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
genes on chromosome band 9p21. This probemix can also be used to detect deletions/duplications in the aforementioned chromosomal region including MIR31
gene on 9p13.
Genomic losses of the 9p21.3 region, encompassing the CDKN2A
genes, are frequent events in many human cancers. This locus encodes three cyclin-dependent kinase inhibitors p14ARF
, 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
genes might open possibilities for alternative treatment for cancer patients. Other genes that are frequently co-deleted with CDKN2A/2B
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.
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
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