INTRODUCTION
Extensive efforts to standardize variant classification criteria in highly penetrant genes have been made by different groups such as the joint consensus of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) (C. S. Richards et al., 2008; S. Richards et al., 2015), ENIGMA consortium forBRCA1/2 genes (Spurdle et al., 2012) or InSiGHT variant interpretation group for MMR genes (Plon et al., 2008). However, there is still an important work to be done in moderate or low-penetrance genes (Katona et al., 2018) since multigene panels for hereditary cancer (HC) include them. A recent publication proposed a framework for classification of variants in low-penetrance genes, in which a variant could be classified as established risk allele (ERA) if it has been assessed in case-control studies of good design and data quality, demonstrated to be cancer-related and determined through robust meta-analysis (Senol-Cosar et al., 2019).
In the present work we have focused in CHEK2 (checkpoint kinase 2; MIM# 604373), which is a tumor suppressor gene associated with different forms of HC, such as breast cancer (BC), colorectal cancer (CRC) and Li-Fraumeni syndrome (Bell et al., 1999; Meijers-Heijboer et al., 2002), among others. CHEK2 is included in most of the in-house and commercial HC panels (Easton et al., 2015). CHEK2mRNA has a total length of 1844-bp distributed in 15 exons, is located at chromosome 22q12.1 and encodes for a human protein of 543-aa, analogue of the yeast checkpoint kinases Cds1 and Rad53 (Matsuoka et al., 2000). CHK2 protein is a kinase involved in several cellular processes, including the control of mitosis and meiosis progression, and plays an important role in the DNA-damage signaling network (Bartek, Falck, & Lukas, 2001; Zannini, Delia, & Buscemi, 2014). ATM activates CHK2 in response to DNA damage. Once activated, CHK2 is capable of phosphorylating many substrates involved in DNA repair, cell cycle regulation, p53 signaling and apoptosis (Zannini et al., 2014).
A few CHEK2 variants have been described as recurrent or founder variants in some populations. The most well-known CHEK2 variant is c.1100delC and it is primarily present in individuals of Northern and Eastern European descent; it results in a premature stop codon within exon 10, impairing the kinase ability of the enzyme (Wu, Webster, & Chen, 2001). A meta-analysis of 44,777 patients and 42,997 controls established a BC odds ratio (OR) of 2.26 for CHEK2 c.1100delC carriers (Schmidt et al., 2016). Another frameshift founder mutation, the deletion of exons 9 and 10, is considered to double BC risk (Cybulski et al., 2007). The missense variant c.470T>C, p(.Ile157Thr) is described to confer a lower risk compared to the two previous ones (OR of 1.58 and 1.67 for BC and CRC, respectively) (Han, Guo, & Liu, 2013). According to a study of 13,087 BC cases and 5,488 controls, the OR for 73 CHEK2 rare missense variants was of 1.36 (95% CI, 0.99-1.87) and of 1.51 (95% CI, 1.02-2.24) if considering only variants in functional domains (Decker et al., 2017; Han et al., 2013). Furthermore, in a recent study of 1,355 BC cases, the OR forCHEK2 missense variants varied between 3.79 and 5.9 (95% CI, 1.86-7.12 and 2.38-14.78) when compared to ExAC and FLOSSIES controls, respectively (Fostira et al., 2020).
The challenge of CHEK2 variant classification is reflected in numerous discrepancies in ClinVar classification (Decker et al., 2017), to the point of being recognized as the gene with more conflicting interpretations in HC diagnosis (Balmaña et al., 2016). Moreover, there is a current controversy whether to use CHEK2 missense variants at clinical level. For instance, the National Comprehensive Cancer Network’s BC management recommendations for CHEK2 carriers only apply to carriers of truncating variants. In the same line, the UK Cancer Genetics Group decided not to take into account non-truncating variants in the clinical routine until a precise utility is stated for missense variants (Taylor et al., 2018).
Here, we present our effort to characterize the CHEK2 mutational spectrum in Spanish HC patients which has resulted in the need to refine ACMG-AMP guidelines for this gene.