Intended purpose
The SALSA MLPA Probemixes P041 ATM-1 and P042 ATM-2 are in vitro diagnostic (IVD)¹ or research use only (RUO) semi-quantitative assays² for the detection of deletions or duplications in the ATM gene in genomic DNA isolated from human peripheral whole blood specimens. P041 ATM-1 and P042 ATM-2 are intended to confirm a potential cause for and clinical diagnosis of Ataxia-Telangiectasia or hereditary predisposition to develop cancer, including but not limited to breast cancer, and for molecular genetic testing of at-risk family members.
In order to cover all ATM exons, both P041 ATM-1 and P042 ATM-2 should be used. Copy number variations (CNVs) detected with P041 ATM-1/P042 ATM-2 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 ATM 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, 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.

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 and Coffalyser.Net analysis software.

Clinical background
Mutations in the ATM gene cause Ataxia-Telangiectasia (A-T, also known as Louis-Bar syndrome). A-T is an autosomal recessive disorder affecting the nervous system, immune system and several other organs. It is characterised by progressive cerebellar ataxia, telangiectases, and a predisposition to malignancy, particularly leukaemia and lymphoma. A-T patients often have a weakened immune system and develop chronic lung infections. It occurs in 1 in 40,000 to 100,000 people worldwide.
The ATM protein is a member of the phosphatidylinositol-3 kinase family of proteins that respond to DNA damage by phosphorylating key substrates involved in DNA repair and/or cell cycle control. This could explain the increased risk in ATM heterozygotes of developing malignancies, in particular breast cancer. Around 1% of breast cancer patients harbour mutations in ATM (Buys et al. 2017, Lerner-Ellis et al. 2015). The relative risk for developing breast cancer is estimated to be two to four fold compared to the general population (Tavtigian et al. 2009, Thompson et al. 2005). Germline heterozygous pathogenic ATM variants have also been reported in several types of leukaemia and lymphoma and hereditary pancreatic cancer (Bullrich et al. 1999, Oguchi et al. 2003, Roberts et al. 2012).

Probemix content
The SALSA MLPA Probemixes P041-B1 ATM-1 and P042-B2 ATM-2 each contain 34 probes for the ATM gene. When used together, a probe for each ATM exon is present. Probemix P041-B1 ATM-1 contains 45 MLPA probes with amplification products between 130 and 485 nucleotides (nt). Probemix P042-B2 ATM-2 contains 45 MLPA probes with amplification products between 131 and 485 nucleotides (nt). In each probemix, 11 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).
Both probemixes contain 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.