Full sequence analysis of the BRCA1 and BRCA2 (BRCA1/2) tumour suppressor genes was introduced more than ten years ago. Unfortunately, a large number of non hot spot regions have been identified and the DNA sequence changes, resulting in an increased risk of developing breast and ovarian cancer, can occur throughout the entire length of the coding regions of these genes, leading to the necessity to perform highly complex sequence analyses. Genetic alteration research is generally performed using genomic DNA extracted from blood or saliva, with automated DNA sequencing representing the gold standard. However, some alternative approaches to direct sequencing do exist, and among these, the most common in widespread use are Denaturing High Performance Liquid Chromatography (DHPLC) and High Resolution Melting (HRM). Genetic testing for germline BRCA1/2 mutations can establish the presence or absence of cancer predisposing alterations related to the disease. The analyses can be interpreted in three possible ways: a mutation that clearly disrupts BRCA1/2 gene function; no variation in the DNA sequence; or a sequence variant of uncertain/unclassified significance (VUS) with unknown function and cancer risk. Indeed, the main problem facing current BRCA genetic analysis techniques is the correct interpretation of these variants. To overcome this difficulty, webbased databases have proven to be useful to link the results obtained from different laboratories, helping researchers and clinicians to correctly interpret the data. However, at this point in time, many questions are still open about analysis methods and, mainly, test results interpretation. In this article we will try to identify and correctly address these important issues.
Keywords: BRCA1, BRCA2, genetic variant, Sequence analysis, unclassified variant, web based database, breast cancer, Breast Cancer Information Core, Protein Truncation Test, Allele-Specific Oligonucleotide Hybridisation