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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 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, p15INK4B and p16INK4A. Genomic deletion of one or both copies of these important cell cycle regulatory genes is the main inactivation mechanism in various cancers. CDKN2A deletion can extend to the MTAP gene, located 110 kb downstream. 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 p14ARF, p15INK4B and p16INK4A proteins, which further results in uncontrolled cell proliferation and tumour development and progression (Wolter et al. 2001).

Alterations of the CDKN2A/2B genes have been also described at the germline level. Germline mutations in the CDKN2A gene are frequently associated with predisposition to malignant cutaneous melanoma and pancreatic cancer (Chan et al. 2021). Up to 40% of familial melanomas are associated with CDKN2A mutations (Hewitt et al. 2002), including point mutations and various intragenic deletions.

This SALSA MLPA probemix is not CE/FDA registered for use in diagnostic procedures. Purchase of this product includes a limited license for research purposes.

Probemix content
The SALSA MLPA Probemix ME024-B3 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. Complete/partial probe sequences and the identity of the genes detected by the reference probes are available in Table 2 of the Product Description and online (

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

Order Items


Item no.
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 25 rxn
€ 281.00
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 50 rxn
€ 550.00
SALSA MLPA Probemix ME024 9p21 CDKN2A/2B region – 100 rxn
€ 1075.00

Required Reagents (Sold Separately)

Item no.
SALSA MLPA Reagent Kit – 100 rxn – FAM (6 vials)
€ 341.00
SALSA MLPA Reagent Kit – 100 rxn – Cy5 (6 vials)
€ 341.00
SALSA MLPA Reagent Kit – 500 rxn – FAM (5×6 vials)
€ 1571.00
SALSA MLPA Reagent Kit – 500 rxn – Cy5 (5×6 vials)
€ 1571.00
SALSA MLPA Reagent Kit – 2000 rxn – FAM (5×6 vials)
€ 6037.00
SALSA HhaI – 115 μl
€ 45.00

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