Intended use: The SALSA MLPA probemix P225 PTEN is an in vitro diagnostic (IVD)¹ or a research use only (RUO) assay for the detection of deletions or duplications in the human PTEN gene in order to confirm a potential cause and clinical diagnosis for PTEN Hamartoma Tumour Syndrome (PHTS). This product can also be used to determine predisposition to PHTS. PHTS includes Cowden syndrome (CS), Bannayan-Riley-Ruvalcaba syndrome (BRRS), PTEN-related Proteus syndrome (PS), and Proteus-like syndrome (PLS). This probemix can be used for copy number detection of the PTEN pseudogene (PTENP1) in a research setting.

This assay is optimised for use with peripheral blood derived genomic DNA. This probemix can be used on tumour tissue to detect deletions and duplications of the PTEN and PTENP1 genes in a research setting. Copy number changes detected by only a single probe always require validation by another method. The results of this test should be interpreted by a clinical molecular geneticist or equivalent.

¹Please note that this probemix is for In Vitro Diagnostic use (IVD) in the countries specified at the end of this product description. In all other countries, the product is for Research Use Only (RUO).

Clinical background: Phosphatase and tensin homolog (PTEN) is a tumour suppressor gene that is mutated in a large number of cancers at high frequency. Defects in the PTEN gene are the main cause of PTEN Hamartoma Tumour Syndrome (PHTS), which is a dominantly inherited cancer predisposition syndrome. PHTS is a spectrum of disorders characterized by multiple hamartomas in several areas of the body. PHTS includes Cowden syndrome (CS), Bannayan-Riley-Ruvalcaba syndrome (BRRS), PTEN-related Proteus syndrome (PS), and Proteus-like syndrome.

Cowden syndrome (CS; OMIM #158350) is inherited in an autosomal dominant manner and comprises 85% of PHTS cases. CS is characterised by hamartomatous polyps of the gastrointestinal tract, mucocutaneous lesions, and by an increased risk of developing breast cancer (with a lifetime risk of 85%), thyroid cancer (with a lifetime risk of 35%), endometrial cancer (with a lifetime risk of approximately 28%), kidney, colon and other cancers. Affected individuals usually present with macrocephaly, trichilemmomas, and papillomatous papules by their late 20s.

Bannayan-Riley-Ruvalcaba syndrome (BRSS) is inherited in an autosomal dominant manner. It is present at birth and is characterized by macrocephaly, intestinal hamartomatous polyposis, lipomas, pigmented macules of the glans penis, intellectual disability (50% of the cases) and development delay. The risk of developing cancer in BRRS patients with a PTEN pathogenic variant is similar to patients with CS.

PTEN-related Proteus syndrome (PS) is a highly variable, severe disorder characterized by progressive segmental or patchy overgrowth of diverse tissues of all germ layers, affecting the skeleton, skin, adipose tissue and central nervous systems. PS is associated with tumours, pulmonary complications, and deep vein thrombosis. Proteus-like syndrome describes individuals that do not meet the diagnostic criteria of Proteus syndrome, but share many of the characteristic signs and symptoms associated with this condition.

More information is available at https://www.ncbi.nlm.nih.gov/books/NBK1488/.

PTENP1 is biologically active as it can regulate cellular levels of PTEN (via binding to mRNAs that target PTEN) and suppress cell growth. It has been shown that PTENP1 is selectively lost in sporadic colon cancer (Poliseno et al. 2010). Specific PTENP1 deletion (not PTEN) was also demonstrated in human melanoma (Poliseno et al. 2011). Furthermore, the importance of PTENP1 as a tumour suppressor has been recently shown in head and neck squamous cell carcinoma (Liu et al. 2017). The PTENP1 copy number detection is of a great importance in cancer research, however the clinical validity of this gene is not yet fully established.

Probemix content: The P225-E1 PTEN probemix contains 49 MLPA probes with amplification products between 130 and 496 nt. It contains 22 probes for the PTEN gene, at least one probe per exon, ten flanking probes, and two probes for the pseudogene PTENP1. In addition, 15 reference probes are included in this probemix. The identity of the genes detected by the reference probes is available in Table 2c and 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 MLPA General Protocol and online at www.mlpa.com.