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SALSA MLPA Probemix P378 MUTYH

MUTYH-associated polyposis (MAP); Polyposis syndrome, hereditary mixed (HMPS1)

Region: MUTYH 1p34.1; SCG5 15q13.3; GREM1 15q13.3

MLPA | CE CO IL
Intended purpose
The SALSA MLPA Probemix P378 MUTYH is an in vitro diagnostic (IVD)1 or research use only (RUO) semi-quantitative assay2 for the detection of deletions or duplications in the MUTYH gene, as well as the presence of the two most common point mutations among people of European descent, c.536A>G (p.Tyr179Cys) and c.1187G>A (p.Gly396Asp), in order to confirm a potential cause and clinical diagnosis of MUTYH-Associated Polyposis (MAP). In addition, P378 MUTYH can be used to detect duplications in the SCG5/GREM1 region in order to confirm a potential cause and clinical diagnosis of Hereditary Mixed Polyposis Syndrome type 1 (HMPS1). This assay is also intended for molecular genetic testing of at-risk family members. P378 MUTYH is for use with genomic DNA isolated from human peripheral whole blood specimens.

Copy number variations (CNVs) detected with P378 MUTYH should be confirmed with a different technique. In particular, CNVs detected by only a single probe as well as the two MUTYH point mutations always require confirmation by another method. Most defects in the MUTYH gene are point mutations, which will not be detected by MLPA, with the exception of the two aforementioned MUTYH point mutations. It is therefore recommended to use this assay in combination with sequence analysis.

Assay results are intended to be used in conjunction with other clinical and diagnostic findings, consistent with professional standards of practice, including confirmation by alternative methods, clinical genetic evaluation, and counselling, as appropriate. The results of this test should be interpreted by a clinical molecular geneticist or equivalent.

This device is not intended to be used for standalone diagnostic purposes, population screening, pre-implantation or prenatal testing. Only in a research setting can this device be used for the detection of, or screening for, acquired or somatic genetic aberrations, e.g. from DNA extracted from formalin-fixed paraffin embedded (FFPE) or fresh tumour materials.

1Please note that this probemix is for in vitro diagnostic (IVD) use in the countries specified at the end of this product description. In all other countries, the product is for research use only (RUO).
2To be used in combination with a SALSA MLPA Reagent Kit, Coffalyser.Net analysis software, and SALSA Binning DNA SD022.

Clinical background
Mutations in the MUTYH gene result in a hereditary predisposition to colon and gastric cancer, which is referred to as MAP. MAP is an autosomal recessive disorder. In MAP patients, ten to several hundred colonic adenomatous polyps develop, and these become evident at a mean age of 50 years. However, colon cancer can also develop in the absence of polyposis. A single defective copy of the MUTYH gene may result in no, or only a small increase in risk for colorectal cancer (CRC). There are two common MUTYH mutations, c.536A>G (p.Tyr179Cys) and c.1187G>A (p.Gly396Asp) that are carried by ~1%-2% of the general population and account for ≥90% of all MUTYH pathogenic variants in northern European populations. Up to 70% of MAP patients harbor at least one of these variants (Aretz et al. 2013). Copy number variations of MUTYH are very rare; they account for <1% of pathogenic alleles. The most frequent CNV in MUTYH - a deletion of exon 4-16 - is reported in multiple patients (Castillejo et al. 2014). More information on MAP is available at http://www.ncbi.nlm.nih.gov/books/NBK107219/.

A recurrent duplication of ~40 kb directly upstream of the GREM1 gene is known to lead to HMPS1. Patients with HMPS1 have a predisposition for developing CRC (Jaeger et al. 2012). Presence of this duplication is predicted to cause reduced bone morphogenetic protein (BMP) pathway activity, a mechanism that underlies tumorigenesis in juvenile polyposis of the large bowel. Several additional duplications in the GREM1 upstream region have been found: e.g. a duplication of the upstream region and the whole GREM1 gene of ~57 kb has been described in one patient with sigmoid colon carcinoma (Venkatachalam et al. 2011); a duplication of ~16 kb has been described in members of a family presenting with atypical FAP (Rohlin et al. 2016); and a duplication of ~24 kb in a patient with multiple colon polyps has been reported (McKenna et al. 2019). These different duplications can be detected by multiple probes in this P378-D1 probemix as is indicated in the table below. More information on HMPS1 is available at http://omim.org/entry/601228.

Probemix content
The SALSA MLPA Probemix P378-D1 MUTYH contains 47 MLPA probes with amplification products between 116 and 471 nucleotides (nt). This includes 18 copy number probes for the MUTYH gene and twelve for the SCG5-GREM1 region. Furthermore, two probes are included for the common c.536A>G (p.Tyr179Cys) and c.1187G>A (p.Gly396Asp) MUTYH mutations, which will only generate a signal when the mutation is present. In addition, 15 reference probes are included that detect relatively copy number stable regions in various cancer types associated with MAP and HMPS1. Complete probe sequences and the identity of the genes detected by the reference probes are available in Table 3 and online (www.mrcholland.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 (www.mrcholland.com).

SALSA Binning DNA SD022
The SALSA Binning DNA SD022 provided with this probemix can be used for binning of all probes, including the two MUTYH mutation-specific probes: the 184 nt probe 18416-SP0654-L23441, detecting the c.536A>G (p.Tyr179Cys) mutation, and the 258 nt probe 18417-SP0655-L23442, detecting the c.1187G>A (p.Gly396Asp) mutation. This Binning DNA is a mixture of genomic DNA from healthy individuals and synthetic DNA that contains the target sequences detected by the above mentioned probes. Inclusion of one reaction with 5 μl Binning DNA SD022 in initial MLPA experiments is essential as it can be used to aid in data binning of the peak pattern using Coffalyser.Net software. Furthermore, Binning DNA should be included in the experiment whenever changes have been applied to the set-up of the capillary electrophoresis device (e.g. when capillaries have been renewed). Binning DNA should never be used as a reference sample in the MLPA data analysis, neither should it be used in quantification of mutation signal(s). It is strongly advised that all samples tested are extracted with the same method and derived from the same source of tissue. For further details, please consult the SALSA Binning DNA SD022 product description, available online: www.mrcholland.com.


Sample DNA
Sample DNA developed for this product:

Order Items

Probemix

Item no.
Description
Technology
Price
P378-025R
SALSA MLPA Probemix P378 MUTYH – 25 rxn
€ 281.00
P378-050R
SALSA MLPA Probemix P378 MUTYH – 50 rxn
€ 550.00
P378-100R
SALSA MLPA Probemix P378 MUTYH – 100 rxn
€ 1075.00

Required Reagents (Sold Separately)

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA Reagent Kit – 100 rxn – FAM (6 vials)
€ 341.00
EK1-Cy5
SALSA MLPA Reagent Kit – 100 rxn – Cy5 (6 vials)
€ 341.00
EK5-FAM
SALSA MLPA Reagent Kit – 500 rxn – FAM (5×6 vials)
€ 1571.00
EK5-Cy5
SALSA MLPA Reagent Kit – 500 rxn – Cy5 (5×6 vials)
€ 1571.00
EK20-FAM
SALSA MLPA Reagent Kit – 2000 rxn – FAM (5×6 vials)
€ 6037.00

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CE-marked products are for In Vitro Diagnostic (IVD) use only in EU (candidate) member states and members of the European Free Trade Association (EFTA), and the UK.

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IVD-registered in Colombia.

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IVD-registered in Israel.