suggested to act as an epigenetic silencer of the CDKN2B gene (Yu et al. 2008). The PAX5 gene, at 9p13, which is essential for normal B-cell lymphopoiesis, is frequently co-deleted with CDKN2A in B-ALL (Kim et al. 2011).

An alternative mechanism of inactivation of the CDKN2A/2B genes is hypermethylation of the promoter regions leading to lack of expression of p14, p15, and p16 proteins, which further results in uncontrolled cell proliferation and tumour development and progression.

Alterations of the CDKN2A/2B genes are described not only in somatic tumour samples but also in the germline. Germline mutations in the CDKN2A gene have been linked to development of malignant cutaneous melanoma in some families with hereditary melanoma. Up to 40% of familial melanoma predisposition cases are associated with CDKN2A mutations (Hewitt et al. 2002). In addition to point mutations, various intragenic deletions within this gene have been identified in hereditary melanoma.

Probemix content: The SALSA MS-MLPA Probemix ME024-B2 9p21 CDKN2A/2B region contains 48 (MS-) MLPA probes with amplification products between 124 and 500 nucleotides (nt). 10 MS-MLPA probes contain an HhaI recognition site and provide information on the methylation status of CDKN2A and CDKN2B promoter regions. All probes present will also give information on copy number changes in the analysed sample. In addition, 12 reference probes are included that are not affected by HhaI digestion and target relatively copy number stable regions in various cancer types. Also, two digestion control probes are included in this probemix indicating whether or not restriction endonuclease digestion in the MS-MLPA reaction was complete. The identity of the genes detected by the reference probes are available in Table 2b of the product description and complete probe sequences are available online (www.mlpa.com).

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 MS-MLPA General Protocol and online at www.mlpa.com.

Order Items

Probemix

Item no.
Description
Technology
Price
ME024-025R
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 25 rxn
€ 243.00
ME024-050R
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 50 rxn
€ 486.00
ME024-100R
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 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 May 26, 2020

SALSA MLPA Probemix P088 Oligodendroglioma 1p-19q

Contains more probes for the CDKN2A and CDKN2B genes, the regions 1p and 19q, and mutation-specific probes for IDH1 and IDH2.

SALSA MLPA Probemix P419 CDKN2A/2B-CDK4

Contains more probes for the CDKN2A, CDKN2B, CDK4, and MTAP genes, and a mutation-specific probe for MITF involved in familial melanoma.

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Improvements

Three target and four reference probes have been replaced and one target probe is added.