: The SALSA MLPA probemix P378 MUTYH is an in vitro diagnostic (IVD)1
or a research use only (RUO) assay for the detection of deletions or duplications in the human MUTYH and GREM1 genes and in specific regions of the human SCG5 gene. It further contains two probes that can detect the presence of the p.Y179C and p.G396D point mutations in the MUTYH gene. The product is intended for confirming a potential cause and clinical diagnosis for MUTYH-Associated Polyposis (MAP) and Hereditary Mixed Polyposis Syndrome (HMPS1). This product can be used for molecular genetic testing of at-risk family members/individuals.
This assay is for use with human DNA extracted from peripheral blood. Deletions or duplications detected with the P378 MUTYH probemix must be verified by another technique. In particular, deletions or duplications detected by only a single probe always require validation by another method. Most defects in the MUTYH gene are point mutations, which will not all be detected by MLPA. It is therefore recommended to use this SALSA MLPA probemix in combination with sequence analysis of the MUTYH gene. This assay is not intended to be used as a standalone assay for clinical decisions. The results of this test must be interpreted by a clinical molecular geneticist or equivalent.
This probemix can be used on tumour material to detect deletions and duplications in a research setting.
Please 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).
: The MUTYH (mutY homolog, E. coli) gene encodes a DNA glycosylase involved in oxidative DNA damage repair. Mutations in this gene result in heritable predisposition to colon cancer, more specifically MUTYH associated polyposis (MAP). MAP is an autosomal recessive trait. A single defective copy of the MUTYH gene may result in no, or only a small increase in risk for colorectal cancer. In case of bi-allelic MUTYH defects, the risk for colorectal cancer is 43% to almost 100% in the absence of timely surveillance, according to the NCBI GeneReview for MAP: http://www.ncbi.nlm.nih.gov/books/NBK107219/
The two most common MUTYH mutations associated with hereditary colorectal cancer are p.Y179C (c.536A>G) in exon 7 and p.G396D (c.1187G>A) in exon 13. These two mutations cover approximately 80% of germline alterations found in patients of European origin. In Eastern Asian populations these hotspot mutations are not prevalent. Patients with homozygous p.G396D or heterozygous p.G396D/p.Y179C mutations show a milder phenotype and later age of onset when compared to homozygous carriers of the p.Y179C mutation (NCBI GeneReview for MAP). A third common mutation is the p.E410Gfs*43 (c.1227_1228dupGG) mutation (Guarinos et al. 2014, Morak et al. 2014). Bi-allelic MUTYH-related colorectal cancer presents without polyps in one-third of the cases.
More information is available in the Clinical Utility Gene Card for MUTYH (http://www.nature.com/ejhg/journal/v21/n1/full/ejhg2012163a.html
A duplication of 40 kb upstream of the GREM1 gene and of the 3’ end of SCG5 is linked to an increased risk of developing colorectal cancer. This syndrome is known as hereditary mixed polyposis syndrome (HMPS1). This duplication leads to increased allele-specific GREM1 expression in the epithelium of the large bowel. Increased GREM1 expression is predicted to cause reduced bone morphogenetic protein (BMP) pathway activity, a mechanism that also underlies tumorigenesis in juvenile polyposis of the large bowel (Jaeger at al. 2012). Another duplication of ~16 kb in this region has been described more recently in members of a family presenting with atypical FAP (Rohlin et al. 2016). Seven probes are included in the P378 probemix to detect the 40 kb duplication (see Table 1 and Table 2b for more information). Copy number alterations detected by only a single probe specific for the SCG5 gene, are unlikely to have a relation to the condition tested for.
More information on HMPS1 is available at http://omim.org/entry/601228
: The P378-D1 MUTYH probemix contains 47 MLPA probes with amplification products between 116 and 471 nt. It contains probes for the MUTYH, SCG5 and GREM1 genes. For the MUTYH gene, the probemix contains 18 copy number probes and two mutation-specific probes, for the SCG5 and GREM1 genes both six copy number probes are included. In addition, the probemix contains 15 reference probes. The identity of the genes detected by the reference probes is available online (www.mlpa.com
) and in Table 2c of the product description.
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 (see the table in the product description). 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
SALSA Binning DNA SD022
: The SD022 Binning DNA provided with this probemix can be used as Binning DNA sample for binning of two mutation-specific probes (MUTYH probe 18416-SP0654-L23441 for the p.Y179C mutation and MUTYH probe 18417-SP0655-L23442 for the p.G396D mutation). SD022 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 SD022 Binning DNA 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), as for this purpose true mutation positive patient samples or cell lines should be used. It is strongly advised to use DNA sample and reference DNA samples extracted with the same method and derived from the same source of tissue. For further details, please consult the SD022 Binning DNA product description provided. This product is for research use only (RUO), except when used in combination with a probemix for in vitro diagnostic (IVD) purpose, as specified at the end of the product description.
Sample DNA developed for this product: