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SALSA MLPA Probemix P248 MLH1-MSH2 Confirmation

Lynch syndrome

Region: MLH1 3p22.2; MSH2 2p21

Intended purpose
The SALSA MLPA probemix P248 MLH1-MSH2 Confirmation is an in vitro diagnostic (IVD)1 or research use only (RUO) semi-quantitative assay2 for the detection of deletions or duplications in the MLH1 and MSH2 genes in genomic DNA isolated from human peripheral whole blood specimens. P248 MLH1-MSH2 Confirmation is intended to confirm a potential cause for and clinical diagnosis of Lynch syndrome, as initially determined using the SALSA MLPA probemix P003 MLH1/MSH2. P248 MLH1-MSH2 Confirmation cannot be used to verify deletions or duplications in EPCAM detected by P003 MLH1/MSH2.

Discordant results between the P248 MLH1-MSH2 Confirmation probemix and the P003 MLH1/MSH2 probemix should be confirmed with a different technique. Most defects in the MLH1 and MSH2 genes are point mutations, none of which will be detected by MLPA.

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, pre-implantation or prenatal testing, population screening, or 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.

1 Please 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).
2 To be used in combination with a SALSA MLPA Reagent Kit and Coffalyser.Net analysis software.

Clinical background
Lynch syndrome, formerly known as hereditary non-polyposis colorectal cancer (HNPCC), is an adult-onset hereditary cancer susceptibility syndrome predisposing to several cancer types, the most prevalent being colorectal cancer, endometrial cancer, ovarian cancer, gastric cancer and small bowel cancer. It is an autosomal dominantly inherited syndrome that is caused by heterozygous germline mutations in one of the four major DNA mismatch repair genes: MLH1, MSH2, MSH6 or PMS2. Another cause of Lynch syndrome is a deletion of the 3’ part of EPCAM, leading to constitutional epigenetic silencing of the downstream MSH2 gene (Lynch et al. 2015). The estimated contribution of the different genes to Lynch syndrome is 15-40% for MLH1, 20-40% for MSH2, 12-35% for MSH6, 5-25% for PMS2 and <10% for EPCAM. More information about Lynch syndrome is available on

Among the various defects in the MLH1 and MSH2 genes that have been found in patients, deletions and duplications of complete exons are usually missed by standard sequence analysis. The MLPA technique can detect most of these deletions and duplications and therefore complements sequence analysis of the MLH1 and MSH2 genes.

Probemix content
The SALSA MLPA Probemix P248-B2 MLH1-MSH2 Confirmation contains 49 MLPA probes with amplification products between 130 and 493 nucleotides (nt). This includes 21 probes for the MLH1 gene, 17 probes for the MSH2 gene and one probe located downstream of the MSH2 gene. In addition, 10 reference probes are included that detect autosomal chromosomal locations. Almost all MLH1 and MSH2 probes included in probemix P003 MLH1/MSH2 have different ligation sites from those in P248, except for the 355 nt MSH2 exon 1 probe (02735-L20467). Complete probe sequences and the identity of the genes detected by the reference probes are available online (

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

Order Items


Item no.
SALSA MLPA Probemix P248 MLH1-MSH2 Confirmation – 25 rxn
€ 281.00
SALSA MLPA Probemix P248 MLH1-MSH2 Confirmation – 50 rxn
€ 550.00
SALSA MLPA Probemix P248 MLH1-MSH2 Confirmation – 100 rxn
€ 1075.00

Required Reagents (Sold Separately)

Item no.
SALSA MLPA Reagent Kit – 100 rxn – FAM
€ 341.00
SALSA MLPA Reagent Kit – 100 rxn – Cy5
€ 341.00
SALSA MLPA Reagent Kit – 500 rxn – FAM
€ 1571.00
SALSA MLPA Reagent Kit – 500 rxn – Cy5
€ 1571.00
SALSA MLPA Reagent Kit – 2000 rxn – FAM
€ 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.