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SALSA MLPA Probemix P190 CHEK2

Susceptibility to breast cancer; Susceptibility to other cancer types

Region: CHEK2 22q12.1; ATM 11q22.3; TP53 17p13.1

MLPA | CE IL
Intended use: The SALSA MLPA probemix P190 CHEK2 is an in vitro diagnostic (IVD)1 or a research use only (RUO) assay for the detection of deletions or duplications in the human CHEK2, ATM and TP53 genes, and the detection of the CHEK2 1100delC variant, in order to determine increased susceptibility to breast cancer. An increased susceptibility to other cancer types, including but not limited to colon cancer, can also be determined with this probemix. This product can also be used for molecular genetic testing of at-risk family members.

Please note that this probemix covers all exons of CHEK2 but not of ATM and TP53. For the latter two genes, the P041/P042 ATM and P056 TP53 probemixes provide a better coverage and may detect aberrations that are not detected by this P190 CHEK2 probemix.

This assay is for use with human DNA extracted from peripheral blood and not for use with DNA extracted from formalin-fixed paraffin embedded or fresh tumour materials. Deletions or duplications detected with the P190 CHEK2 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 aforementioned genes are point mutations, the majority of which are not detected by MLPA. It is therefore recommended to use this SALSA MLPA probemix in combination with sequence analysis of these genes. This probemix is not intended to be used as a standalone assay for clinical decisions. 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: CHEK2, ATM and TP53 all play important roles in DNA damage repair. A defect in one of these genes can lead to an increased risk of tumour formation. For breast cancer, autosomal dominant mutations in the genes BRCA1 and BRCA2 are the most frequent cause, followed by mutations in CHEK2, ATM and PALB2, though with a much lower frequency (Buys et al. 2017). Mutations in CHEK2 may also increase the risk of developing colorectal cancer (Xiang et al. 2011) and other cancers, including prostate cancer (Cybulski et al. 2006). Mutations in CHEK2, and the 1100delC mutation in particular, have also been suggested as an underlying cause of Li-Fraumeni syndrome (LFS) type 2. Moreover, a deletion in CHEK2 was found in a patient fulfilling Li-Fraumeni-Like (LFL) criteria (Ruijs et al. 2009). Researchers are uncertain whether CHEK2 mutations actually cause LFS or are merely associated with an increased risk of several types of cancer, including cancers seen in LFS. For more information: https://omim.org/entry/609265.

Exons 11-15 of CHEK2 share a high sequence homology with several CHEK2 pseudogenes, which can result in a pseudogene-mediated gene conversion (Pan et al. 2017).

Autosomal dominant mutations in ATM are linked to an increased risk of cancer, with breast cancer in particular. Autosomal recessive mutations of ATM cause Ataxia-Telangiectasia, which is characterized by progressive cerebellar ataxia, telangiectases, and a predisposition to malignancy, particularly leukaemia and lymphoma. For more information: https://www.ncbi.nlm.nih.gov/books/NBK26468/.

Autosomal dominant TP53 mutations result in LFS. The most common types of tumours in LFS are soft tissue sarcomas and osteosarcomas, pre-menopausal breast cancer, brain tumours, leukaemia, and adrenocortical carcinoma. Families presenting incomplete features of LFS are referred to as having LFL, and around 20-40% of these patients have a germline mutation in TP53 (Ruijs et al. 2010). More information on LFS: https://www.ncbi.nlm.nih.gov/books/NBK1311/.

Probemix content: This SALSA MLPA probemix P190 CHEK2 contains 53 probes with amplification products between 124 and 500 nt (Table 2), including ten reference probes. At least one probe is present for each exon of CHEK2 and one probe is included just upstream of CHEK2. Moreover, there is one probe specific for the CHEK2 1100delC mutation, which will only generate a signal when this mutation is present. Nineteen probes for ATM and four probes for TP53 are also present. These probes target sequences in various parts of the genes, including in the first and last exon. The identity of the genes detected by the reference probes is available 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.

SALSA Binning DNA SD078: The SD078 Binning DNA provided with this probemix can be used as Binning DNA sample for binning of one mutation-specific probe (313 nt probe 22034-SP0468-L31261 CHEK2 1100delC mutation). SD078 Binning DNA is a mixture of genomic DNA from healthy individuals and synthetic DNA that contains the target sequence detected by the above mentioned probe. Inclusion of one reaction with 5 μl SD078 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/SNP 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 SD078 Binning DNA product description.

Sample DNA
Sample DNA developed for this product:

Order Items

Probemix

Item no.
Description
Technology
Price
P190-025R
SALSA MLPA Probemix P190 CHEK2 – 25 rxn
€ 243.00
P190-050R
SALSA MLPA Probemix P190 CHEK2 – 50 rxn
€ 486.00
P190-100R
SALSA MLPA Probemix P190 CHEK2 – 100 rxn
€ 972.00

Required Reagents

Item no.
Description
Technology
Price
EK1-FAM
SALSA MLPA EK1 reagent kit – 100 rxn – FAM
€ 300.00
EK1-Cy5
SALSA MLPA EK1 reagent kit – 100 rxn – Cy5
€ 300.00
EK5-FAM
SALSA MLPA EK5 reagent kit – 500 rxn – FAM
€ 1380.00
EK5-Cy5
SALSA MLPA EK5 reagent kit – 500 rxn – Cy5
€ 1380.00
EK20-FAM
SALSA MLPA EK20 reagent kit – 2000 rxn – FAM
€ 5295.00

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CE

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).

IL

IVD-registered in Israel.