Intended purpose
The SALSA MLPA Probemix P056 TP53 is an in vitro diagnostic (IVD)¹ or research use only (RUO) semi-quantitative assay² for the detection of deletions or duplications in TP53 gene in genomic DNA isolated from human peripheral whole blood specimens. P056 TP53 is intended to confirm a potential cause for and clinical diagnosis of Li-Fraumeni syndrome (LFS1) or Li-Fraumeni-like syndrome (LFL) and for molecular genetic testing of at-risk family members. In addition, this assay can be used to detect deletions or duplications in the human CHEK2 gene exons 8, 10 and 13 and the 1100delC mutation, to determine a suggested cause for Li-Fraumeni syndrome (LFS2) in a research setting.

Copy number variations (CNVs) detected with P056 TP53 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 TP53 gene are point mutations, none of which will be detected by MLPA. 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, pre-implantation or prenatal testing, population screening, or for the detection of, or screening for, acquired or somatic genetic aberrations. In a research setting this assay can be used on tumour tissue-derived DNA.

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, SALSA Binning DNA SD067 and Coffalyser.Net analysis software.

Clinical background
Li-Fraumeni syndrome (LFS or LFS1) is a clinically and genetically heterogeneous inherited cancer syndrome. LFS is characterised by autosomal dominant inheritance and early onset of tumours, multiple tumours within an individual, and multiple affected family members. The most common types of tumours are adrenocortical carcinomas, breast cancer, central nervous system tumours, osteosarcomas, and soft-tissue sarcomas. Approximately 92% of LFS cases contain germline mutations in the tumour suppressor gene TP53. Families presenting incomplete features of LFS are referred to as having Li-Fraumeni-like syndrome (LFL), and 20-40% of these patients have a germline mutation in TP53 (Ruijs et al. 2010). Around 50% of the individuals carrying germline mutations in TP53 will develop cancer by the age of 30 years, with a lifetime cancer risk of ≥70% in men and almost ≥90% in women. Individuals with a germline TP53 pathogenic variant are managed by increased surveillance and are eligible for prophylactic surgery. Next to germline mutations, somatic pathogenic variants in TP53 are found in about 50% of all tumours, making it one of the most frequently altered genes in human cancers. For more information: https://www.ncbi.nlm.nih.gov/books/NBK1311/.

A second form of LFS (LFS2) has been suggested to be caused by mutations in the CHEK2 gene, in particular the CHEK2 1100delC variant. However, it is currently still under debate whether CHEK2 gene mutations actually cause LFS or are merely associated with an increased risk of several types of cancer, including those cancers often seen in LFS. Importantly, pathogenic CHEK2 variants still pose an increased risk of developing cancer, even if CHEK2 might not be associated with LFS. For more information: https://omim.org/entry/609265.

Probemix content
The SALSA MLPA Probemix P056-D1 TP53 contains 40 MLPA probes with amplification products between 129 and 490 nucleotides (nt). This includes 15 probes for the TP53 gene with at least one probe for each exon, and seven flanking probes to determine the extent of the deletion/duplication. Furthermore, there are four probes present for CHEK2 including a mutation-specific probe for the 1100delC mutation, which will only generate a signal when the mutation is present. In addition, 14 reference probes are included that detect autosomal chromosomal locations. 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 at www.mrcholland.com.

SALSA Binning DNA SD067
The SD067 Binning DNA provided with this probemix can be used for binning of all probes including the CHEK2 1100delC mutation-specific probe (208 nt probe 18318-L26751). SD067 Binning DNA is a mixture of genomic DNA from healthy individuals and plasmid DNA that contains the target sequence detected by the above mentioned probe. Inclusion of one reaction with 5 μl SD067 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. 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 SD067 Binning DNA product description, available online: www.mrcholland.com.

Sample DNA
Sample DNA developed for this product:

• SD067 Binning DNA - included with this probemix.