The SALSA MLPA Probemix P041 ATM-1 and SALSA MLPA Probemix P042 ATM-2 are in vitro diagnostic (IVD) or research use only (RUO) semi-quantitative manual assays 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 (in the context biallelic pathogenic variants in ATM) or ATM-related cancer susceptibility (in the context of a monoallelic variant in ATM), and for molecular genetic testing of at-risk family members. Since only CNVs can be detected with P041 ATM-1 and P042 ATM-2, using an additional method is needed to exclude the possibility of an undetected variant.

For the full intended purpose, see the product description.

Ataxia-telangiectasia (A-T) is a rare autosomal recessive neurodegenerative disorder characterized by progressive cerebellar ataxia, ocular apraxia, immunodeficiency, conjunctival and cutaneous telangiectasia, elevated serum α-fetoprotein concentration, radiosensitivity, cancer predisposition (particularly for leukemia and lymphoma) and a spectrum of immunological abnormalities (GeneReviews). It occurs in 1 in 40,000 to 300,000 individuals worldwide, with substantially higher estimates observed in some founder communities. It is estimated that up to 1% of individuals are asymptomatic carriers of a heterozygous ATM mutation. Although they show no clinical manifestations, they are affected by an 1.5–3-fold increase of cancer risk (Suspitsin et al. 2020).

The clinical spectrum of A-T ranges from classic A-T, a severe form of the disease, and variant A-T, with a milder associated phenotype. In classic A-T, progressive neurologic manifestations followed by immunodeficiency, pulmonary disease, and increased malignancy risk are typical. These grave symptoms, combined with infections, lead to decreased life expectancy. One key difference in variant A-T is that extrapyramidal movement disorders are observed without compromised immune function, infections, or pulmonary disease. However, particularly in premenopausal women, there is an increased risk of developing breast cancer and hematologic malignancies.

A-T is caused by biallelic inactivation of the ATM gene on chromosome 11q22.3 (Gene Reviews). The ATM protein has a central role in the cellular response to DNA double-strand breaks by phosphorylating key substrates involved in repair. Severe forms of A-T are associated with total loss of ATM protein; milder forms are associated with the presence of residual ATM kinase activity, principally caused by missense or splice site variants. The spectrum of ATM pathogenic variants is extremely diverse, including nonsense or missense mutations, small insertions/deletions (indels), splicing alterations, and large genomic rearrangements. There have also been reports of several distinct pathogenic variants in the noncoding region of ATM (Castellví-Bel et al. 1999, Cremin et al. 2020, Fiévet et al. 2019, Klee et al. 2021, McConville et al. 1996, Schon et al. 2019). Large deletions/duplications account for 5-10% of the ATM pathogenic variants, while the remaining 90-95% are SNVs.

It has been shown that specific ATM pathogenic variants are associated with cancer susceptibility syndromes (Gene Reviews). In particular, heterozygous ATM c.7271T>G is associated with high-penetrance for breast cancer risk. Heterozygosity for other ATM variants (including large deletions or duplications (Lepkes et al. 2021, Parenti et al. 2021, Rolfes et al. 2022)) is associated with moderate-penetrance for breast cancer risk and an increased risk for other tumour types such as pancreatic cancer and prostate cancer.

SALSA MLPA Probemix P042 ATM-2 is CE-marked under the IVDR for in vitro diagnostic (IVD) use in Europe. This assay has also been registered for IVD use in Israel.

This assay is for research use only (RUO) in all other territories.

Inclusion of a positive sample is usually not required, but can be useful for the analysis of your experiments. MRC Holland has very limited access to positive samples and cannot supply such samples. We recommend using positive samples from your own collection. Alternatively, you can use positive samples from an online biorepository, such as the Coriell Institute.

The commercially available positive samples below can be used with P041-B1 and P042-B2.

P041 & P042

• Coriell NA00959: Heterozygous duplication affecting the probes for ATM.
• Coriell NA08618: Heterozygous duplication affecting the probes for ATM.
• Coriell NA09596: Heterozygous deletion affecting the probes for ATM.
• Coriell NA15099: Heterozygous duplication affecting the probes for ATM.
• Coriell HG03694: Heterozygous duplication affecting the probes for ATM intron 61 at 474 nt and 419 nt, and ATM exon 62-63.

Various related products

• P002 BRCA1: Hereditary breast cancer, screening BRCA1.
• P037 CLL-1: Tumour mix that contains probes for genes involved in chronic lymphocyte leukaemia. Several ATM probes are included.
• P038 CLL-2: Tumour mix that contains probes for genes involved in chronic lymphocyte leukaemia. Several ATM probes are included.
• P040 CLL: Tumour mix that contains probes for genes involved in chronic lymphocyte leukaemia. Several ATM probes are included.
• P041 ATM-1: Ataxia-telangiectasia (AT); Predisposition to develop cancer, hereditary. Contains probes for all ATM exons when used together with P042.
• P045 BRCA2/CHEK2: Hereditary breast cancer, screening BRCA2.
• P077 BRCA2 Confirmation: Hereditary breast cancer, screening BRCA2.
• P087 BRCA1 Confirmation: Hereditary breast cancer, screening BRCA1.
• P090 BRCA2: Hereditary breast cancer, screening BRCA2.
• P190 CHEK2: Contains probes for CHEK2, ATM and TP53 involved in predisposition to cancer.
• P316 Recessive Ataxias: Contains probes for APTX, SETX, FXN, involved in recessive ataxias.
• P377 Hematologic Malignancies: Tumour mix that contains probes for genes involved in hematologic malignancies. Several ATM probes are included.
• P489 BARD1: Contains probes for BARD1, involved in hereditary breast cancer.

General MLPA resources

• MLPA technique overview
• Coffalyser.Net overview

MLPA education

• Getting started with MLPA
• Using Coffalyser.Net to analyse MLPA data
• Help centre with other learning resources

Selected publications using P042 ATM-2

• Bartsch O et al. (2012). A girl with an atypical form of ataxia telangiectasia and an additional de novo 3.14 Mb microduplication in region 19q12. Eur J Med Genet. 55:49-55.
• Cavalieri S et al. (2008). Large genomic mutations within the ATM gene detected by MLPA, including a duplication of 41 kb from exon 4 to 20. Ann Hum Genet. 72:10-8.
• Chessa L et al. (2009). Founder effects for ATM gene mutations in Italian Ataxia Telangiectasia families. Ann Hum Genet. 73:532-9.
• Claes K et al. (2013). Variant ataxia telangiectasia: clinical and molecular findings and evaluation of radiosensitive phenotypes in a patient and relatives. Neuromolecular Med. 15:447-57.
• Huang Y et al. (2013). Twelve novel Atm mutations identified in Chinese ataxia telangiectasia patients. Neuromolecular Med. 15:536-40.
• Jacquemin V et al. (2012). Underexpression and abnormal localization of ATM products in ataxia telangiectasia patients bearing ATM missense mutations. Eur J Hum Genet. 20:305-12.
• Micol R et al. (2011). Morbidity and mortality from ataxia-telangiectasia are associated with ATM genotype. J Allergy Clin Immunol. 128:382-9.e1.
• Nakamura K et al. (2012). Functional characterization and targeted correction of ATM mutations identified in Japanese patients with ataxia-telangiectasia. Hum Mutat. 33:198-208.
• Podralska MJ et al. (2014). Ten new ATM alterations in Polish patients with ataxia-telangiectasia. Mol Genet Genomic Med. 2:504-11.
• Soukupova J et al. (2011). Characterisation of ATM mutations in Slavic Ataxia telangiectasia patients. Neuromolecular Med. 13:204-11.
• Verhagen MMM et al. (2012). Presence of ATM protein and residual kinase activity correlates with the phenotype in ataxia-telangiectasia: a genotype-phenotype study. Hum Mutat. 33:561-71.

References

• Castellví-Bel S et al. (1999). New mutations, polymorphisms, and rare variants in the ATM gene detected by a novel SSCP strategy. Hum Mutat. 14:156-62.
• Cremin C et al. (2020). Burden of hereditary cancer susceptibility in unselected patients with pancreatic ductal adenocarcinoma referred for germline screening. Cancer Med. 9:4004-13.
• Fiévet A et al. (2019). Functional classification of ATM variants in ataxia-telangiectasia patients. Hum Mutat. 40:1713-40.
• Klee EW et al. (2021). Impact of integrated translational research on clinical exome sequencing. Genet Med. 23:498-507.
• Lepkes L et al. (2021). Performance of In Silico Prediction Tools for the Detection of Germline Copy Number Variations in Cancer Predisposition Genes in 4208 Female Index Patients with Familial Breast and Ovarian Cancer. Cancers (Basel). 13:118.
• McConville CM et al. (1996). Mutations associated with variant phenotypes in ataxia-telangiectasia. Am J Hum Genet. 59:320-30.
• Parenti S et al. (2021). Characterization of New ATM Deletion Associated with Hereditary Breast Cancer. Genes (Basel). 12:136.
• Rolfes M et al. (2022). Prevalence of Cancer Predisposition Germline Variants in Male Breast Cancer Patients: Results of the German Consortium for Hereditary Breast and Ovarian Cancer. Cancers (Basel). 14:3292.
• Schon K et al. (2019). Genotype, extrapyramidal features, and severity of variant ataxia-telangiectasia. Ann Neurol. 85:170-80.
• Suspitsin E et al. (2020). ATM mutation spectrum in Russian children with ataxia-telangiectasia. Eur J Med Genet. 63:103630.