SALSA MLPA P225 PTEN probemix

application: Cowden syndrome and tumour analysis
region: PTEN 10q23
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version: D2
sold since: 2015-06-10

item no. description price
P225-025R SALSA MLPA P225 PTEN probemix – 25 rxn € 237
P225-050R SALSA MLPA P225 PTEN probemix – 50 rxn € 474
P225-100R SALSA MLPA P225 PTEN probemix – 100 rxn € 948
EK1-FAM SALSA MLPA EK1 reagent kit – 100 rxn - FAM € 294
EK1-Cy5 SALSA MLPA EK1 reagent kit – 100 rxn - Cy5 € 294
EK5-FAM SALSA MLPA EK5 reagent kit – 500 rxn - FAM € 1355
EK5-Cy5 SALSA MLPA EK5 reagent kit – 500 rxn - Cy5 € 1355

Please note that both a probemix and reagent kit are needed to perform MLPA.

PTEN is a tumour suppressor gene that is mutated in a large number of cancers at high frequency. The protein encoded by PTEN is able to modify other proteins and lipids by removing phosphate groups. The main mechanism by which PTEN functions as a tumour suppressor is negative regulation of the AKT-PKB signalling pathway. Defects in the PTEN gene are the main cause of Cowden syndrome, which is a dominantly inherited cancer predisposition syndrome. Cowden syndrome is characterised by hamartomatous polyps of the gastrointestinal tract, mucocutaneous lesions, and by increased risk of developing neoplasms in the breast, thyroid, kidney, colon and skin.

Promoter hypermethylation represents an alternative mechanism of PTEN inactivation. Moreover, KLLN, a gene which shares a bidirectional promoter region with PTEN, has been shown to be epigenetically regulated in renal cell carcinoma (Bennett KL et al., 2011, Genes Chromosomes Cancer. 50:654-61) and in the germline of Cowden syndrome or Cowden-like syndrome patients (Nizialek EA et al., 2015, Eur J Hum Genet. 23:1538-43; Bennett KL et al., 2010, JAMA. 304:2724-31); the latter differential germline methylation region is not covered by the P225-D2 probemix. Also, a potential oncosuppressive role has been demonstrated for PTEN pseudogene PTENP1, which is affected by genomic deletions in various human malignancies (Poliseno L et al., 2010, Nature. 465:1033-8).

The PTEN gene comprises nine exons, spanning about 105 kb of genomic DNA and is located on chromosome 10q23.31, ~90 Mb from the p-telomere. This P225-D2 PTEN probemix contains at least two probes for each of these nine exons. The total number of PTEN probes included in this probemix is 21. In addition, it contains 14 probes located elsewhere on chromosome 10 that can help to distinguish focal PTEN deletions in tumour-derived DNA samples from loss of the complete 10q arm or a chromosome 10 aneuploidy. This probemix contains also two probes for copy number detection of the pseudogene PTENP1 (at 9p13.3). Moreover, five MS-MLPA probes are included in this probemix to determine the methylation status of the shared promoter region of the PTEN and KLLN genes that are unmethylated in most blood-derived DNA samples. Upon HhaI digestion, the peak signal obtained in unmethylated samples will be very low or absent for these five probes. In contrast, when tested on methylated human DNA in vitro, these probes do generate a signal. We have no data showing that methylation detected by a particular probe directly influences the corresponding mRNA levels. Finally, 14 reference probes are included in this probemix, detecting several different autosomal chromosomal locations, which are relatively stable in human cancers, and are not affected by HhaI digestion.

This SALSA® MLPA® probemix is designed to detect deletions/duplications of one or more sequences in the PTEN gene and other chromosome 10 sequences and the PTENP1 pseudogene in a DNA sample. Heterozygous deletions of recognition sequences should give a 35-50% reduced relative peak height of the amplification product of that probe. Note that a mutation or polymorphism in the sequence detected by a probe can also cause a reduction in relative peak height, even when not located exactly on the ligation site! In addition, some probe signals are more sensitive to sample purity and small changes in experimental conditions. Therefore, deletions and duplications detected by MLPA should always be confirmed by other methods. Not all deletions and duplications detected by MLPA will be pathogenic; users should always verify the latest scientific literature when interpreting their findings. We have no information on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Finally, note that most defects in this gene are expected to be small (point) mutations which will not be detected by this SALSA® MLPA® test.

This probemix can also be used to detect aberrant methylation of one or more sequences of the PTEN and/or KLLN genes. Methylation levels can be different for different tissues. If possible, use identically treated test and reference samples (same tissue type and extraction method).

related products
SALSA MLPA P158 Juvenile polyposis syndrome (JPS) probemix
Juvenile Polyposis: Contains probes for SMAD4, BMPR1A and PTEN.

product history
version D2: As compared to the previous lot (D1-0613), one probe has a small change in length but no change in the sequence detected.
version D1: One probe for PTEN exon 3 and one flanking probe for PTEN is added and four flanking probes replaced. Moreover, an HhaI digestion control probe is included and several reference probes replaced.
version C1: Several new target and reference probes. P225 may also be used now to detect methylation of PTEN and KLLN.
version B3: The 88 and 96 nt control fragments have been replaced (QDX2).
version B2: Major change. The number of PTEN probes has been increased to 25.
version A1: Extra control fragments at 88, 96, 100 and 105 nt have been added.

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