ABSTRACT
Genetic screening for predisposition to hereditary breast ovarian/cancer has proven to be essential for early diagnosis and successful treatment. Th e widespread testing of the BRCA1 gene for individuals with a family history of breast/ovarian cancer has over the last fi ft een years, uncovered a large number of missense Variants of Uncertain clinical Signifi cance (VUSs) concentrated at the protein’s BRCT domain. It is essential for cancer patients and their families that these variants are successfully classifi ed in order to improve the interpretation of cancer susceptibility test results. Th is classifi cation task has proven to be very challenging since most of the missense variants are rare worldwide. A considerable research eff ort is thus being placed towards using genetic epidemiology and bioinformatics methodologies as well as biochemical and biophysical approaches, aiming at accurately determining whether a missense mutation is pathogenic or neutral. To provide an updated status of the classifi cations of all the variants entered in the BIC (breast cancer mutation) database, concerning the BRCT domain, a Table listing is presented (Table 2). Color coding is used to highlight the currently proposed pathogenicity Class in order to facilitate the reading. Th e Table incorporates all of the published assigned grades from studies that used integrative genetic methods to assess the missense-variant pathogenicity as well as grades assigned from comprehensive analyses based on experimental structural and functional data at the protein level. Results from smaller-scale studies focused on specifi c variants are also included. In 2007, a systematic risk assessment for 1,433 VUSs was based on data that included co-occurrence with known deleterious mutations, personal and family history of the patients and cosegregation of the variant with the disease within pedigrees (Easton et al. 2007). Th e risks reported in the study can then be assigned to Classes according to the classifi cation scheme proposed by the International Agency for Research in Cancer (IARC) (Plon et al. 2008). Class 1 corresponds to the classifi cation “not pathogenic” or “no clinical signifi cance” with likelihood of less than 0.1% for pathogenicity; Class 2 is “likely not pathogenic” with 0.1 – 0.5% likelihood of pathogenicity; Class 3 is “uncertain” (5 to 95%); Class 4 is “likely pathogenic” (95 to 99%) and Class 5 is “pathogenic” (>99%). Carriers of Class 4 and 5 variants are advised to undergo surveillance and cancer prevention treatments. Class 4 and Class 2 variants may change to Class 5 and Class 3 respectively as more genetic data
are accumulated with time, although it is highly unlikely that Class 2 will turn to Class 4 or 5. Class 3 variants carry suffi cient uncertainty that no predictive testing should be advised for relatives and the clinical advice should depend solely on the pattern of cancer in the family and tumor histology and should not concern the presence of the variant. Of very high value for risk assessment and the interpretation of genetic testing results is the comprehensive analysis of BRCT missense variants by Le et al. (Lee et al. 2010). For this study in vitro protein folding, phosphopeptide binding and cell-based transcriptional assays were used to assess the functional consequences from missense variants of the BRCT domain of BRCA1. Based on the results the variants are grouped in fi ve categories: Strong Functional Eff ect, Moderate Functional Eff ect, Uncertain Result, Low and fi nally No Functional Eff ect. Th e results are then correlated with the Classes defi ned by the genetic assessment of Easton et al. (Easton et al. 2007) and other genetic assessment studies to produce a validation set of likely pathogenic and likely neutral variants. Th ese variants have been highlighted by red or blue respectively in the list presented in column one of the Missense Variant Table (Table 2). Proposed classifi cation schemes of the BRCA1-BRCT VUS, based on biophysical assays involving the changes in the thermodynamic stability of the wild-type and the calorimetric assessment of the binding ability of the variants to phosphopeptides are also included in the Table. Based on the results by Rowling et al., (Rowling et al. 2010) the following Classifi cation scheme was proposed: Very Destabilizing, Moderately Destabilizing, Mildly Destabilizing and No Destabilizing Eff ect.
