Intended purpose
The SALSA MLPA Probemix P190 CHEK2 is an in vitro diagnostic (IVD)
1 or research use only (RUO) semi-quantitative assay
2 for the detection of deletions or duplications in the human
CHEK2,
ATM and
TP53 genes, and for the detection of the
CHEK2 c.1100delC variant in genomic DNA isolated from human peripheral whole blood specimens. P190 CHEK2 is intended to confirm a potential cause for breast cancer in patients who are negative for
BRCA1,
BRCA2 and
PALB2 mutations, and for other
CHEK2-related cancer types, including colorectal cancer. This product can also be used to determine increased cancer susceptibility in at-risk family members.
Copy number variations (CNVs) detected with P190 CHEK2 should be confirmed with a different technique. In particular, CNVs detected by only a single probe always require confirmation by another method. Most defects in the
CHEK2,
ATM and
TP53 genes are point mutations, of which only the
CHEK2 c.1100delC mutation will be detected by MLPA. It is therefore recommended to use this assay in combination with sequence analysis.
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.
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, Coffalyser.Net analysis software, and SALSA Binning DNA SD078.
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 c.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.
CHEK2 exons 11-15 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 (see Table 1 in the Product Description). 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
The SALSA MLPA Probemix P190-D1 CHEK2 contains 53 MLPA probes with amplification products between 124 and 500 nucleotides (nt). This includes 19 probes for the
CHEK2 gene and one probe for the
HSCB gene, just upstream of
CHEK2. This probemix also contains one probe specific for the
CHEK2 c.1100delC mutation, which will only generate a signal when the mutation is present. Moreover, 19 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. In addition, ten reference probes are included that detect autosomal chromosomal locations. Complete probe sequences and the identity of the genes detected by the reference probes are available 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 at
www.mrcholland.com.
Sample DNA
Sample DNA developed for this product: